DreINT0049616 @ danRer10
Intron Retention
Gene
ENSDARG00000011407 | col2a1b
Description
collagen, type II, alpha 1b [Source:ZFIN;Acc:ZDB-GENE-050302-9]
Coordinates
chr11:39675-40321:-
Coord C1 exon
chr11:40268-40321
Coord A exon
chr11:39729-40267
Coord C2 exon
chr11:39675-39728
Length
539 bp
Sequences
Splice sites
5' ss Seq
AGAGTAAGA
5' ss Score
5.73
3' ss Seq
GCTGCTTTGTGTCTTTACAGGGT
3' ss Score
10.18
Exon sequences
Seq C1 exon
GGCGATAATGGAGATAAGGGACCAGAAGGAGCTCCGGGTAAAGACGGCTCAAGA
Seq A exon
GTAAGAGTCCACATCTCTCTGTTCCTCCAGTAGACATCAGACAAACCTTCAACATTCTCTTGATCTTGGATTTGTGTCACCTTCAGGATGTGTTGTGTGTGTTCTCTCTAAACAGCATTAACTAATTTCAGCTAACATCTGATGTGTGCTTCAGCATTGAAGAGCTGGTCCAGTCATTATGAATGAAATGAAAGATTAAAGCTTCTGTTTAATGTTCATTTTTCCAAATAAAGCTGGAATCTGGCCACAGTGCAGCGCCGCCGGCGTGTCTGTTCAGTGGCCAACATGATGAACAGAACTCACATATTAATGTTTAGTAAAGCGGGTCCTGTGTTGGTCTGCAGTATATAAAATACTTCAGTCAAACTAAATAAAGAGAGTCAGCTGTAGTGATCGGCCAGTGGATGAGCTGCTGTGAGTTCAGTTCTGCATGAATGTTGTGGATTCATATGTGTGAGAGTCATTAAGAGTTTTATTCAGCATTTCTGCTAAAGGTCATGAACACCAGTGCATGAAGAGGCTGCTTTGTGTCTTTACAG
Seq C2 exon
GGTTTAACGGGTCCAATTGGTCCAACAGGTCCTGCGGGACCCAACGGTGAAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000011407:ENSDART00000159169:7
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(17.5=100),PF0139113=Collagen=PU(2.6=11.1)
A:
NA
C2:
PF0139113=Collagen=FE(17.5=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]