DreINT0052178 @ danRer10
Intron Retention
Gene
ENSDARG00000059826 | crtac1a
Description
cartilage acidic protein 1a [Source:ZFIN;Acc:ZDB-GENE-030131-9704]
Coordinates
chr1:54260482-54261955:-
Coord C1 exon
chr1:54261855-54261955
Coord A exon
chr1:54260651-54261854
Coord C2 exon
chr1:54260482-54260650
Length
1204 bp
Sequences
Splice sites
5' ss Seq
CAGGTACGA
5' ss Score
10.03
3' ss Seq
CCATCTATATATTTCTGCAGGGC
3' ss Score
8.63
Exon sequences
Seq C1 exon
GAGCCACAATAACAGATTTTGATGGAGACGGTCTGCTGGATCTGCTGGTGGCTCATGGTGAAAGCGCTTCTCAGCCCATCTCTGTGTTTAAGGTCAACCAG
Seq A exon
GTACGACACAATCTTTATGTACACACTGTCACGATTGTATAATGTGGTTTAAATGATTAAAGAGCTAATAAATAGTGAGATTATGAAGATTGTCTGTTTTGGTGATTTGACATAAGGAAATCTATTGCCACATATGGAAATAACTATATATAAAATACTTGACGTTATATAATTTGAATAGTTGAATGGTTAATTTTTGCAATATTCAAATATATTTAATTTGTATTATAGTCATATATATATCATATTTATATTACATCCAAACATGAACTTGTATGTTTAACATGTGATTTGCATTTATTACCTACTGTATATCAGATTTCTGTATTGGGGCTTTGTCATTTTTTTCCCCTGTATTTATTTATTAACTGCATATTATTGTGATGAACTGATATTTGTAAGTTGTCCTATTGCACCTTTAAACAATTTATTAATTAACTTATTTTAATAATTAATATAAATGAATAATAATTGATAAATTATTGTTTATTATTATTTACAAGTATAGGGTTGCAGCTGGAAGGGCATTTGCTGTGTAAATCATACGCCAGAATAGTTGGTGGTTCATTCCCCTGGGGTGACCCCTGATGAATCAGAGAGTAAAGCTGGAGGAAAATGAATGAATGAAGGAATGAATGTAAATTATTTTTAGGTAATTTTTTGCATTTTGTAAATGTAAGAATACGCACAAAATGGCGTACATGTAATACACAAACAACACACAGACAATTTGCTCATTTTCTCAGCAACAAGTAGTAAGCATTGCAGGTGTTTGAAGCTTTAGTTACAGCTATTCGCAGGGAGATGTCATGTAAATGCAATTTACACATGCAGTCACGCTCTACGTCTTAATCCCTGGTAAAGCCGTCATGAAATCGAAAGTGAAAGTGAAAGTAAACGACGCACGTTTGAAACGGTGTCTTTGTGGATTTAGTGATCTATGTCTCCCCTTTGTGCCTTTTAATGGAATTGCAGCAAATCCAGACAAATAACACAACCTTCTTTAACTTAAATAATCACAATTATTTATTGTTTATTTAATAATCCCGGCAGGTCTATTTTATAAGAGTTATATCAGACTCAAGGACCTAATTTCCCAGTACACATTTTCACTTCTGAATATTGACTCTTCTAGCGTATGTGAACATTTTAATCATCAGCTGATCACTTTTAATATCCATTTTCCATCTATATATTTCTGCAG
Seq C2 exon
GGCTCCAGTAATAATTGGCTGCGTGTGATTCCTCGCACACGTTTCGGGGCATTTGCAAGAGGAGCGAAAGTTGTGATGTTCACCAAACACAGCGGCTCACACACCCGCATCATTGATGGAGGATCGGGATATCTGTGCGAGATGGAGCCGGTGGCGCACTTTGGTTTAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000059826:ENSDART00000129710:10
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.118 A=NA C2=0.012
Domain overlap (PFAM):
C1:
PF0183918=FG-GAP=FE(71.7=100)
A:
NA
C2:
PF0183918=FG-GAP=PD(17.4=14.0),PF075937=UnbV_ASPIC=PU(55.7=68.4)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GAGCCACAATAACAGATTTTGATGGA
R:
CTAAACCAAAGTGCGCCACCG
Band lengths:
270-1474
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]