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Annotation From Genomic Level
Wanding Zhou edited this page Mar 20, 2016
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Annotation from genomic level is handled by the ganno subcommand in TransVar.
This is the forward annotation
$ transvar ganno --ccds -i 'chr3:g.178936091G>A'outputs
chr3:g.178936091G>A CCDS43171 (protein_coding) PIK3CA +
chr3:g.178936091G>A/c.1633G>A/p.E545K inside_[cds_in_exon_9]
CSQN=Missense;dbsnp=rs104886003(chr3:178936091G>A);codon_pos=178936091-178936
092-178936093;ref_codon_seq=GAG;source=CCDS
Another example:
$ transvar ganno -i "chr9:g.135782704C>G" --ccdsoutputs
chr9:g.135782704C>G CCDS6956 (protein_coding) TSC1 -
chr9:g.135782704C>G/c.1317G>C/p.L439L inside_[cds_in_exon_11]
CSQN=Synonymous;dbsnp=rs770692313(chr9:135782704C>G);codon_pos=135782704-1357
82705-135782706;ref_codon_seq=CTG;source=CCDS
chr9:g.135782704C>G CCDS55350 (protein_coding) TSC1 -
chr9:g.135782704C>G/c.1164G>C/p.L388L inside_[cds_in_exon_10]
CSQN=Synonymous;dbsnp=rs770692313(chr9:135782704C>G);codon_pos=135782704-1357
82705-135782706;ref_codon_seq=CTG;source=CCDS
and a nonsense mutation:
$ transvar ganno -i 'chr1:g.115256530G>A' --ensembloutputs
chr1:g.115256530G>A ENST00000369535 (protein_coding) NRAS -
chr1:g.115256530G>A/c.181C>T/p.Q61* inside_[cds_in_exon_3]
CSQN=Nonsense;codon_pos=115256528-115256529-115256530;ref_codon_seq=CAA;alias
es=ENSP00000358548;source=Ensembl
CSQN fields indicates a nonsense mutation.
To annotate a short genomic region in a gene,
$ transvar ganno --ccds -i 'chr3:g.178936091_178936192'outputs
chr3:g.178936091_178936192 CCDS43171 (protein_coding) PIK3CA +
chr3:g.178936091_178936192/c.1633_1664+70/p.E545_R555 from_[cds_in_exon_9]_to_[intron_between_exon_9_and_10]
C2=donor_splice_site_on_exon_9_at_chr3:178936123_included;start_codon=1789360
91-178936092-178936093;end_codon=178936121-178936122-178936984;source=CCDS
Results indicates the beginning position is at coding region while ending position is at intronic region (c.1633_1664+70). Note that there is no consequence label (CSQN tag) when performing a region annotation (instead of a variant).
For intergenic sites, TransVar also reports the identity and distance to the gene upstream and downstream. For example, chr6:116991832 is simply annotated as intergenic in the original annotation. TransVar reveals that it is 1,875 bp downstream to ZUFSP and 10,518 bp upstream to KPNA5 showing a vicinity to the gene ZUFSP. There is no limit in the reported distance. If a site is at the end of the chromosome, TransVar is able to report the distance to the telomere.
$ transvar ganno -i '9:g.133750356_137990357' --ccdsoutputs
9:g.133750356_137990357 CCDS35165 (protein_coding),CCDS6986 (protein_coding) . .
chr9:g.133750356_137990357/./. from_[cds_in_exon_7;ABL1]_to_[intron_between_exon_4_and_5;OLFM1]_spanning_[51_genes]
.
9:g.133750356_137990357 CCDS35166 (protein_coding),CCDS6986 (protein_coding) . .
chr9:g.133750356_137990357/./. from_[cds_in_exon_7;ABL1]_to_[intron_between_exon_4_and_5;OLFM1]_spanning_[51_genes]
.
The result indicates that the region span 53 genes. The beginning of the region resides in the coding sequence of ABL1, c.1187A and the ending region resides in the intronic region of OLFM1, c.622+6C. 2 different usage of transcripts in annotating the starting position is represented in two lines, each line corresponding to a combination of transcript usage. This annotation not only shows the coverage of the region, also reveals the fine structure of the boundary.
In another example, where the ending position exceeds the length of the chromosome, TransVar truncates the region and outputs upstream and downstream information of the ending position.
