DreINT0007197 @ danRer10
Intron Retention
Gene
ENSDARG00000091398 | COL13A1
Description
collagen, type XIII, alpha 1 [Source:HGNC Symbol;Acc:HGNC:2190]
Coordinates
chr13:7735391-7735686:+
Coord C1 exon
chr13:7735391-7735483
Coord A exon
chr13:7735484-7735641
Coord C2 exon
chr13:7735642-7735686
Length
158 bp
Sequences
Splice sites
5' ss Seq
CAAGCAAAT
5' ss Score
-3.32
3' ss Seq
CCCTTGTTTTTTGTCACTAGGGT
3' ss Score
10.37
Exon sequences
Seq C1 exon
GGTTTAGATGGCCCTACTGGAGAAAAGGGGGTTTCAGGGCCCCCTGGCCATATTGGATTGCCAGGCCCAATGGTACGCAATGGTGGTCCTCAA
Seq A exon
GCAAATAGATGTCATAGTTGAAAAGACATCAAAGTACACTGGGGTTGTGGGGGGAGGGGGTTGGGGGAGGAGCAATGTATTTCATCATGCCAGTTTTGAATTCTGTTAAATGAATGATACAGTTGAGTCTTCCCTCTCCCCTTGTTTTTTGTCACTAG
Seq C2 exon
GGTCAGAAGGGTGAACCTGGGGAGAAAGGAGATAAAGCAGAGCTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000091398:ENSDART00000040379:27
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(42.2=87.1),PF0139113=Collagen=PU(15.8=29.0)
A:
NA
C2:
PF0139113=Collagen=FE(16.7=100),PF0139113=Collagen=FE(22.6=100),PF0139113=Collagen=PU(3.4=13.3)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGTTTAGATGGCCCTACTGGAG
R:
CAGCTCTGCTTTATCTCCTTTCTCC
Band lengths:
138-296
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]