BtaINT0042255 @ bosTau6
Intron Retention
Gene
ENSBTAG00000012837 | COL6A6
Description
collagen, type VI, alpha 6 [Source:HGNC Symbol;Acc:HGNC:27023]
Coordinates
chr1:153331553-153336354:-
Coord C1 exon
chr1:153335683-153336354
Coord A exon
chr1:153331650-153335682
Coord C2 exon
chr1:153331553-153331649
Length
4033 bp
Sequences
Splice sites
5' ss Seq
GGCGTAAGT
5' ss Score
9.39
3' ss Seq
GATTTTCTTTTTCTTCCTAGGTG
3' ss Score
10.85
Exon sequences
Seq C1 exon
ATGTATGCAAGCCGGACGCTTCTTGCGATCAAGCCAGACCACCCCCTGTGCCATCTTACGTGGACGCTGCTTTCCTTCTGGACGGCTCCCGGCATGTGGGAAGTGCAGAATTTGAAGACATACGAGGATTCTTGGGGGCGCTGTTAGATCACTTCGAAATCACCCCAGAGCCCGAGTCCTCTGTCACCGGAGACCGGGTGGCCCTATTAAGCCTCAGTCCCCCTCACTTCCTACCCAACACTCAGAGGAGCCCTGTTAGAAGCGAATTCAACCTGACCACCTACAAGAGCAAACGCCTCATGAAGAGACACGTGGAAGAATCCGTTCAGCAGCCAAATGGAGATGCTTTTATTGGTCACGCCCTCCAGTGGACTCTGGACAATGTCTTCTCAAGGACACCCAATCTGAGAAGGAATAAAGTCATTTTTGTGGTATCTGCTGGGGAAACCAGTCACTTGGACAGGGAAACCTTAAAGCAAGAATCCTTGAGGGCCAAGTGTCAAGGTTATACCCTGTTTGTGTTTTCCCTTGGGCCTTCTTGGAATGACCAGGAACTGGAAGATCTAGCCAGCTACCCTTTGGATCACCACTTGATCCAGCTTGGCCGCATTCATAAGCCTGACCACAGATACGCTGTGAAGTTTGTGAAGGCTTTTATAAGCTCAGTCAGGC
Seq A exon
GTAAGTCATAAAATCATATTCTTTCTTGCACATTTCAGTATATTTGGGATTCCCCAAAGAAGGGCTGATGAACTGACATGGATTCTTGGAAGCCTCTGTCTTCAAGGGCACTGCAGGGTGAGAAAGGAAAACAGGGAATGATGGATGGTGCAGGGAGGAAGCCTATGATTTCTAAGCATTGAATTCTCTGGCTCCTCTTTTTTATGCCTCTGGTTTCTATGGAGAAGCAGTCATAACAAACAGCTACTCACACATCTGTAGTCACAGCCGGGATACTAGCCACAAAGTAGAAACGCTTGCCATATAACATTATCACGCTGCCCTTTGATGGAAAGTTTGACCAGTTAACACTCCGAGAGAGAGCTAGAGAAAAATTCAACAATCCTTGGCTTTGCTTTTACAAGTTCTAAAGGCAGAGTCTGAAGTTTTAGGAGGTACCACTTTACATGTCAGAATGAAAGATGCATCCTTGCAAAACTTTCTTAGCTTTGTTAATGATTCTTTATGACGCCAGTAATTAGTGTAACTGTTGCCCATAAAAAAAGAAACATGGGTTATATTTCTTGGCAGGAGCTTGTCTCGAAAGTTTGCAATTCATTTTGAATGCAGCAGGATGGATTCAGAGAAGCCTGGTCCTGATATGGCTATGGAGGTCGAAAAGCACTGTCAGACTTCTGATGATTTTACTTTTGGAGTTCAGACAAGGGAAAGCGGACATGCAGGCTAAAGGGCACCCAGTGCCACATCCTAGGTCGCAAACTTGTCACTGACATTCACCGTGAGACCAGCTAAGGCTGCAGCTGCAAAGACCCTGACTGGTCAGGGCCGGGGAGGTCTGAGGGGCCTTGGGGAATAGTCGGTGGGGCTGATGCCGTGTCCTCGAGTTCTCTACTACTCGAGGAGTGAGTCTAGGACCAATGTCCCAGCATCTCCTGGGAGCCTGTGAAAAATGCGGACTCTCCCGCCCCACCCCAGACATTTTGTTCCAGAATCTGCATTTTATCAAGATCCCCAGTGATTCCTATATACATTATATGGTTTGAGAAACACTGATGCACGAGGCATATGCTCCTAGAATAAAATTTCTGTGGATTGGGTTCTGGAATAGGAACCAGAAAGAAGAGCTGGGAAAATGAGGGGGAAAAAATAAGTGAAGGCCAGGGGTCGTTTGGAAAGAAGAACTCATGAGGCATTTGTAAGGGTAAAACAGAAGAGCACCTTGAAACTCAGCCACTGAAAAGCCACTGACTCTGTTTATTAGCATTCCCCTCCCCCTCCTTCCTTCTCCTCTCTGCAAACGTGTTCTCCTGTCCTTCAGATCAGATCAGATCAGATCAGTCGCTCAGTCGTGTCCGACTCTTTGCGACCCCATGAATCGCAGCACGCCAGGCCTCCCTGTCCATCACCAACTCCTGGAGTTCACTCAGATTCATGTCCATCGAGGCAGTGATGCCATCCAGCCATCTCATCCTCCGTCATCCCCTTCTCCTCCTGCCCCCAATCCCTCCCAGCATCAGAGTCTTTTCCAATGAGTCAACACTTCGCATGAGGTGGCCAAAGTACTGGAGTTTCAGCTTTAGCATCATTCCTTCCAAAGAAATCCCAGGGCTGATCTCCTTCAGAATGGACTGGTTGGATCTCCTTGCAGTCCAAGGGACTCTCAAGAGTCTTCTCCAACACCACAGTTCAAAAGCATCAATTCTTCGGTGCTCAGCCTTCTTCACAGTCCAACTCTCACATCCATACATGACCACAGGAAAAACCATAGCCTTGACTAGACGAACCTTTTGCTTGTGGCTTGCAATGTTCCAGACCCTGAATTACAAGTGTCTGCTGATCCCAAATAAACCCATTTTCATGGAAAAGCAGAACAGAAAACACCTTGAAAGACTGAGAAATTTGTCAAGAAACACTCCTTATAAGGCAAAAAGTTGAAAGGAGGTTAAGATGGAATTTACTTCCCTGGCCCCACAAAATTCTTAGTGGTGTTTCATGGTAACGAGTCAAACTATATGATTAGATAAATCACCACCCAGGGAAAGGGGAGGAGATGCTTTAAGAAGAATTACTTGGGGTGGGTGAGAAATATATAAAGTGCTTGTGAAAAACTATAGTCATGACACCACTTTTCTAAAAAGTATCTAGAAATCTCCAACATTTATTTTTTTGTGTGTGTAATAAAGTTTTATTAAAGTATAAAGGAGATAGAGAAAGCTTCTGACATAGGCATCAGAAGGGGGCAGAAAGAGTACTCCCCTGCTAGTCTTCAGCTGGATGTTATACAGTCACTGCTGCTACTGCTGCTAAGTCGCTTCAGTCGTGTCCGATTCTGCGCAACCCCATAGACGGCAACCCACCATGCTCCCCCATCCATGGGATTCTCCAGGCAAGAACACTGGAGTGGGTTGCCATTTCCTTCTCCTAGAAATCTCCAACATTTAAACTATAGCTTTCAAAGTACAAAAAGTTGAAAAGATTTTGACATTCAGTTTAGCTGCTCAGTCATGTCTGACTCTTAGTGACCCCATGGACTGTAGCAGGTCAGGCCTCCCTGTCCATCATCAACTCCCGGAGCTTGCTCAAACTCATGTCCATTGATTTGGTGATGCCATCCGACCATCTCATCCTCTATTGTCTCCTTCTCCTCCTGCCTTCAATTCTGCCGTTAACAGGGTCGTTTCCAAAGAGTCAGTTCTTCGCATTAGATGGCCAAACTATGACTTTGACATAATCATATTCAATCCCACATCCTCCATTCAGAGCAGGCCCCCAGACCCACACGCACCTCTTCAATATTAACACATATGTAGGGGCTTCTCAGGTGGCTCAGGGGTAGAGAATCCACCTGCCAATGCAGGAGATGCAGGATATGTGGGTTCAATCCCTGGGTTGAGAAGATCCCCCAGAGGCAGAAATGGCAACCAACTCCAGTATGCTTGCCTGAAAACTCCCATGGACAGAGGACAGGCTCCAGTCCACGGGGTCACAAAGAGTCAGACACGACTGAGCAAATAGGCACACGGCACATTAGGTACCTACTTTGAGCCACTGACTGTTGAGGGACGGGGTATCAAGAAGGGACCAAAGTAGATCTGGTCCCAACCCTCCCAGGCATGCCCATCCAGCTCCCTAAGTAACTCCTGTTTATCCCGCTACTGTGACAGAATTGGCTACCAGACACAATTCACAGAATAAACATATTTTCTAAGCAAAACTACTACTGACAAAAGCTATTGCTGATACTTAGAGTGAAGACAGATAACGAAAAATCAGATGCGCATAAAGGAAACACCCCAGTCTGGGCCGTTCAGTCTAGAAGCACACAGCTCAGTCTGCAACAGCAGCTCAGGAGATGGTGCTGGGTCACAGTCCAGGACCAACTTGTAACTACGGGGACCCAGGATCACCAGGAAGAGGTTTAATCATGTTTAACATACAATTAAATTAAAGGCTTCAAGGAAATAAATAGTGCAATTTTAAAGTTTCTCATCAAAAAAAGGCTTTTTAATGTTTTAAATGGTATCGGAATAAGCATGCTTTAGTATTATGAAAAAATAATATATTTCAGATGAAATGAATCATAATGAATTAAACCCAAAATGGACCACAGTTACTGTTGCTGTTAATGATGCAGAGAACATAAAAGGAATATCCTTTTCCCTTTGCAATTTGGCATTTCAAAGGAGCAAATAAAAAATAACTATTCTGATTAGTTCAGGTCAGTTAGAGGCCAGACTTTTAGGATGGGCTCATGATTTCTCCTCTAATGTTCAATGGACTTTGGGAGCTAAGAGCATCTTACTGAAAAGTAAGTTGAATTCTCTACTTATACATTTGGCCGTCGTGACTTTTCTCAGCCTAGTTTAGAGACTCCATGAGAAATCTGCTTTCATCTCACGTGGCCACCCTAGTTGGTGTCTTTCTTTCATGGGTGTTGAGTACAGTGATGTGATGCTTTGCACGCAAAGCAGATTGCGGTCATGTTCATTGCTGTGAATAAGAGTCTCCTCACAGATTTTCTTTTTCTTCCTAG
Seq C2 exon
GTGCAATCAACAAATATCCACCAATAAATATCAAAGCAAAGTGCAACAGACTCAGCTCTATGGAGCCGCAGCAGCACCCACTCCAGTTTGTGCGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000012837:ENSBTAT00000017057:34
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.062 A=NA C2=0.121
Domain overlap (PFAM):
C1:
PF0009223=VWA=WD(100=79.6)
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
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