$ transvar ganno -i '9:g.133750356_1337503570' --ccdsoutputs
9:g.133750356_1337503570 CCDS35165 (protein_coding), . .
chr9:g.133750356_141213431/./. from_[cds_in_exon_7;ABL1]_to_[intergenic_between_EHMT1(484,026_bp_downstream)_and_3'-telomere(0_bp)]_spanning_[136_genes]
.
9:g.133750356_1337503570 CCDS35166 (protein_coding), . .
chr9:g.133750356_141213431/./. from_[cds_in_exon_7;ABL1]_to_[intergenic_between_EHMT1(484,026_bp_downstream)_and_3'-telomere(0_bp)]_spanning_[136_genes]
.
A frameshift deletion
$ transvar ganno -i "chr2:g.234183368_234183380del" --ccdsoutputs
chr2:g.234183368_234183380del CCDS2502 (protein_coding) ATG16L1 +
chr2:g.234183368_234183380del13/c.841_853del13/p.T281Lfs*5 inside_[cds_in_exon_8]
CSQN=Frameshift;left_align_gDNA=g.234183367_234183379del13;unaligned_gDNA=g.2
34183368_234183380del13;left_align_cDNA=c.840_852del13;unalign_cDNA=c.841_853
del13;source=CCDS
chr2:g.234183368_234183380del CCDS2503 (protein_coding) ATG16L1 +
chr2:g.234183368_234183380del13/c.898_910del13/p.T300Lfs*5 inside_[cds_in_exon_9]
CSQN=Frameshift;left_align_gDNA=g.234183367_234183379del13;unaligned_gDNA=g.2
34183368_234183380del13;left_align_cDNA=c.897_909del13;unalign_cDNA=c.898_910
del13;source=CCDS
chr2:g.234183368_234183380del CCDS54438 (protein_coding) ATG16L1 +
chr2:g.234183368_234183380del13/c.409_421del13/p.T137Lfs*5 inside_[cds_in_exon_5]
CSQN=Frameshift;left_align_gDNA=g.234183367_234183379del13;unaligned_gDNA=g.2
34183368_234183380del13;left_align_cDNA=c.408_420del13;unalign_cDNA=c.409_421
del13;source=CCDS
Note the difference between left-aligned identifier and the right aligned identifier.
An in-frame deletion
$ transvar ganno -i "chr2:g.234183368_234183379del" --ccdsoutputs
chr2:g.234183368_234183379del CCDS2502 (protein_coding) ATG16L1 +
chr2:g.234183368_234183379del12/c.841_852del12/p.T281_G284delTHPG inside_[cds_in_exon_8]
CSQN=InFrameDeletion;left_align_gDNA=g.234183367_234183378del12;unaligned_gDN
A=g.234183368_234183379del12;left_align_cDNA=c.840_851del12;unalign_cDNA=c.84
1_852del12;left_align_protein=p.T281_G284delTHPG;unalign_protein=p.T281_G284d
elTHPG;source=CCDS
chr2:g.234183368_234183379del CCDS2503 (protein_coding) ATG16L1 +
chr2:g.234183368_234183379del12/c.898_909del12/p.T300_G303delTHPG inside_[cds_in_exon_9]
CSQN=InFrameDeletion;left_align_gDNA=g.234183367_234183378del12;unaligned_gDN
A=g.234183368_234183379del12;left_align_cDNA=c.897_908del12;unalign_cDNA=c.89
8_909del12;left_align_protein=p.T300_G303delTHPG;unalign_protein=p.T300_G303d
elTHPG;source=CCDS
chr2:g.234183368_234183379del CCDS54438 (protein_coding) ATG16L1 +
chr2:g.234183368_234183379del12/c.409_420del12/p.T137_G140delTHPG inside_[cds_in_exon_5]
CSQN=InFrameDeletion;left_align_gDNA=g.234183367_234183378del12;unaligned_gDN
A=g.234183368_234183379del12;left_align_cDNA=c.408_419del12;unalign_cDNA=c.40
9_420del12;left_align_protein=p.T137_G140delTHPG;unalign_protein=p.T137_G140d
elTHPG;source=CCDS
Another example
$ transvar ganno --ccds -i 'chr12:g.53703425_53703427del'outputs
chr12:g.53703425_53703427del CCDS8856 (protein_coding) AAAS -
chr12:g.53703427_53703429delCCC/c.769_771delGGG/p.G257delG inside_[cds_in_exon_8]
CSQN=InFrameDeletion;left_align_gDNA=g.53703424_53703426delCCC;unaligned_gDNA
=g.53703425_53703427delCCC;left_align_cDNA=c.766_768delGGG;unalign_cDNA=c.768
_770delGGG;left_align_protein=p.G256delG;unalign_protein=p.G256delG;source=CC
DS
chr12:g.53703425_53703427del CCDS53797 (protein_coding) AAAS -
chr12:g.53703427_53703429delCCC/c.670_672delGGG/p.G224delG inside_[cds_in_exon_7]
CSQN=InFrameDeletion;left_align_gDNA=g.53703424_53703426delCCC;unaligned_gDNA
=g.53703425_53703427delCCC;left_align_cDNA=c.667_669delGGG;unalign_cDNA=c.669
_671delGGG;left_align_protein=p.G223delG;unalign_protein=p.G223delG;source=CC
DS
Note the difference between left and right-aligned identifiers on both protein level and cDNA level.
