BtaINT0042225 @ bosTau6
Intron Retention
Gene
ENSBTAG00000030190 | COL6A3
Description
collagen, type VI, alpha 3 [Source:HGNC Symbol;Acc:HGNC:2213]
Coordinates
chr3:117465614-117468086:-
Coord C1 exon
chr3:117467487-117468086
Coord A exon
chr3:117466187-117467486
Coord C2 exon
chr3:117465614-117466186
Length
1300 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAAG
5' ss Score
9.65
3' ss Seq
ACGACCCACTTTTGTTGCAGAGA
3' ss Score
8.03
Exon sequences
Seq C1 exon
TTCGCGTAAACAAAAGGGATATCATCTTTCTTTTGGATGGATCGTCCAACGTCGGAGAGACCAATTTCCCTTATGTGCGGGACTTTGTCATGAACCTAGTTAACAGCCTTGATGTTGGAAGCGACCACATTCGGGTCGGTCTAGTGCAATTTAGTGACACTCCGGTGACGGAGTTCTCCCTAAACACCTACCCGACCAAGTCAGAGTTGCTAGCTCACCTGAGGCAGATGCAGCTCCAGGGGGGGTCGGTCCTGAACACGGGCGCGGCCCTGAGCTATGTGCATGCCAACCACTTCACCGAAGCTGGCGGCAGCAGGATCCAGGACCACGTGCCGCAGCTGCTACTCCTGCTCACGGCCGGGCAGTCTGAGGACTCCTATTTGCAAGCCGCCAACGCCCTGGCGCGCGCGGGCATCCTGACCTTTTGTGTGGGCACTAGCCAGGCCGATAGGGCGGAGCTTGAGGAGATTGCTTTTAACCCGGGCCTGGTGTATCTCATGGATGATTTCAGCTCCTTGCCAGCTTTGCCTCAACAGCTGATTCAGCCCCTAACCACTTATGTTAGCGGAGGTGTGGAGGAGGTGCCTCTTGCCCAGCCAG
Seq A exon
GTAAAGCTCTGCGATTGCTCGGGGCTCCCTCTCCCCTACCCCCAGACACCTCTTTGGTGGGCAGGTGGCCCGGGCTGAACTCCAGAGGCTGGCGACGAGCTGTGCAGAGATGATGGGGTCCCTTTGGTTCATGGATTTTTGAAGGGAGGCTCAAGACACTGTACCAGCAAGCTTAGGTCCTCTGTCTAAAGGGTGTTTGTCCTTGAACGTCTAGAAAATCCAGTTTATGTTCTACCCAGGTTATCCCACCCTGGATTCAGAAGCTTTTACTTACTTTTTTTTTTTTTTTGCCCCAATGTCTCTGAAGATACTGGCATGCAAATCCGGATGGAAATGGGAGAAAAACAGAGAGAGAAAGCTGGATCCCCTTTTATACATGAGTATACATTGGGAACATTTAAAAGTGGAATTGATTTTCTTGATAGGATGTTTTTATATTCCAAATCTGCTGTATCTAGAAAAATTTTTGTCATAAACCCAACAAAGGCTGTGTCTTTTTGTGATGGTAAAGTGGTTTCCAAAGGCAGCCTAGGTGATGATGATTATGGTGGCAAATTAGTAAGATGATGAGTTATGGACCCTTACTTACACCAGTTGCTGACATCACGCAGATGGGTAGCTAGATGGAGCCCACTGAAGCCTAATCAAAATAGTTCTAAGAGTGGTTTGAACAGAAAATTATATTCACGTGACACATTGTAGCCCCTGACTGGCTGCTGCTGGGTTTTCTGTAGTCTGACCACAGCAGACTGGAAGTCACTGACAGAGATCCTTACCCACAGAGTCGTGATAGACACTATCTTGGGTTCTAACCCATAACCTCAAATTTAATGGAAAGAGAATCCAAATAGAGCATTGATGACACCTGATTATGTGTCAGTTACACTTGGGTGGATAACCCATAGCAGCCTTTGTCACTAGAGACAGAATTGATTTTTAAGCACAATGTTTTCAGAAGTTGGTAACAATTTGAAAACACCATCTGTTCTCCCAGAATGATTGGCACTGATGCTAGAACAGACCCCCGAGGCCTTTCTCTGGCTTGCAGCGTTGAGGAAGCAGGGCACTAGATTGGGCAAACGGTCCAGTGGTCCCAGCCCTGTGCACAGATGCACTGCTTTGAGAGGGGGCATTTGAATGACAGCTGGTGTGAGTTTTCTCTTCCCTTGCTGGTACAGTGATCATCAGGTGAATTGCCTGAATTCCCATGACTGAAAGCTGGCAGTGCTGGGCTGAGGTCGGTTTGGAGCCTATTGTGTTTTTGTCCCTCACTGTGCCCCACGACCCACTTTTGTTGCAG
Seq C2 exon
AGAGCAAGCGAGACATCCTGTTCCTTTTCGACGGCTCAGCCAACCTCATGGGCCAGTTCACTGCCGCCCGTGACTTTCTCTACAAGGTCATCGACGAGCTGGATGTGAAACCTGAGGGGACCCGGGTTGCAGTGGCTCAGTTCAGTGATGATGTCAAGGTGGAGTCCCGTTTTGACCAGCACCAGAATAAGCCTGAGATCCTGAATCTCGTGAAGAGGATGAAGCTCAAGACAGGCAAAGCCCTCAACCTGGGCTACGCCTTGGATTACGCACAGAGGTACATCTTTGTGAAGTCCGCTGGAAGCCGGATTGAGGATGGAGTGCTTCAGTTCCTGGTGCTGCTGGTGGCGGGAAAGTCATCGGACCGGGTGGATACACCCGCACTCAACCTGAAGCAGAGCGGGGTGGTGCCCTTCATCCTCCAGGCGAAAAACGCGGACCCTGCTGAGTTGGAGCTGATCGTACCATCCCCAGCCTTTATTTTGGTTGCGGAGTCCCTTCCTAAGATTGGAGACCTGCAACCACAGATTGTGAACCTCTTAAAATCAGTGCAAAATGGGGCACCGGCACCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000030190:ENSBTAT00000018479:6
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=0.000
Domain overlap (PFAM):
C1:
PF0009223=VWA=WD(100=88.6)
A:
NA
C2:
PF0009223=VWA=WD(100=90.1)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ATGCCAACCACTTCACCGAAG
R:
GCCGTCGAAAAGGAACAGGAT
Band lengths:
353-1653
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]