DreINT0076254 @ danRer10
Intron Retention
Gene
ENSDARG00000057498 | habp2
Description
hyaluronan binding protein 2 [Source:ZFIN;Acc:ZDB-GENE-030131-4721]
Coordinates
chr12:31603040-31604134:+
Coord C1 exon
chr12:31603040-31603182
Coord A exon
chr12:31603183-31603999
Coord C2 exon
chr12:31604000-31604134
Length
817 bp
Sequences
Splice sites
5' ss Seq
TAGGTCAGT
5' ss Score
6.39
3' ss Seq
TTGTTTCTCATCTATGAAAGCCC
3' ss Score
3.65
Exon sequences
Seq C1 exon
CGATGAGAATGATGAGGTGAGGGTGGAGTTGGGTGGTGTGAACCTGGAGAAAGATGACCCTGATAAACAGTTTGTGGAGGTGGAGAAAATCATTGTTCATGAGAACTACACAGAGACTTTTGACGCCCTCTATAATGATATAG
Seq A exon
GTCAGTGATTCACTATTTATGTGAACTATCTGTCTATAGTTTATCCATCTTCCTGCGCTCACATGATTTTGCTGCTTGTACAGACTAATTATTAAAAATGAGCTGAAACAACACTTGATGAAACACTGAAACACACAATTCATTTTAAGTTCAATCGTAGTCAACACAAAAATGTGGCACAAAAGTGGTTTTTAAAATTCAAATTGTACTAAGACACAAATAGATGCTGTTCAATAATTTTAGAAAAAAATTTAAGGTTTTGATCCACTTCAAATGTTGATCGATCCATCCATTCATCCATCCGTCCATCCATCTGTCTGTCTGTCTGTCTGTCAGTCTATCTATCTATCCGTCTTTCTATATTTCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTTTCCACCCACCCATCTATCCGTCTATCTGTCTGTTCATCTGTCGATCATCTATCTATCCATCCATCTCTCAGTATAATCATCAAAATTTTAAAGATACACTATTGCTGTATAGCCTACCATCCATTTTGCAAACAAGCCTTGTGATCAATGAAAAGTGTTTCTGAAGTACATAGAATTGATTTTATGTTGTGAAATGAAATATTCCTTTAAAAAATGATATACACAACACATTGTGTTTCCAATGGTTTCAAACAGGATAATCCATATTAAGTGAAATGTGAAAATAAAAACTATAGTTTACTTATTTTTAACCAGTTATGCTCACATCACAGTGCTTTTGTTTCTCATCTATGAAAG
Seq C2 exon
CCCTCCTGAAACTGAAGGGACGGAATGGACGGTGTGCCAATGAGTCCAGGTCTGTCAGGGCAGCTTGCCTTCCCACCGATTTATTCCCTGAAGGAACACGGTGCACAATATCAGGCTATGGAGCTACTGAGAAAC
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000057498:ENSDART00000122379:10
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.082 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0008921=Trypsin=FE(20.3=100)
A:
NA
C2:
PF0008921=Trypsin=FE(19.0=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:
AGAATGATGAGGTGAGGGTGGA
R:
GCTCCATAGCCTGATATTGTGCA
Band lengths:
262-1079
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]