An in-frame out-of-phase deletion
$ transvar ganno -i "chr2:g.234183372_234183383del" --ccdsoutputs
chr2:g.234183372_234183383del CCDS2502 (protein_coding) ATG16L1 +
chr2:g.234183372_234183383del12/c.845_856del12/p.H282_G286delinsR inside_[cds_in_exon_8]
CSQN=MultiAAMissense;left_align_gDNA=g.234183372_234183383del12;unaligned_gDN
A=g.234183372_234183383del12;left_align_cDNA=c.845_856del12;unalign_cDNA=c.84
5_856del12;source=CCDS
chr2:g.234183372_234183383del CCDS2503 (protein_coding) ATG16L1 +
chr2:g.234183372_234183383del12/c.902_913del12/p.H301_G305delinsR inside_[cds_in_exon_9]
CSQN=MultiAAMissense;left_align_gDNA=g.234183372_234183383del12;unaligned_gDN
A=g.234183372_234183383del12;left_align_cDNA=c.902_913del12;unalign_cDNA=c.90
2_913del12;source=CCDS
chr2:g.234183372_234183383del CCDS54438 (protein_coding) ATG16L1 +
chr2:g.234183372_234183383del12/c.413_424del12/p.H138_G142delinsR inside_[cds_in_exon_5]
CSQN=MultiAAMissense;left_align_gDNA=g.234183372_234183383del12;unaligned_gDN
A=g.234183372_234183383del12;left_align_cDNA=c.413_424del12;unalign_cDNA=c.41
3_424del12;source=CCDS
TransVar reduces the reference sequence in a deletion to its length when the deleted reference sequence is too long. For example
$ transvar ganno -i 'chr14:g.101347000_101347023del' --ensembloutputs
chr14:g.101347000_101347023del ENST00000534062 (protein_coding) RTL1 -
chr14:g.101347000_101347023del24/c.4074+29_4074+52del24/. inside_[3-UTR;noncoding_exon_1]
CSQN=3-UTRDeletion;left_align_gDNA=g.101347000_101347023del24;unaligned_gDNA=
g.101347000_101347023del24;left_align_cDNA=c.4074+29_4074+52del24;unalign_cDN
A=c.4074+29_4074+52del24;aliases=ENSP00000435342;source=Ensembl
where the deletion sequence is reduced to its length (del24). The --seqmax option changes the length threshold (default:10) when this behavior occur. When --seqmax is given a negative number, the threshold is lifted such that the reference sequence is always reported regardless of its length, i.e.,
$ transvar ganno -i 'chr14:g.101347000_101347023del' --ensembl --seqmax -1outputs the full reference sequence:
chr14:g.101347000_101347023del ENST00000534062 (protein_coding) RTL1 -
chr14:g.101347000_101347023delTTGGGGTGAGAAATAGAGGGGACT/c.4074+29_4074+52delAGTCCCCTCTATTTCTCACCCCAA/. inside_[3-UTR;noncoding_exon_1]
CSQN=3-UTRDeletion;left_align_gDNA=g.101347000_101347023delTTGGGGTGAGAAATAGAG
GGGACT;unaligned_gDNA=g.101347000_101347023delTTGGGGTGAGAAATAGAGGGGACT;left_a
lign_cDNA=c.4074+29_4074+52delAGTCCCCTCTATTTCTCACCCCAA;unalign_cDNA=c.4074+29
_4074+52delAGTCCCCTCTATTTCTCACCCCAA;aliases=ENSP00000435342;source=Ensembl
An in-frame insertion of three nucleotides
$ transvar ganno -i 'chr2:g.69741762_69741763insTGC' --ccdsoutputs
