BtaINT0041603 @ bosTau6
Intron Retention
Gene
ENSBTAG00000021466 | COL3A1
Description
collagen alpha-1(III) chain precursor [Source:RefSeq peptide;Acc:NP_001070299]
Coordinates
chr2:7345848-7346345:-
Coord C1 exon
chr2:7346143-7346345
Coord A exon
chr2:7345899-7346142
Coord C2 exon
chr2:7345848-7345898
Length
244 bp
Sequences
Splice sites
5' ss Seq
GCTGTGAGT
5' ss Score
7.39
3' ss Seq
ATATCTTTTCCATTTATTAGCCC
3' ss Score
4.93
Exon sequences
Seq C1 exon
CTGTTGACGGAGGATGCTCCCATCTCGGTCAGTCTTATGCAGATAGAGATGTATGGAAACCAGAACCGTGCCAAATATGCGTCTGTGACTCAGGATCCGTTCTCTGTGATGACATAATATGTGACGACCAAGAATTAGACTGCCCCAACCCTGAAATCCCGTTTGGAGAATGTTGTGCAGTTTGCCCACAGCCTCCAACAGCT
Seq A exon
GTGAGTTGAAAGAAAATCTGTATATATTCATGATTCTTATTTAAACACATGAGTAGTTCCTATGTCATAGGAGCCAGAAAGGAAATGAAGGTAATATCTGGCAAACAGTCAAATGGGCATTACCAGTAAAAGGTGAACCTTCCTATTTAAAACCAGGGGTTAGATGTGATTTAGGGTAAGAAATTGGGACATATTTGATGGAAAATTTTTTCTGTGTTTAATCTATATCTTTTCCATTTATTAG
Seq C2 exon
CCCACTCGCCCTCCTAATGGTCAAGGACCTCAAGGCCCCAAGGGAGATCCA
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000021466:ENSBTAT00000028617:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.074 A=NA C2=1.000
Domain overlap (PFAM):
C1:
PF0009313=VWC=WD(100=83.8)
A:
NA
C2:
PF0139113=Collagen=PU(28.3=88.2)
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:
CTGTTGACGGAGGATGCTCC
R:
GATCTCCCTTGGGGCCTTGAG
Band lengths:
252-496
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]