BtaINT0041622 @ bosTau6
Intron Retention
Gene
ENSBTAG00000021466 | COL3A1
Description
collagen alpha-1(III) chain precursor [Source:RefSeq peptide;Acc:NP_001070299]
Coordinates
chr2:7328853-7329043:-
Coord C1 exon
chr2:7328990-7329043
Coord A exon
chr2:7328907-7328989
Coord C2 exon
chr2:7328853-7328906
Length
83 bp
Sequences
Splice sites
5' ss Seq
AAGGTAACA
5' ss Score
8.92
3' ss Seq
TTTTTTTTTTCTTTTTTAAGGGT
3' ss Score
11.56
Exon sequences
Seq C1 exon
GGTCCCACTGGTCCCATTGGTCCTCCTGGCCCAGCTGGTCAGCCTGGAGATAAG
Seq A exon
GTAACACTTAACACTGTTTAGAAACAGAAAGTGTCTTTTGTTGCTGTTTGGATGAAGGACAATTTTTTTTTTTCTTTTTTAAG
Seq C2 exon
GGTGAAAGTGGTGCCCCTGGAGTTCCGGGTATAGCTGGTCCTCGCGGTGGCCCT
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000021466:ENSBTAT00000028617:37
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=FE(20.7=100)
A:
NA
C2:
PF0139113=Collagen=FE(20.7=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTCCCACTGGTCCCATTGGTC
R:
AGGACCAGCTATACCCGGAAC
Band lengths:
95-178
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]