chr2:g.69741762_69741763insTGC CCDS1893 (protein_coding) AAK1 -
chr2:g.69741780_69741782dupCTG/c.1614_1616dupGCA/p.Q546dupQ inside_[cds_in_exon_12]
CSQN=InFrameInsertion;left_align_gDNA=g.69741762_69741763insTGC;unalign_gDNA=
g.69741762_69741763insTGC;left_align_cDNA=c.1596_1597insCAG;unalign_cDNA=c.16
14_1616dupGCA;left_align_protein=p.Y532_Q533insQ;unalign_protein=p.Q539dupQ;p
hase=2;source=CCDS
Note the proper right-alignment of protein level insertion Q. The left-aligned identifier is also given in the LEFTALN field.
A frame-shift insertion of two nucleotides
$ transvar ganno -i 'chr7:g.121753754_121753755insCA' --ccdsoutputs
chr7:g.121753754_121753755insCA CCDS5783 (protein_coding) AASS -
chr7:g.121753754_121753755insCA/c.1064_1065insGT/p.I355Mfs*10 inside_[cds_in_exon_9]
CSQN=Frameshift;left_align_gDNA=g.121753753_121753754insAC;unalign_gDNA=g.121
753754_121753755insCA;left_align_cDNA=c.1063_1064insTG;unalign_cDNA=c.1063_10
64insTG;source=CCDS
$ transvar ganno -i 'chr17:g.79093270_79093271insGGGCGT' --ccdsoutputs
chr17:g.79093270_79093271insGGGCGT CCDS45807 (protein_coding) AATK -
chr17:g.79093282_79093287dupTGGGCG/c.3988_3993dupACGCCC/p.T1330_P1331dupTP inside_[cds_in_exon_13]
CSQN=InFrameInsertion;left_align_gDNA=g.79093270_79093271insGGGCGT;unalign_gD
NA=g.79093270_79093271insGGGCGT;left_align_cDNA=c.3976_3977insCGCCCA;unalign_
cDNA=c.3988_3993dupACGCCC;left_align_protein=p.A1326_P1327insPT;unalign_prote
in=p.T1330_P1331dupTP;phase=0;source=CCDS
Notice the difference in the inserted sequence when left-alignment and right-alignment conventions are followed.
A frame-shift insertion of one nucleotides in a homopolymer
$ transvar ganno -i 'chr7:g.117230474_117230475insA' --ccdsoutputs
chr7:g.117230474_117230475insA CCDS5773 (protein_coding) CFTR +
chr7:g.117230479dupA/c.1752dupA/p.E585Rfs*4 inside_[cds_in_exon_13]
CSQN=Frameshift;left_align_gDNA=g.117230474_117230475insA;unalign_gDNA=g.1172
30474_117230475insA;left_align_cDNA=c.1747_1748insA;unalign_cDNA=c.1747_1748i
nsA;source=CCDS
Notice the right alignment of cDNA level insertion and the left alignment reported as additional information.
A in-frame, in-phase insertion
$ transvar ganno -i 'chr12:g.109702119_109702120insACC' --ccdschr12:g.109702119_109702120insACC CCDS31898 (protein_coding) ACACB +
chr12:g.109702119_109702120insACC/c.6870_6871insACC/p.Y2290_H2291insT inside_[cds_in_exon_49]
CSQN=InFrameInsertion;left_align_gDNA=g.109702118_109702119insCAC;unalign_gDN
A=g.109702119_109702120insACC;left_align_cDNA=c.6869_6870insCAC;unalign_cDNA=
c.6870_6871insACC;left_align_protein=p.Y2290_H2291insT;unalign_protein=p.Y229
0_H2291insT;phase=0;source=CCDS
A block-substitution that results in a frameshift.
