DreINT0076426 @ danRer10
Intron Retention
Gene
ENSDARG00000018542 | hapln4
Description
hyaluronan and proteoglycan link protein 4 [Source:ZFIN;Acc:ZDB-GENE-060503-243]
Coordinates
chr22:17803289-17803968:+
Coord C1 exon
chr22:17803289-17803509
Coord A exon
chr22:17803510-17803605
Coord C2 exon
chr22:17803606-17803968
Length
96 bp
Sequences
Splice sites
5' ss Seq
GAAGTGCGT
5' ss Score
4.88
3' ss Seq
CCTCCTTCTTCTTTTCCTAGAGG
3' ss Score
9.74
Exon sequences
Seq C1 exon
AGGCCCTGTCCACACGAACACAGGTGTTTACAAAACCTCACTTTTTTTTTGCAGTTTTTCCACACTAAAACAGTGTCCAGTGAATGAAACAGAAACTTTCATTAAACTCCAGCCAGGGTGATGATTTTCTAAAACATGTCGGCATCCCCGAGGTTGCACAGATGATTGAAGGCTACGTCAACTGTCACTGAGTTACTGTTCACTACTGATGTTTAATGGAA
Seq A exon
GTGCGTTTATTTTAAACCATGATCCAAACCTTCTGGAAATACTTGTGCATTAAATTAGTTTATTGTATAAATGAAACCTCCTTCTTCTTTTCCTAG
Seq C2 exon
AGGACGATACTGGGGCAGTTATAGTCCAGACTGCTCCAGGTAAGGTGGTCACTCATCGTGGTGGAACCATCACCCTTCCCTGCCGATACCACCATGAACCAGAGGACATTGATCCTAACCGCATTCGCATCAAATGGACGAAGGTTTCTGATGCTTTCCAGTTTGAAGATGTATTTGTGGCACTGGGTCGACAACAGAAGGCATTTGGGTCTTACCAAGAGCGAGTGTCTCTAGAGCAAGCAGGACCTGGAGATGCTTCGGTTATAATTCACAACATCACCTTGGAAGACTACGGTCGATATGAATGCGAGGTCACTAATGACATGGAGGATGACACAGGATTTGTCAATCTGGACCTTGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000018542:ENSDART00000136016:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.025
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0768612=V-set=WD(100=95.9),PF0019312=Xlink=PU(0.1=0.0)
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:
CCCGAGGTTGCACAGATGATT
R:
TGTCCTCTGGTTCATGGTGGT
Band lengths:
183-279
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]