BtaINT0041605 @ bosTau6
Intron Retention
Gene
ENSBTAG00000021466 | COL3A1
Description
collagen alpha-1(III) chain precursor [Source:RefSeq peptide;Acc:NP_001070299]
Coordinates
chr2:7335959-7336249:-
Coord C1 exon
chr2:7336205-7336249
Coord A exon
chr2:7336058-7336204
Coord C2 exon
chr2:7335959-7336057
Length
147 bp
Sequences
Splice sites
5' ss Seq
ATGGTAAGA
5' ss Score
9.48
3' ss Seq
TGTGCTTGGATTGTTTCCAGGGT
3' ss Score
7.31
Exon sequences
Seq C1 exon
GGGCCTCCTGGGAGTAATGGTAGTCCTGGTGGCAAAGGTGAAATG
Seq A exon
GTAAGATGTCCCCACAACTCACCCGCATCTCAGTTCAACACACATTTTTGGCTTCCTTTGTATTTAGCATGATAAGACATTTAAGTTGGTTACTTAGAAAAGAAAATTCAAGTCTGGCTCATGTTAATGTGCTTGGATTGTTTCCAG
Seq C2 exon
GGTCCTGCTGGCATTCCTGGGGCTCCTGGGCTGATAGGAGCTCGTGGTCCTCCAGGGCCACCTGGCACCAATGGTGTTCCCGGGCAACGAGGTGCTGCA
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000021466:ENSBTAT00000028617:21
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(15.4=100)
A:
NA
C2:
PF0139113=Collagen=PD(22.1=45.5),PF0139113=Collagen=PU(37.2=97.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGCCTCCTGGGAGTAATGGTA
R:
CACCTCGTTGCCCGGGAA
Band lengths:
138-285
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]