$ transvar ganno -i 'chr10:g.27329002_27329002delinsAT' --ccdschr10:g.27329002_27329002delinsAT CCDS41499 (protein_coding) ANKRD26 -
chr10:g.27329009dupT/c.2266dupA/p.M756Nfs*6 inside_[cds_in_exon_21]
CSQN=Frameshift;left_align_gDNA=g.27329002_27329003insT;unalign_gDNA=g.273290
02_27329003insT;left_align_cDNA=c.2259_2260insA;unalign_cDNA=c.2266dupA;sourc
e=CCDS
A block-substitution that is in-frame,
$ transvar ganno -i 'chr10:g.52595929_52595930delinsAA' --ccdschr10:g.52595929_52595930delinsAA CCDS7243 (protein_coding) A1CF -
chr10:g.52595929_52595930delinsAA/c.532_533delinsTT/p.P178L inside_[cds_in_exon_4]
CSQN=Missense;codon_cDNA=532-533-534;source=CCDS
chr10:g.52595929_52595930delinsAA CCDS7241 (protein_coding) A1CF -
chr10:g.52595929_52595930delinsAA/c.508_509delinsTT/p.P170L inside_[cds_in_exon_4]
CSQN=Missense;codon_cDNA=508-509-510;source=CCDS
chr10:g.52595929_52595930delinsAA CCDS7242 (protein_coding) A1CF -
chr10:g.52595929_52595930delinsAA/c.508_509delinsTT/p.P170L inside_[cds_in_exon_4]
CSQN=Missense;codon_cDNA=508-509-510;source=CCDS
One can define the promoter boundary through the --prombeg and --promend option. Default promoter region is defined from 1000bp upstream of the transcription start site to the transcription start site. One could customize this setting to e.g., [-1000bp, 2000bp] by
$ transvar ganno -i 'chr19:g.41950335_41951908' --ensembl --prombeg 2000 --promend 1000 --refversion mm10chr19:g.41950335_41951908 ENSMUST00000167927 (nonsense_mediated_decay) MMS19 -
chr19:g.41950335_41951908/c.1071+3684_1071+5257/. from_[intron_between_exon_20_and_21]_to_[intron_between_exon_19_and_20]
whole_exon_[20]_included;aliases=ENSMUSP00000132483;source=Ensembl
chr19:g.41950335_41951908 ENSMUST00000171561 (protein_coding) MMS19 -
chr19:g.41950335_41951908/c.1915+499_2016-252/p.E639_E672 from_[intron_between_exon_20_and_21]_to_[intron_between_exon_19_and_20]
whole_exon_[20]_included;start_codon=41950753-41950752-41950083;end_codon=419
52407-41950851-41950850;aliases=ENSMUSP00000130900;source=Ensembl
chr19:g.41950335_41951908 ENSMUST00000170209 (retained_intron) MMS19 -
chr19:g.41950335_41951908/c.2251+499_2352-252/. from_[intron_between_exon_16_and_17]_to_[intron_between_exon_15_and_16]
whole_exon_[16]_included;source=Ensembl
chr19:g.41950335_41951908 ENSMUST00000163287 (protein_coding) MMS19 -
chr19:g.41950335_41951908/c.1477+499_1578-252/p.E493_E526 from_[intron_between_exon_17_and_18]_to_[intron_between_exon_16_and_17]
whole_exon_[17]_included;start_codon=41950753-41950752-41950083;end_codon=419
52407-41950851-41950850;aliases=ENSMUSP00000128653;source=Ensembl
chr19:g.41950335_41951908 ENSMUST00000163398 (nonsense_mediated_decay) MMS19 -
chr19:g.41950335_41951908/c.225+12487_225+14060/. from_[intron_between_exon_19_and_20]_to_[intron_between_exon_18_and_19]
whole_exon_[19]_included;aliases=ENSMUSP00000126864;source=Ensembl
chr19:g.41950335_41951908 ENSMUST00000164776 (nonsense_mediated_decay) MMS19 -
chr19:g.41950335_41951908/c.225+12487_225+14060/. from_[intron_between_exon_19_and_20]_to_[intron_between_exon_18_and_19]
