BtaINT0041615 @ bosTau6
Intron Retention
Gene
ENSBTAG00000021466 | COL3A1
Description
collagen alpha-1(III) chain precursor [Source:RefSeq peptide;Acc:NP_001070299]
Coordinates
chr2:7332485-7332922:-
Coord C1 exon
chr2:7332869-7332922
Coord A exon
chr2:7332539-7332868
Coord C2 exon
chr2:7332485-7332538
Length
330 bp
Sequences
Splice sites
5' ss Seq
ACTGTAAGT
5' ss Score
8.59
3' ss Seq
CGTATTATGTTTTTACATAGGGC
3' ss Score
7.45
Exon sequences
Seq C1 exon
GGTCCTGCTGGAAAGAATGGTGAGACCGGACCTCAGGGTCCTCCAGGACCTACT
Seq A exon
GTAAGTTTCCTCGCGTGAACTGGAAACGGAAGTGGATGGGAGTGGGCCTGAGGGAAGACTTTGGGAATTATACAGTCTCTGCCACTGTATTGGTATAGCTCACCAAAGCAATTATGAAGATTGTTTATTTAATCAGCTAGCTAAATACTGACACTGAGTAAAGTTTGTGCCGTATATGTCTTCCTTACACCACTTCCACAAGCCAGACTCTGCCTTCCTTCATACCATTAATTTTTAAATTAAGCAATTGGCCTGATGAGATGAAAAATATGTGGATAAATATGAAAAGATATTTTATAGTGAAGCATCTCGTATTATGTTTTTACATAG
Seq C2 exon
GGCCCTTCTGGTGACAAAGGAGACACAGGACCCCCTGGTCCACAAGGACTACAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000021466:ENSBTAT00000028617:30
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(21.0=100),PF0139113=Collagen=PU(14.1=61.1)
A:
NA
C2:
PF0139113=Collagen=FE(21.0=100),PF0139113=Collagen=FE(21.8=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]