DreINT0049390 @ danRer10
Intron Retention
Gene
ENSDARG00000035809 | col1a1b
Description
collagen, type I, alpha 1b [Source:ZFIN;Acc:ZDB-GENE-030131-4400]
Coordinates
chr12:3089217-3089703:-
Coord C1 exon
chr12:3089605-3089703
Coord A exon
chr12:3089262-3089604
Coord C2 exon
chr12:3089217-3089261
Length
343 bp
Sequences
Splice sites
5' ss Seq
GCTGTGAGT
5' ss Score
7.39
3' ss Seq
CTTTTGTTCTTTCTCCATAGGGA
3' ss Score
13.12
Exon sequences
Seq C1 exon
GGAGAAACTGGTGCTGCTGGAGGTCGTGGTTCAGAGGGACCTCAGGGACCCCGTGGTGAGCCTGGTAACCCTGGACCTGCTGGTGCTGCCGGCCCTGCT
Seq A exon
GTGAGTATTTGCTATATTAAAAAAGAAAATCTTGCTAATTTGATAGAAAGATTTCTAAATTTTGAAAGAGAATCGGTATACATTGGTGGTTTAATTAGAAATAGAGAAAGTTGGATTATCTACAAAATAGTAATTTATTAAATGCATTTTTTAAGTGTTGTGTTTATCCAATTAATTTGTTCATTTGACAAAATTTAAATGTACTTTTGGGAATGGATAAAACTTTAAAAAGCTAATGCAACAAACACAATATAATGATTGGCTGTTTATTACAGTGTGTGGTGAATAAGATAAACGTCATCAGCTTTTAATAGCGAACTTCTCTTTTGTTCTTTCTCCATAG
Seq C2 exon
GGAGGACCTGGTTCTGATGGCACTCCTGGTGGCAAAGGATCTCCT
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000035809:ENSDART00000015092:17
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(3.0=6.1),PF0139113=Collagen=FE(39.5=100),PF0139113=Collagen=PU(6.9=15.2)
A:
NA
C2:
PF0139113=Collagen=FE(17.3=100),PF0139113=Collagen=FE(19.4=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
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]