whole_exon_[19]_included;aliases=ENSMUSP00000129478;source=Ensembl
chr19:g.41950335_41951908 ENSMUST00000026168 (protein_coding) MMS19 -
chr19:g.41950335_41951908/c.1786+499_1887-252/p.E596_E629 from_[intron_between_exon_19_and_20]_to_[intron_between_exon_18_and_19]
whole_exon_[19]_included;start_codon=41950753-41950752-41950083;end_codon=419
52407-41950851-41950850;aliases=ENSMUSP00000026168;source=Ensembl
chr19:g.41950335_41951908 ENSMUST00000166090 (nonsense_mediated_decay) MMS19 -
chr19:g.41950335_41951908/c.636+499_737-252/. from_[intron_between_exon_7_and_8]_to_[intron_between_exon_6_and_7]
whole_exon_[7]_included;aliases=ENSMUSP00000131219;source=Ensembl
chr19:g.41950335_41951908 ENSMUST00000171755 (retained_intron) MMS19 -
chr19:g.41950335_41951908/c.1941+499_2042-252/. from_[intron_between_exon_20_and_21]_to_[intron_between_exon_19_and_20]
whole_exon_[20]_included;source=Ensembl
chr19:g.41950335_41951908 ENSMUST00000167820 (protein_coding) MMS19 -
chr19:g.41950335_41951908/c.179-1057_279-252/p.E60_E93 from_[intron_between_exon_3_and_4]_to_[intron_between_exon_2_and_3]
whole_exon_[3]_included;start_codon=41950753-41950752-41950083;end_codon=4195
3669-41950851-41950850;aliases=ENSMUSP00000130399;source=Ensembl
chr19:g.41950335_41951908 ENSMUST00000169775 (nonsense_mediated_decay) MMS19 -
chr19:g.41950335_41951908/c.522+11101_522+12674/. from_[intron_between_exon_20_and_21]_to_[intron_between_exon_19_and_20]
whole_exon_[20]_included;aliases=ENSMUSP00000128234;source=Ensembl
chr19:g.41950335_41951908 ENSMUST00000166517 (retained_intron) MMS19 -
chr19:g.41950335_41951908/c.1-564_594-252/. from_[intron_between_exon_1_and_2]_to_[intergenic_between_MMS19(564_bp_upstream)_and_MMS19(1,189_bp_downstream)]
promoter_region_of_[MMS19]_overlaping_1565_bp(99.43%);whole_exon_[1]_included
;source=Ensembl
The result shows that 99.43% of the target region is inside the promoter region. The overlap is as long as 1564 base pairs.
$ transvar ganno -i 'chr2:25564781G>T' --refseqresults in a UTR-containing CSQN field
chr2:25564781G>T NM_022552 (protein_coding) DNMT3A -
chr2:g.25564781G>T/c.1-27928C>A/. inside_[5-UTR;noncoding_exon_1]
CSQN=5-UTRSNV;dbxref=GeneID:1788,HGNC:2978,HPRD:04141,MIM:602769;aliases=NP_0
72046;source=RefSeq
chr2:25564781G>T NM_175629 (protein_coding) DNMT3A -
chr2:g.25564781G>T/c.1-27928C>A/. inside_[5-UTR;intron_between_exon_1_and_2]
CSQN=IntronicSNV;dbxref=GeneID:1788,HGNC:2978,HPRD:04141,MIM:602769;aliases=N
P_783328;source=RefSeq
chr2:25564781G>T NM_175630 (protein_coding) DNMT3A -
chr2:g.25564781G>T/c.1-27928C>A/. inside_[5-UTR;intron_between_exon_1_and_2]
CSQN=IntronicSNV;dbxref=GeneID:1788,HGNC:2978,HPRD:04141,MIM:602769;aliases=N
P_783329;source=RefSeq
Given Ensembl, GENCODE or RefSeq database, one could annotate non-coding transcripts such as lncRNA. E.g.,
$ transvar ganno --gencode -i 'chr1:g.3985200_3985300' --refversion mm10results in
chr1:g.3985200_3985300 ENSMUST00000194643 (lincRNA) RP23-333I7.1 -
