BtaINT0041612 @ bosTau6
Intron Retention
Gene
ENSBTAG00000021466 | COL3A1
Description
collagen alpha-1(III) chain precursor [Source:RefSeq peptide;Acc:NP_001070299]
Coordinates
chr2:7333234-7333719:-
Coord C1 exon
chr2:7333621-7333719
Coord A exon
chr2:7333288-7333620
Coord C2 exon
chr2:7333234-7333287
Length
333 bp
Sequences
Splice sites
5' ss Seq
GATGTGAGT
5' ss Score
7.77
3' ss Seq
AATACTGGCTACTTCTTTAGGGT
3' ss Score
6.64
Exon sequences
Seq C1 exon
GGAAGCCAAGGAGAGACGGGTCGACCCGGTCCTCCAGGTTCACCTGGTCCGCGAGGCCAGCCTGGTGTCATGGGCTTCCCTGGTCCCAAAGGAAACGAT
Seq A exon
GTGAGTTCCTTCCTTCATTTCTTCAATAAATAGGTGATGGAAGTTCTTTTATTTTCCATATGGGGGTGCAGATGGCCCCAAACTGATTTCCACTTCAAAGCACAGAAGAGTATAAGAGAAAGAAGCTTCCCTCTACCGTGTAAGAAGGGAGCTAACGTATTTTCTTCTGGAGTTCCGGGCAAAGAGCAGAACACTTATGGAAGCCTAGTCTAGAAATAAGTTTTCAGTTGGGGATATATACATGTGTGAGTAGGGGGAAGATCAAAAAGATGAGAGAACATGATAATGAATAATTTCCTTTTGAGATTTAGTAAATACTGGCTACTTCTTTAG
Seq C2 exon
GGTGCTCCTGGAAAAAATGGAGAACGAGGTGGCCCTGGAGGTCCTGGCCCTCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000021466:ENSBTAT00000028617:28
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(46.4=100),PF0139113=Collagen=PU(17.3=42.4)
A:
NA
C2:
PF0139113=Collagen=PD(17.4=66.7),PF0139113=Collagen=FE(21.0=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:
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]