BtaINT0041611 @ bosTau6
Intron Retention
Gene
ENSBTAG00000021466 | COL3A1
Description
collagen alpha-1(III) chain precursor [Source:RefSeq peptide;Acc:NP_001070299]
Coordinates
chr2:7333621-7333929:-
Coord C1 exon
chr2:7333876-7333929
Coord A exon
chr2:7333720-7333875
Coord C2 exon
chr2:7333621-7333719
Length
156 bp
Sequences
Splice sites
5' ss Seq
CCTGTAAGT
5' ss Score
7.52
3' ss Seq
ATATAATTTTTTCTTATTAGGGA
3' ss Score
7.84
Exon sequences
Seq C1 exon
GGTATTCCTGGTAGCCCCGGAGGACCAGGCAGTGATGGGAAACCAGGGCCTCCT
Seq A exon
GTAAGTACATTTTCAACATCTCATTTTACAAGTCCAGAGAATGGTTAAATGCACAATTTGGACTAGCCTTCATGTATATTGTATAGCTTTAGGATGTACATTGCATATTCTATCAGACTTTTTGAAATTTCTGTTAATATAATTTTTTCTTATTAG
Seq C2 exon
GGAAGCCAAGGAGAGACGGGTCGACCCGGTCCTCCAGGTTCACCTGGTCCGCGAGGCCAGCCTGGTGTCATGGGCTTCCCTGGTCCCAAAGGAAACGAT
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000021466:ENSBTAT00000028617:27
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(14.7=61.1),PF0139113=Collagen=FE(24.3=100)
A:
NA
C2:
PF0139113=Collagen=FE(46.4=100),PF0139113=Collagen=PU(17.3=42.4)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTATTCCTGGTAGCCCCGGAG
R:
ATCGTTTCCTTTGGGACCAGG
Band lengths:
152-308
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]