chr1:g.3985200_3985300/c.121_221/. inside_[noncoding_exon_2]
source=GENCODE
chr1:g.3985200_3985300 ENSMUST00000192427 (lincRNA) RP23-333I7.1 -
chr1:g.3985200_3985300/c.685_785/. inside_[noncoding_exon_1]
source=GENCODE
or
$ transvar ganno --refseq -i 'chr14:g.20568338_20569581' --refversion mm10results in
chr14:g.20568338_20569581 NR_033571 (lncRNA) 1810062O18RIK +
chr14:g.20568338_20569581/c.260-1532_260-289/. inside_[intron_between_exon_4_and_5]
dbxref=GeneID:75602,MGI:MGI:1922852;source=RefSeq
chr14:g.20568338_20569581 XM_011245228 (protein_coding) USP54 -
chr14:g.20568338_20569581/c.1357+667_1357+1910/. inside_[intron_between_exon_6_and_7]
dbxref=GeneID:78787,MGI:MGI:1926037;aliases=XP_011243530;source=RefSeq
chr14:g.20568338_20569581 XM_011245226 (protein_coding) USP54 -
chr14:g.20568338_20569581/c.1972+667_1972+1910/. inside_[intron_between_exon_13_and_14]
dbxref=GeneID:78787,MGI:MGI:1926037;aliases=XP_011243528;source=RefSeq
chr14:g.20568338_20569581 NM_030180 (protein_coding) USP54 -
chr14:g.20568338_20569581/c.2188+667_2188+1910/. inside_[intron_between_exon_15_and_16]
dbxref=GeneID:78787,MGI:MGI:1926037;aliases=NP_084456;source=RefSeq
chr14:g.20568338_20569581 XM_011245225 (protein_coding) USP54 -
chr14:g.20568338_20569581/c.2359+667_2359+1910/. inside_[intron_between_exon_16_and_17]
dbxref=GeneID:78787,MGI:MGI:1926037;aliases=XP_011243527;source=RefSeq
chr14:g.20568338_20569581 XM_006519705 (protein_coding) USP54 -
chr14:g.20568338_20569581/c.2188+667_2188+1910/. inside_[intron_between_exon_15_and_16]
dbxref=GeneID:78787,MGI:MGI:1926037;aliases=XP_006519768;source=RefSeq
chr14:g.20568338_20569581 XM_006519703 (protein_coding) USP54 -
chr14:g.20568338_20569581/c.2359+667_2359+1910/. inside_[intron_between_exon_16_and_17]
dbxref=GeneID:78787,MGI:MGI:1926037;aliases=XP_006519766;source=RefSeq
chr14:g.20568338_20569581 XM_011245227 (protein_coding) USP54 -
chr14:g.20568338_20569581/c.2359+667_2359+1910/. inside_[intron_between_exon_16_and_17]
dbxref=GeneID:78787,MGI:MGI:1926037;aliases=XP_011243529;source=RefSeq
chr14:g.20568338_20569581 XM_006519709 (protein_coding) USP54 -
chr14:g.20568338_20569581/c.2359+667_2359+1910/. inside_[intron_between_exon_16_and_17]
dbxref=GeneID:78787,MGI:MGI:1926037;aliases=XP_006519772;source=RefSeq
chr14:g.20568338_20569581 XM_006519708 (protein_coding) USP54 -
chr14:g.20568338_20569581/c.2359+667_2359+1910/. inside_[intron_between_exon_16_and_17]
dbxref=GeneID:78787,MGI:MGI:1926037;aliases=XP_006519771;source=RefSeq
or using Ensembl
$ transvar ganno --ensembl -i 'chr1:g.29560_29570'results in
chr1:g.29560_29570 ENST00000488147 (unprocessed_pseudogene) WASH7P -
chr1:g.29560_29570/c.1_11/. inside_[noncoding_exon_1]
promoter_region_of_[WASH7P]_overlaping_1_bp(9.09%);source=Ensembl
chr1:g.29560_29570 ENST00000538476 (unprocessed_pseudogene) WASH7P -
chr1:g.29560_29570/c.237_247/. inside_[noncoding_exon_1]
source=Ensembl
chr1:g.29560_29570 ENST00000473358 (lincRNA) MIR1302-10 +
chr1:g.29560_29570/c.7_17/. inside_[noncoding_exon_1]
source=Ensembl