BtaINT0040912 @ bosTau6
Intron Retention
Gene
ENSBTAG00000011741 | COL13A1
Description
Bos taurus collagen, type XIII, alpha 1 (COL13A1), mRNA. [Source:RefSeq mRNA;Acc:NM_001105433]
Coordinates
chr28:26376472-26377261:+
Coord C1 exon
chr28:26376472-26376624
Coord A exon
chr28:26376625-26377162
Coord C2 exon
chr28:26377163-26377261
Length
538 bp
Sequences
Splice sites
5' ss Seq
CCGGTGAGC
5' ss Score
8.69
3' ss Seq
AGATCTTTGTCAATCCATAGGGT
3' ss Score
7.48
Exon sequences
Seq C1 exon
GGACCTCGAGGCAAACCAGGAGATGTGGGCCCTCCTGGTCCCCAAGGCCCCCCAGGAAAGCCTGGGCCTGCAGGAATGAAGGGAGAAGACGGCCTCCCGGGGAGCCCAGGAGAGAAGGGGGAGAAAGGGGAGACGGGGCAGCCGGGACCACCG
Seq A exon
GTGAGCGCCAGGGCCCACCTAGCATGATACAGCTGTGTACTGTGCCAGGTGCAGCTGGAAACAGGGTTGGGAGCCGGGCACAGGGGCTCACCTGCTTTCTCCTCCAGCCTTACTTTATGAAAGCTAGTTTCCTGCCTCAAGAGACCTGGGTCCTGCTCTGTCACCTCCCATTCGCAGGAAAGTCACTGAGCCTGGCAGAGCCTCAGTTTCCTCATCTGTAAAATGGGGATGATAATGCCATCCCTGGATACCTCCCTGGGTTGTTGGGAAGATAAAGTTGTGGGTGTAAAACTGTCTCTTGGGACAGCATACAGAAGCCCTAGACCCAGGAGAGGTACAAACAAGGAACCTTGCCCAGGCCAGCTAGGTTTGACCTAGGAACCTTCTTTGGGCCTCACAGCTTCCTTCTGAGAAATGGACGGCACCCTAGACATCCGCTCTCGGGGGAAGGGGGTCCCACGTGCAGGCCGCAGCTTGTCCGCAGACCTCAGTGTGACGACCTGGCCCTTGATTAACAGAGATCTTTGTCAATCCATAG
Seq C2 exon
GGTCTAGACGGCCCAACTGGGGAGAAAGGAGAACCAGGTGACCAAGGGAGACCCGGAGCGACTGGACTTCCTGGCCCAATCGGGCTCCCAGGATTTATA
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000011741:ENSBTAT00000039811:26
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=PD(37.1=45.1),PF0139113=Collagen=FE(58.8=100),PF0139113=Collagen=PU(9.0=15.7)
A:
NA
C2:
PF0139113=Collagen=PD(41.1=90.9),PF0139113=Collagen=PU(29.4=60.6)
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:
CTCGAGGCAAACCAGGAGATG
R:
TAAATCCTGGGAGCCCGATTG
Band lengths:
246-784
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]