DreINT0076424 @ danRer10
Intron Retention
Gene
ENSDARG00000045802 | hapln3
Description
hyaluronan and proteoglycan link protein 3 [Source:ZFIN;Acc:ZDB-GENE-040426-2089]
Coordinates
chr25:19104535-19106252:+
Coord C1 exon
chr25:19104535-19104906
Coord A exon
chr25:19104907-19105949
Coord C2 exon
chr25:19105950-19106252
Length
1043 bp
Sequences
Splice sites
5' ss Seq
GAGGTCAGT
5' ss Score
7.7
3' ss Seq
TCTCATTTTGCACTCCACAGGTG
3' ss Score
9.82
Exon sequences
Seq C1 exon
TTTACTTACACAAGATCCGTCTTCATGTTGAATCCCCGGAGACTCTGGTGTCCGCTGTTCAGGGCAGTAACGTGACGCTGCCGTGTCATTACCGCTACGAGCCCGCGCTCAGTGCGCCCCGCAGGACGCGGGTCAAGTGGTTCTGGCAACCCGTGAACGGCGAAGGCCAGGAACATGACGTCATGGTTGCCATCGGCACACGTCACCGGAGTTACGGAGACTTCAAAGGACGCGTGCGGCTCCGGCGTAGCGCTCCGGGCGACGCGTCTCTCGTCATCAACCCGCTACAGTCCGACGATACCGGCCGCTACCGGTGCGAAATTATAGATGGTCTGGAGGACGAGAGCGTCACCATGCAGCTGAAGTTTCGAG
Seq A exon
GTCAGTCATAGAAAAAAACCTTATAGTCCTTCATTACCTTTACACTAAAACAGCCACAATTCTATAGATGTTGTAGGCTATTATTATTATTAATAACATTAAATACTCTTATCAATATAGGCTCATGATTAGTATATTAACATAAACATTCATTAATTCATTCATTTTCTTTTCGGCTTAGTCCCTTTATTAATCAGGGGTCGCCACAGCAGAATGAACCGCCAACTTATCTAGCAAATGTTTTTACACAGCGGATACCCTTCCAGCTGCAACCCATCAGGAAACATCCATACACACTTATTTACACACACTAACACACTATGGTCAAGTTGATCATATTGACGTGCTACCCACTGCGCCACCTAACATAAACATAAAATGTAGAATTAGCACATCAAACAAAATATATCATTTTTGAGTTTTATTACTAACAATTAGGCCTACTTATATGATTAAGTTATGAAATAATGTGTTGGTTTTTATATTACACAAATTATTTAGTTTGGAAATGCATTCTTATTTTCTAATTGTGAAATAATTATTTATAAAATAATTAATTAGCAAGTAAAATATTTTATTTCCCAGAGATGGGTTGCGGCTGGAGGAGCATCCGCTGCGTAAAAACTTGCTGGATAAGTTGGCGGTTCATTCCGCTGTGGCAACCCCGGATTAATAAAGGGACTAAGCCGACAAGAAAATGAATGAATAAAATGTTTTACTTAAAATCCTCAAATTTAGTAGGATTTAAGCAAGTTTATAATATTTGTCTTATTCTACAAATGTCTGTCTTCCAAACTTAAAGCTTTCTCATCAAAAGATTACAGAATATAACAAAGTTTTGCTCACACACACACACACACACACACACACACACACACACATATATAACCTAACTATAGATCACATTTTTATAAAATGTTTGTTTTTAGATTATTATATAGAAAATATAATTGCCAAACAATTGATTGACTATAGGTCTACAAAATACTCTCAAAGCAACAGAATAAAGAGCATCCGTCAATTTCTCATTTTGCACTCCACAG
Seq C2 exon
GTGTGGTGTTCCCCTATTACTCCTCCAAGGGGCGCTATTTGATGAACTATCACGAGGCAAAAGAAGCCTGTGAGAAGCAGGATGCACACCTGGCCACCTTTGAACAGCTGTTTGCTGCTTGGGAAGAGGGGCTGGATTGGTGTAACGCTGGATGGCTCACTGACGGGACGGCTCAATATCCTGTCTCAGTGCCCCGAGTGGCCTGTGGAGGCACCAACATGGCAGCTGGTGTAAGGAGCTATGGCATTCGAGACAAAGATCTAGATCGGTTTGATGCCTTCTGCTTCACTGCATCTATAAGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000045802:ENSDART00000067323:3
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.024 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0768612=V-set=PU(97.5=94.4),PF0019312=Xlink=PU(0.1=0.0)
A:
NA
C2:
PF0768612=V-set=PD(1.7=2.0),PF0019312=Xlink=WD(100=94.1),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:
TCTCGTCATCAACCCGCTACA
R:
CTCCTTACACCAGCTGCCATG
Band lengths:
342-1385
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]