BtaINT0042227 @ bosTau6
Intron Retention
Gene
ENSBTAG00000030190 | COL6A3
Description
collagen, type VI, alpha 3 [Source:HGNC Symbol;Acc:HGNC:2213]
Coordinates
chr3:117459803-117463542:-
Coord C1 exon
chr3:117462934-117463542
Coord A exon
chr3:117460409-117462933
Coord C2 exon
chr3:117459803-117460408
Length
2525 bp
Sequences
Splice sites
5' ss Seq
CGGGTAAGG
5' ss Score
10.17
3' ss Seq
TGATAACATTTGATTCACAGTGG
3' ss Score
3.96
Exon sequences
Seq C1 exon
TTTCAGTTGAAAAGGATGTGGTGTTCCTGATTGATGGCTCCGAGGGTGTCAGGAGCGGCTTCCCACTGCTGAAGGAGTTCGTCCAGAGAGTGGTGGAGAGCCTGGACGTGGGACCAGACCGGGTGCGTGTGGCCGTGGTGCAGTACAGCGACCGGACCAGACCTGAGTTCTACCTGAATTCCTACATGGACCAGCAGAGTGTGGTCGGAGCCATCCGTGGGCTGACCCTGCTGGGCGGGCCGGCCCCCAACACAGGGGCTGCCCTGGAGTTCGTCCTGAGGAACATCCTGGTGGGCTCTGCTGGGAGCCGCATAGCAGAAGGTGTCCCCCAGCTCCTGATTGTCCTCACGGCCGACAGGTCTGGGGATGACGTGAGGGGCCCCTCTGTGGTCCTGAGGAGGGGAGGGGCCGTGCCCATCGGCATCGGCATTGGGAACGCTGACATCACCGAGATGCAGACCCTCTCCTTCGTCCCGGACTTCGCCGTGGTCATCCCCACCTTCCGGCAGCTGGGGACCATCCAACAGGTCATCTCGGAGAGAGTGACCCAGCTCAGCCGCGAGGAACTGAGCAGGCTGCAGGCGTCTGTCACCCCCTTGACGACTCCGG
Seq A exon
GTAAGGAGCCAATTCTCTGGCACTTCCTTCCTTAAAATATCTGGGGCTATTGGGACTGCGGGTTACAAAGGCCTCTCAGTTTTGTTTCCTCCTCCATGGGGTGTGGAAACTAGGCTTACATGAAGAATTAGGAGCCGCTTGGCCTTGGTGGCCAGAAACGACTTGGGGAGAGGCCGAGAGTCGTGTTTTTAGCCAAATTTAAGTCTCAAAAGAGAAGTGGGCTTGGTTTACAGTTCAGACCCCTAACTCTGCATGAAGGCTTCTGTGCTGATAACTGAAGAGAGGGGCCATCTAGTTGATAAAACTCCCGTGCAGTGCCAGGTCCTCGTTACCCTTGGGGGTTCAGCTGGCAGCCTCCGATGGTCAGGGAAGGTGTTCATCCCAGTTGCCTCTGTCAAGCTTGGGCACCGTTTCTGAAATGTTGGTATTCTCAGAGCCCAAGTGTGAAGATGGCGTTTGAATTTGCTCAGCGCAGAGAAGGGAGTGTCTGAACTGGCAGGAGGGCCACCTGGCTCTTCTGACCTTGGCTTATTCTACTTCCTGTTCCGCTTCCCCAGGCTTGATGCAGAAGAAAGGGGGCTTAGATAGGCCCACCCTTCCAAGAAGGCCCACAGAGGAGCTCCTCTCCCTGGGGCCTCGGGTTGGGAGGGCACAGTGGAGAACAGGCACACACAACGTCACCCCTGCGTGGTTCACATGCCTCACAACAGCATCTGCATCCAGGGATGGGGAGGCTGGGGTCGGCAGGCGGGGAGGGAAGAGTGAAAGCAATCGAGAGAAAAGTAGATGCAGGAAACCATTAGGGCGGGTGAGAGAGGGGGCAGCGTCCCCTCGCTGGTGTCCACGCAGAACAGCACTCCCTGTGAGCCTTCCTTGGAATGTTCTACAGGGCTCACCATCCAATAAATTGGGGGAAGCTGTGGGATAAATGCAGTGAGGGTTTTGTTGGCTGTTCCCTAGTTGAAGTGTTTTATGTGTCCCCCATACAATAGGGGAGCACTTTCCAAAACTTGTTTGGCTGCAGGAATCTCTCTCTTTTTTTAGTTTTTAATTTATATTGGAACACCATTGATTTACAATGTTGTGTTTGCTTCAGATGTACTGCGGAGTGATTCAGTCATACATATACATATATCTGTTCTTTTTAAAATCCTTTTCCCATTTAGGTTATCACAGCCTACTGAGTAGAGTTCTGTGTGCTCTATAGTAGGTTCTTGTTGGTTATTTTTTTAAATATAGTGGTGCGTATATGTCAACTCCAAACTCCGACTTTATCCCCCACCCCACCCACCACCTTTTTTGTGGTGCATTTGAGGCAGTGGCGCTCCCAGGAAGGCACTTTGGAAATGCTGGTATCGCGTGTGGCAGCTTCTTTAAACATAAGCACGTTTCTACAGCAGTGTGGCTCCTGGTCCGTTTGCTTTCCCCCTCTTCAGGATAACTATTTTCTACCTTTTCCTCATTCTGCTTCATCTACACCTTTCCCTCTTCAGTTAACTCTGAGCTGGTGATCTTGATTTCCATTTCACTGAGAAAGTATAAGTAAAATCAAAGAACATCTCTGCTTCCTCTAACAGTCTGCCTCCTCCCTATTCAAGAGTGCCTCCTGCAACTCTCCTGTCTCCTGCATCATTGATTCTCCGATGTACTGTATAGATCCTTTCATGATATGTACGCAGTGCCTTTTCTTCTCTCGTAAAAACCCTCTGGATGCCCTGCTCTCCCCTTCAGGAGGGTCCCGGTCTCCTTTTTTTTTTAATTAAAAAAAATTAATTTACTTCTTTTAATTAAATTGTATAATTTATACAATACTGTGTGGTTTTTGCCATACACTGACATGAATCAGCCACGGGTGTACATGAGTTCCCCGTCCTGAACCCCCCTCCCACCTCCCTCCCATCCCATCCCTCTGGGTTGTCCCCATGCACCGGCTTTGAGTGCCCTGTTTCATGCATCGAACTTGGACTGGCGATCTAGTTCACATATGGTAATATACGTGTTTCAGTATTATTCTCTCAAATCATCCCACCCTGGTCTCCTTTATAAGCATCATCTTCACTGCCTATAGTTCTCTCTGAACTCACCCTAGCCTGTTGTTAGCTCTCTCTGCTCCACAGAAAGTGTGCTGGGCAAAGTCCCTCCATCTGGCAAATCCCAGTGGTCAGTGTTGGGTGCTGTTACGCTTGACCCATGAGTGCCATCTGTCACAGCGGTGACCCCCTCCTTCCTAGAATGCCATGCTCCCTCGGTCCAGATTCGGCTCTTGTGTGTCTAGGTTCTTCCTCCTGCAGAGTCATTCTTCCTTATCCTCTGCTGGTTCTTCCTCTTCTCTCTTCCTCTTCTTCTCTTCATCACTGAATTCCCCAGGATCCTCTCCTGGGACTGGTGTTTTAACTTGAATAGTCTGAATTAGGACGCCTCGCCTGCCAGGTGGCAATTCTGTGACAAACTGGGAGGCGGCTCATTCGACACAAAGGCTCTGGTGCCAGTGGAGCTGAAGCCCTGTGATAACATTTGATTCACAG
Seq C2 exon
TGGTCAGCAGCAAGAGGGACGTGGTCTTTCTCATCGATGGGTCCCAGAGTGCTGGCCCCGAGTTCCAGTACATCCGAACGCTCATCGAGAGGCTGGTGGACTACCTGGATGTGGGCTTCGACACGACCCGGGTGGCGGTCATCCAGTTCAGCGATGACCCCAGGGTGGAGTTCCTGTTGAACGTCCACTCCAGCAAGGACGAGGTGCAGAACGCCGTGCGGCGGCTGCGGCCCAAAGGTGGGAGGCAGGTCAACGTTGGGGGTGCCCTGGAGTACGTGGCCAGGAACATCTTCAAGAGGCCCCTGGGGAGCCGGATTGAGGAGGGTGTCCCTCAGTTCCTGGTCCTCATTTCCTCCGGGAAGTCGGATGATGAGGTGGAGGACTCGGCCATAGAGCTCAAGCAGTTTGGCGTGGCGCCACTCACGATCGCCAGGAACGTGGACCAGGAAGAGCTGGTGAAGATCTCGCTGAGCCCCGAGTACGTGTTCTCAGTGAACACCTTCCGGGAGCTCCCCAGCCTGGAGCAGAAACTGCTGACACCGCTCACCACCCTGACTGCCGGGCAGATACAGCAGCTCCTGGCCAGCACGCGCTACCCGCCTCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000030190:ENSBTAT00000018479:8
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.015
Domain overlap (PFAM):
C1:
PF0009223=VWA=WD(100=85.3)
A:
NA
C2:
PF0009223=VWA=WD(100=84.7)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
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]