BtaINT0040842 @ bosTau6
Intron Retention
Gene
ENSBTAG00000020056 | COL12A1
Description
collagen, type XII, alpha 1 [Source:HGNC Symbol;Acc:HGNC:2188]
Coordinates
chr9:14935332-14938475:-
Coord C1 exon
chr9:14938329-14938475
Coord A exon
chr9:14935472-14938328
Coord C2 exon
chr9:14935332-14935471
Length
2857 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAGG
5' ss Score
11.08
3' ss Seq
TACTTCATTTCCATGTGCAGGTG
3' ss Score
9.07
Exon sequences
Seq C1 exon
GTATTAAAAATGCTGATGAAGTTGAGTTAAAGATGATTGCAACAGATCCTGATGATATCCACGCGTACAACGTGGCGGATTTTGATTCACTTTCTAGGATCGTGGATGACCTCACCAACAACTTGTGTAACAGTGTCAAAGGTCCAG
Seq A exon
GTAAGGTTAGCCCAGGTTCTTACCCTCAGAACTGTTGGTATTTTGGTCCATTTAATTCTTTGTAGAATGGAGGGAGTGGATTACTTTGTGCATTGTGAGATGTTTAGCAGCATCCCTGAACACTGCCCACCGGATACCAGTAGTATCCCCTGAGTTATGACAACTAAAAATACCTTCAGAATGTGCTGAACGTCTGCTGGGGAGAACACTGCCCCCAGTTGAGAATCATTGATTTAGTCCTTGGGTTTTCTCTGATGGCATCAAACTGTAAATGACTTCTAGTTTATTTGGGGATACATTTAGTTTAAATGTGCCTGTATCAAACACATGCTTCCTAGGTGGCTCAGTGGTAAAGAATCCTCCTGCCAATAAAGGAGATGCAGTTTTGATCCCTGGGTCAGGAAGATCCCCTGGAGAAGGAAGTGGCAACCCACTCTAGTATTCTTGCTGGGATAATCCCTTGAACAGAGGAGCCTGGTGGGCTATGGTCCATGTGGTTGCAAAGACTTGGACATGATGGAGCGACTGCACACGTGTGCACCACACACACAGACACATACACAAGTGAGATTAGGGAATAAAGAGGTGCTTTCTCTCCTGGTGTATATTTTTCTCTGGTAAACCATCCTCACTCCATATCACTACTAAGTTACTATTAAATGCCCCAACCAGAGATGATCACATTTGATACTTTGCACTTGTAACTTCTAAACATAAAGACAAGTTACAGTTTAGAGTGTGGATTTTTAGAAAGGTTAGAGTGTGGATTTTTAGAAAGGGTATCATCTCTCTTTACCACTGAAGAAATAGATTTAGAGAAATACAGTTACTTACTCAAAGTCAGATGGGTAAAGATGTTTTGAGAGGTCCTTGAAAAAAGGTAGCTATTGATAAGGAATGAAGATTTAGAAATAAAATTATAGAAGTGAATTTGTAGTGGTAAGTGGTATAAAATAATTACTACCTGTGTAAATTGTAGGACAAACCATGGTAAATACTAAATTGAAGGTATTTTGAAAATTAATGATAAAATGATGGTTCTTATTGTATGAGAAAAATTTCTTTTAAGTAAGTGTAGATTCTGGTAAAGATTGTCTTTCATTAATTTACTCTGGTTTTGGAAAGTTGGAATGAGTTTAACAAAGTGGTAGAAATGGTTCACGTGCTTTGGATACTAAGGATACATTTATTTGAATGTTCCTTCTTGAATTTCTCTCTTCAAAATTTTGCAGATTTTCTTTTTGGATTTTGAACAATAGAGTGACCTTTTCCCAGGAGAAATAGAGCAGCCAGGAAGCCAGAATTTGTAGGCGTCTGGCTTTGGATTAGCTGAGAGAGTTGTAGTTTTATTTAGTTGGAGAGAACTTTGAGTGGGGATGAAAACATCTTTTATCTGTTTTACTTTATTTTTTTTACATCAGCTATGTAATAGTTGCATTCATTTAGTTTCCCAGACAGTAAAATTGCTTGATAATTTTGTAGGCTTGATTATGACCCAAGTACAATAAAGGTTAGGATACTAAGAATGGAAATGCTTTTTCCCAGCTTTGGCTTACAAAGAAAGTAGGAAGAGTTCATATGAGAATGATTTGCCATGCTCATGGAGTCACTGTATTAGCTCTCCTATGATTATTATTTGAGATGTCTCTCTAGTTAATGGTCTTATTGAGCCCAATATTTCTATTTTCACTTATATTGATTCCAAATATTTTTATATATTTGTCATTTCACCTACACTTATGAACAGAAAAAAACAAACACAGCAGTAGGATATTCCTAAATTTTAGAAGACTTGGTTGTTTCTCTCTGAGTGAGAAAGGAAGTAGGTTCTCTTACCACTGAATTAGATCCTGAAAAGGAACTAAACATGAATAAAAAATCACTTCTGTCCTCACAGAGCATAACTTATGGTTAAGAAGATAAGACATGAATGTAAATAATCAACATGATGATGAAGGCAGTGAACTTGGGTGGTACCAATAGCGATAGAGGCGATAGAGTTGTCAGGCCCCATGTTGTCATTTACTGATACATGCAGAAGGTGGGAGAGCAGAGAGAGTATCCGGGATGAGTCGGAGGTATTGAATCTAGGTGACTGATAAACTGTGATGCTGTCAGGATGAGGGGAGCGGCTTTTAAAGGATGACAAGAGCTCAGATTTGAATTTCCTGAGGGTGAAGAATCTTAGGCCACCCATTCAGAGAGGACTTAGGGGCACTGGGCTGATTTACTGGAGAAGACTCTTGAGAGTCCCTTGGACTGCAAGGAGATCAAACCAGTCCATCGTGAAGGAAATCAGTCCTGAATATTCATTGGAAGGACTGATGCTGAAGCTGAAGCTCCTATGCGTCGGCCACCGGATGCAAAGAGCTGGCTCATTAGAAAAGACCCCTGATGCTGGGGAAGATTGAGAGCAGGAAGAGAAGGGGGCAGCGGAGGATGAGATGGTTCGATAGCATCACCAACTCAATGGACATGAATTTGAGCGAACTCCAGGAGATAGTGGAGGACAGGAGCCTGGCCTGCTGCAGCCCATGGGGTTACAAAGAGTTAGATGTGATTTAGCAACTGAACAAGAACAACTGTAACTTGTTAGTATATGAAAGAATGTGTACAACTGTAACTTGTTAGTATATGAAAGAATGTGTACAACTGTAACTTGTTAGTATATGAAAGAATGTGTACAACTGTAACTTGTTAATATATGAAAGAATGTGTACAACTGTAACTTGTTAGTATATGAAAGAATGTGTACAAAAGCTTGAAATACGGAGAGGAACGCCACTGCAACCTAATTTAAATACCGTCATCTTGCTGTGATAATGAAAAAGTCTATGTACTTCATTTCCATGTGCAG
Seq C2 exon
GTGACTTGGAAGCACCTTCCAACCTAGTTCTTTCTGAGCGGACCCATCGTTCTATGAGAGTGAGCTGGACACCTCCTTCTGACAGCGTGGACAGGTACAAGGTGGAATACTACCCAGTGTCAGGAGGGAAACGGCAAGAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000020056:ENSBTAT00000026725:20
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.060 A=NA C2=0.234
Domain overlap (PFAM):
C1:
PF0009223=VWA=PD(21.4=74.0)
A:
NA
C2:
PF0004116=fn3=PU(53.8=91.5)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping 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]