BtaINT0042239 @ bosTau6
Intron Retention
Gene
ENSBTAG00000012837 | COL6A6
Description
collagen, type VI, alpha 6 [Source:HGNC Symbol;Acc:HGNC:27023]
Coordinates
chr1:153383991-153390977:-
Coord C1 exon
chr1:153390924-153390977
Coord A exon
chr1:153384027-153390923
Coord C2 exon
chr1:153383991-153384026
Length
6897 bp
Sequences
Splice sites
5' ss Seq
ACAGTAAGG
5' ss Score
5.42
3' ss Seq
TACTTTTTTCCCTATTGTAGGCA
3' ss Score
9.97
Exon sequences
Seq C1 exon
GGAAGAAGAGGCCAGCCAGGGCCCCCTGGAACTCCCGGCTCCAGAAGGACGACA
Seq A exon
GTAAGGACCCACAGAGGCCAAGTGGCCCACTCTGGAGGAGCTGAAGTGGGGTGATGAAATGGCTGATGTGGGGCGGTTCCCCAGGACTTACTACCCTGAGGAAACTGACTCAGGGCAGAGCTGGCAAAGGAGGCAGGAAGGGCCTGAAGCCAAGGCCAGACGGCGCTGGCTGCAGGGGAAATGACCACATCGGAGGAAAGCGCTGCCCAAGGAGAACACAAGAGTAGCCAACTAGGGGAAGAGTAGTCAAAGTCTGGCCTGCTCACTAGGCCCATGGAGGTTTGAAGTCCAAGGCTCCATTCCTCTGCCAAGTTTTATGACTGCTTAGAAAAGTCAGTCCTGATGCGAGTGCTCTGGTCTCCTTTCCATTTTCTCTGACTCGAAGAGGAATGTGCTCCAAGATATAAAAATATTTTCTTGGATGAACTACAATATATGGTTCTGTGAATTTCTCCTCAGAAAACAGAATGCATAATGAATGCAATATATTAAACTAGTGTTTATTTGTGCTAAATTTTTAAATGTTATAAATATATATTTTACTGAGATGTGATAGATAATATTAGTTTCAGATGTACAACATAATGATTCCATGTATGTATATATTACAAGATGATCACCATTCAGCTAGTAAGTCTAGTTAACATCCATCACCACACATAGTTATGATTCTTTTTTTCTTGTGATGAAAACTTTTTAAGATCTGCTCTGTTGTTGTGTAGTTGCTATGTTGTGTCCAGTTCTTTTATGATTCCATGGACTGTAGCCCACCAGACTCCTCTGTCCATGGGATTTCCCAGGCAAAAATACTGAAGAAAAAAAAAAAAAAAAAGAATACTGAAGAAGGGTTACCATTTCCCTCTCCAGGGGATCTTCCTAACCCAGGGATTAAACCCATGTCTCCTGCACTGACAGGCAGATTCTTTACCACTGAGCCACCAGGAAAGCCCTTCTACTCTCTTAGCAACTTTTAAATATACAATATAGTTTTACTGGGCTTCCCTAGTGGCTCAGCAATAAAGAATCTGTCTGCCAATGCAGGAGACACAGGTTCAATTTCCGGGTCAAGAAGATCCCCTGGAGAAGGAAATGGCAATCCACTCTAGTATTCTTGCCTGGGAAATCCCATAGAGAGAGGAGCCTGGTGGGCTATAGTCCATGGGGTCGCAAAAGAATCGGACACAATGCAGAAACTACACAGCAACATACTATTATTGACGATAGTTACCATGTGAAGTGAAGTGAAGTGAAAGTCGTTCAGTCATGTCCAACTGTTTGCGACCCCATGGACTAGCCCATGGAATTTTCCAGGCCAGAATACTGGAGTGGGTAGCCTTTCCCTTCCCCAGGGCACCTTCCCAACCAGAGGTTGAACCCAGGTCTCTGACATTGCAGGCAGATTCTTTACCAGCTGAGGCACCAGGGAAGCCCAAGAATACTGGAGTGGGTAGCCTATCTCTTCTCCAGGGGATCTTCCCAACCCAGGAATAGAACTGGGGTCTCCTGCATTGCAGACAGATTCTTTACCAACTGAGCTATCATGCTATACATTAAATCCCATGACTTATTTATTTTCTAACTGGAAGTTTATGCCTTTTGATTCCCTCTACCCATGTCACACTACCCCCCACTCCTCAGCTCTGTTCTCTGTATCTATGAGTTTAGCTGGTTGGTTTATTTGTTTTGTTAAGATTCCACATATAAGTGAGATCATAGGGTATTGGTCTTTTTCTGACTTATTTCACTCAGTGTAATGCCTTCAGGACTCCCCTGTAGCTCAGACAGTAAAGAATCCTCCTGCAATGCAGAGACCTGGGTTCGATCCCTGGGTCAGAAGATCCCCTGGANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNCCCAGAAGTGGAATTTCTGGAAGATACGGTATTTCTATATTTAAGTTTCTTTGAGGACACTCTGTACTGCTAAAGAGATTATATATAATACCTGAAAGTGAAAGTGATGTCGCTCAGTCGTGTCCAACTCTTTGCGACCCCATGGACTGTAGCCTACCAGGCTCCTCCCTCCATGGGATTCTCCAGGCAAGAATACTGGAGAGGGTTGCCATTTCCTTCTCCAGGGGATCTTCTAATACATGCCTATAAAAACATATCTGAGGGCAATATTAGGTCACTCGCTTATGAAACCTTTTGGGATCTTTCTCGTTATTTTTTTCAATAAGTATAAGAGTTTCTGTGCTTGACTTCTTGGAAAAGAATTGACATTATAAAATAAAATCTTTATCCGTTAAGAAAATATAACTTCAATAAAATATACTTAAATGCCTGCATTGGGTTCTGAACTAGAACCCAAGGTCTCTTCTTATGGTGCAATGCTTTCTTTCCATTCTTTATTTAGTTATCCAGCCTTTTCCGACTTCCTTCATCCCTCCCTGCCCACTACATGTAAGGATAGATGTTAACTAGATTTATTAGCTGAATGATGGTCTTCTTGCAGTATATACATATATGGAATCATTATGTTGTACATCTGAAACTAATACAATTTTAACATTTTAAATTTGAGGACAAATAAAAACTGTTTTAACATATTGCATTATTATGCATTGTATTTTCTGAGCAGAAGCTCATAAAACCAGCTATTATACTCCAACAGGAAAATATTTTTATATGTTGGAACATACTTTTATTCTTTGTAAGACAGAGAAAAATAAGAACAGGGATTATGTTTAAAACCTGCAGAATTTAATTGGTGGGAAAGCCCTTTCTAATGCATCTAAAGATTTTTAAAAGTACATTTGCTATTTATTTGACTTTCTAAAAGGGTGTAGCCAGTTTACATACCCCAGGAAAGTATTTTGAACTTAAAGAATATCATCCAAAAAATCCTGGTGTGGGAGATGAACTTTTCTTACTTTATAGAGGCTATAATCTCTCTGGAGGATAAGGCAATATCACCATGTATTAGCTAAACTATACAACTCCTGAGAAATATGGCCCCTTCTTGAGTTATAGATTCAGCAGTGTCATTTAGGAGTAAAAACAGAATTCCACCTAAAGATGGTAAAGTCAAGGGATTTTTTTTTATACTACTCCACTTCTATGCAACTCACCAAAAACAATAAAAGAAATTTAAGATGAATTAACAAAAAATGACCACAACTTCAAGCCACACATGATGACAGATATTGGCCAACTATTTTATTTTTAGAGGTTTTACTTTATTTTGTGGAAATACAGTTGATTGTTGTATTAATTTCTACTGTACAGCAAAGTGATTCAGTTATATGTATACATGTATATATATATATATATATATATTCCTTTTCGTATTCCTTTCCATATGTTTTATTACAGGATATTGAATATAGTCCCCTGTGCTATAAAATAGGATCTTGTTTTCTACCCATTCTATATACAGTAGTTTGCATCTGCTAATCCCAAACTCCCAGTCCATTGCTCTCCCACATGCCCTCCCCCTTGGCAATCACGAGTCTGTTCTCTATGTCTATGAGTCTGTTTCTCTTCCATAGGTATATTCATTTGTCTCCACTTTTAGATTCCACACATAAATGATATCATATGGAATTTGCCTTTCTTTTTCTGACTTACCTCACTTAGTATGATAATCTCTAGTCCATCCATCGTGCTGCAAATGGCATTATTTCCTTCTTTTTTACGGCTAATATTCCACTGTATATATGGACCACGTCTGCTTCTGTTCATCTGTCAATAGACATTCAGGTCACTTCCATGTCTTGGCTATTATCAATAGTGCTACAGTGAACACTGGGGTACATGTGCTTTTGAACTTATAGTTTTGTCTAAATATACGCCCAGGAATGGGATTGCTGGATCATCTGGCAACTCGATTTTTAGTTTCTTGAGGAACCTCCGCATTGTTCTGCATAGTAGCTGCATCAATTTATATTCCCACTACCAGGGTCAGAGGGTTTCCTATTCTCCACAGTCTCTCTGATGGCCATTCTGCCTGGTGTGAAGTGGTTGTTGTTCAGCCACTCAGTCGTGTCTGACTCTGGAGCCACATGGACTGCAGCACACCAGACTTCCCTGTCCTTCACCATCTCCCAGAGACTACTCAAACTCATGTCCATTGAGTCAGTAATGCCATCCAACCATCTCATCCTCTGTCATCCCCTTCTCCTCCCGCCTTCAGTCTTCCCAGCATCAGGGTCTTTTCCAATGAGTCAGTTCTTTGCATCAGGTGGCCAAAGCTTCAGCATCAGCCCTGAATATTCAGGATTGATTTCCTTCAAGGTCGACTGGTTTGATCTCCTTGCAGTCCAAGGGACTCTGAAGAGTCTTCTCAACACCATAGTTCAGAAGCACCAATTCTTTGGCATTCAGCCTTCTTTGTGGTCCAATTCTCACATCCGTACATGACTACCAGAAAAACCATAGCTTTGACTATATGGACCTTTGTCAACAAAGTAATGTCTCTGCTTTTTAATACACTGTCTTGTGGTCATAACTTTTCTTCCAAGGAGCAATCATCTTTTAATTTCATGGCTGCAGTCACCATCTGCAGTGATTTTGGAGCCCCAAAATAAAGTCTGTCATTGTTTCCATTGTTTGCTCGTCTATTTGCTATGAAGTGATGTGACCGGATGCCATGATCTTAGCTTTTTGAATGTTGAGTTTTAAGCCAGCTTTTTCCACTCTCCTTTTTCACCTTCATCAAGACACTCTTTAGTTCCTCTTCACTTTCTGTCATAAGGGTGGTGTAATCTGTGTATCTCAGGTTATTGATATTTCTCCCAGCATTCTTAATTCCAGCTTGTGCTTTATCCAGCCCAGCATTTCACATGATATACTCTGCATGTAAGTTAAATAAGCAGGGTGACAGTATACAGCCTTGACATACTCCTTCCCCAATTTGGAACCAGTCCATTGTTCCATGTCCAGTTCTAAGTGTTGCTTCTTGACCTACATACAGATTCCTCAGGAAGCAGGTAAAATGCTCTGGTATGTCCGTCTCTTTAAGAATTTTCTACTGTTTGTTGCAATCCACACAGTCAAAAGCTTTAGAGCAGTCAGTGAAGCAAAAGTAGATGTTTTTCTGGAACTCCCTTGCTTTTTCTATGATCCAACAGTGTGAAGTGTGCTTCATTGTAATTTTGATTTGCATTTATGTAGTAATTAGCGATGTTGAGCATCTTTTCATGTGCCTGTTGGCCATCTATTTTTCTTCTTTGGAGAAATGTCTATTAAGTCATTTTTCAATTGGGAGAAACCCATATTTCTGTCTTCCCCTTTCTTACGGCATCTGATATATTCTGTCTTGTAAATATTTACAGTATTTATCTCCTCCCCACTAACCCAAGTGGTGAGGACCTTCTGAGGTCAAGAACTGTATGTCACCTTTATGATCCTATGGTTCCCATGCTACATACTTTGTGGATAGTAGCTGTTGGATAGATATTTTTCTGAATGAAACTGCTGTGAATTGAACCAGAAAAGATAAATCCTTATGTGAAAGAGTAGAGAAAACTGCTCTTCATCCCTTTGATATGGACGTTTTGACATTCATCATTTGGTGTTAAAGAAATAGGCCTCTAATCATATCCCAGACACATAGTCTCTTTCCTAAATAACAAGAGATTTTCACTGAAATATAATTAGAAGAATTTAAAATTTTCAAGACCAGCCTCACATAGAAATTTGACTTGACTATCTCAAATAAATTTCCATCACAAAAATGTCTGATATGTATTGAATTTTACAAATCCTGGATATCAGTCATGCTCTAATCTGAGTTAGACAATAAAATGTCTTTGTCTCTTGATTCCCATATTTATGAAATATTGATCTAGAAATACTGAGATTTTCACTTTATACATGAGAGTAGCAGGAAAAATCCATTTAGTCTAGCCATTTATTTTTCGATCAAGTATTTTGTTAACATACTAAACTGAGTAATCTTGAGTGCTTAAGTTGATTTTTCATTTTTGACAGGTAAGCATATCTGACTTCTTGAAGGGGAAGAGGGATAAAATTAGTTTTGCTATCAATAGCTTCTGAAGTCCATCTATAATAATGTTGATGAATCCTCCTAGTGTTTCCTCTGGGTTCCTGCCTTTTGGCCATTTCTATACTTAATTTCTGGCTTACTTTGTAACACTTTGGAAAAATGAAAAGAAATACAATTCGAATCAGCCAATTTTGGTGCTTATGCTAAGTTCTAGTAGTAATTTAGTAGAGGATGAATTACTGATGACAATCTGTTCCAACAAGTATGTATAGATTTACATTGTCTATGGTTTTATTCATCTGTTGCCCTAGGATAGAAATTCAGAGTTGGCAATATTTTGCTTTCACGGTGCAGTCAGTAATTTAAAGCAGTATGTGGTAACTTTTTGTTTTAATGTCGATGCCCCAAGGGGTCTGTTATTAATTTAAGTTAAACTTTAGAAAGAATTTTTCAGGGTTAATGATATCTACTTTTTTCCCTATTGTAG
Seq C2 exon
GCAGCTCATGGCCAGAGGGGACATACAGGCCCACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000012837:ENSBTAT00000017057:19
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=1.000
Domain overlap (PFAM):
C1:
PF0139113=Collagen=FE(17.9=100),PF0139113=Collagen=FE(28.3=100)
A:
NA
C2:
PF0139113=Collagen=PD(0.1=0.0),PF0139113=Collagen=FE(18.3=100),PF0139113=Collagen=PU(11.8=83.3)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development