DreINT0076262 @ danRer10
Intron Retention
Gene
ENSDARG00000057498 | habp2
Description
hyaluronan binding protein 2 [Source:ZFIN;Acc:ZDB-GENE-030131-4721]
Coordinates
chr12:31601911-31602619:+
Coord C1 exon
chr12:31601911-31602064
Coord A exon
chr12:31602065-31602524
Coord C2 exon
chr12:31602525-31602619
Length
460 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAAA
5' ss Score
8.59
3' ss Seq
CACTATCGTTATTGTTTAAGGAA
3' ss Score
5.88
Exon sequences
Seq C1 exon
GTTCAAACGATTGCTATGAAGGGAATGGGGAATCATACAGAGGCAATGTCAGTGAAACAATAGAAGAAATTGAGTGTTTACCCTGGAACCACAATCTTATTCCTTACAAAGAGTTTGAAGGGAATGAGAGCATTGGAGAACACAATTACTGCAG
Seq A exon
GTAAAATCCACCGTAAACCAGCATGAACTCAGTGTTGGTCCAGGCTGGTCGGAGCTGGTTTAGTGCTAATCTACACAGTCAAAAATACAAGGTATGATAGCTGTCACTGGGGTGGTATAAAAGGTTTATATTTTTAACTAAATAGTCCTAATTATTACCTCAAGGGTACATACTACTACCTAAAAAAGTATGCGTACCTCTTGAAATTTGTAGGTACTAATAAGAGAAACTAATATTGAGCTACCAATATGGACCCTTTAAGTACAACATTTGTGGTACACATTTGACAGCACAGTGACAGAACTCGTACCTTTATTCATACCCTGTGCAGCCAAACAGGTCTGGAGTGCATCTTGCATTGACCAGAGACTGACTGACTGAGATATAAAGCAACCAATGAGTTTTTGTATTACATGTCATATTAAACATTGTCGTCTTATCACTATCGTTATTGTTTAAG
Seq C2 exon
GAATCCAGATGGAGACCGAGAACCTTGGTGCTTTGTAAAGGAAAAGGGAAAGCTTCAGTGGAACTACTGCAATGTCAAGCCATGCTCTGAAACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000057498:ENSDART00000122379:7
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.019 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0005113=Kringle=PU(61.8=90.4)
A:
NA
C2:
PF0005113=Kringle=PD(36.8=84.8)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TCAAACGATTGCTATGAAGGGA
R:
TGTTTCAGAGCATGGCTTGACA
Band lengths:
246-706
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]