BtaINT0041270 @ bosTau6
Intron Retention
Gene
ENSBTAG00000013472 | COL1A2
Description
Bos taurus collagen, type I, alpha 2 (COL1A2), mRNA. [Source:RefSeq mRNA;Acc:NM_174520]
Coordinates
chr4:11642247-11642773:+
Coord C1 exon
chr4:11642247-11642345
Coord A exon
chr4:11642346-11642719
Coord C2 exon
chr4:11642720-11642773
Length
374 bp
Sequences
Splice sites
5' ss Seq
AGTGTAAGA
5' ss Score
4.57
3' ss Seq
TTTTTAAATGTTTATTATAGGGT
3' ss Score
7.84
Exon sequences
Seq C1 exon
GGTCTCCCTGGTATTGACGGCAGACCTGGGCCCATTGGCCCAGCGGGAGCAAGAGGAGAGCCTGGCAACATTGGATTCCCTGGACCCAAAGGCCCCAGT
Seq A exon
GTAAGAATCACCACCACCTCCTCTCCCTCAGCACTTCTTTGCGTCACATTTCATCAAAACTCTCATTTCTCTCTGGCATCAGTCCCCTCTACCTCAAGGGGTCCCTTTCAACACAAGAAAACCGTAACTTACCACTTAGCACATTAAAAGTTGACCTCCAGTATGTCATTGTGAAAACTCACATCCTGAGTTGCTTACGTCTGCGGACACAGCTGGACTTTATTGTAATCTAGATCTGCACAATGATGGGTCATGCCTTAGATAACAGAATTCAAGGATGAGGAAGCTAAAAAAAAAAAACCAAGATATTCATATTTCAGAATTGTCATGGTTAATTTGACATTAAATGTATGTTTTTTAAATGTTTATTATAG
Seq C2 exon
GGTGATCCTGGCAAAGCTGGTGAAAAAGGTCATGCTGGTCTTGCTGGTGCTCGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000013472:ENSBTAT00000033863:25
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(6.0=12.1)
A:
NA
C2:
NO
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]