DreINT0049408 @ danRer10
Intron Retention
Gene
ENSDARG00000035809 | col1a1b
Description
collagen, type I, alpha 1b [Source:ZFIN;Acc:ZDB-GENE-030131-4400]
Coordinates
chr12:3079945-3080269:-
Coord C1 exon
chr12:3080162-3080269
Coord A exon
chr12:3079999-3080161
Coord C2 exon
chr12:3079945-3079998
Length
163 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAAG
5' ss Score
9.06
3' ss Seq
TGTATTTGGTTGTGTTTTAGGGA
3' ss Score
9.73
Exon sequences
Seq C1 exon
GGTGATGGTGGTCCTAAGGGTCCTGATGGTGCTCCTGGCAAAGATGGCGTGCGTGGCATGACCGGCCCTATTGGACCTCCTGGACCCAGTGGTGCTCCTGGTGATAAG
Seq A exon
GTAAAGACATATGAAACATTTATTAGATAGCATTGAAAGATTAACACTAATGTTGTCAAGCAATTACGTTTCAGCTTCAAAGTCATTTTGAATTGGTCACTAAATAAAAGGATAAAAGAATAATGTTGATACTAAATCAGCTTTGTATTTGGTTGTGTTTTAG
Seq C2 exon
GGAGAGCCTGGTGCTGTTGGACCCCCAGGATTGACTGGACCTCGTGGAGGCCCT
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000035809:ENSDART00000015092:33
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(49.3=100),PF0139113=Collagen=PU(22.7=47.2)
A:
NA
C2:
PF0139113=Collagen=PD(5.6=22.2),PF0139113=Collagen=FE(22.7=100)
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:
TGATGGTGGTCCTAAGGGTCC
R:
TCCACGAGGTCCAGTCAATCC
Band lengths:
154-317
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]