DreINT0047565 @ danRer10
Intron Retention
Gene
ENSDARG00000078722 | clip1a
Description
CAP-GLY domain containing linker protein 1a [Source:ZFIN;Acc:ZDB-GENE-060526-282]
Coordinates
chr5:66511844-66513829:-
Coord C1 exon
chr5:66513777-66513829
Coord A exon
chr5:66511975-66513776
Coord C2 exon
chr5:66511844-66511974
Length
1802 bp
Sequences
Splice sites
5' ss Seq
CAGGTACGC
5' ss Score
10.12
3' ss Seq
TATTGTTATTTGTTTGGAAGGTT
3' ss Score
5.27
Exon sequences
Seq C1 exon
ATGATTCTGCCTTAAGAATGTGGAAGGAGGCAAAGGAGAATGCCGAGCATCAG
Seq A exon
GTACGCCGAGTGTTTTTCCATCTGTAAACTTTTCCTCATTTATAAAAAGCCTTATTTAAAGTGTCAGAGTAAAAACTGTAGAAATGTTTGAAATGTATTCTGTTGTCTTAAAATACATCACAAAAAAATTTTTACTTGTTGAGAACTTTGAGTTTATAGTCATTTAACATTTAAAAATTAAAGATGTTTTTTTAAAGGGCGCCAATGATGAAAATCATCTTTTTTGAGCTGTTTGGAGAGAACTGTGTGTGTAATGTGTCCACAGCCATACTGGAGTGATAGAAACACAATAAGACTTTTTTTATTATATTTTTATTTTCTGATGTTAAAATAGGATCCAAATCCCTCTCATTTTGAGGCTGACTGCAACTTGACGTCCCCGCCCACTGAATTGATTGACAGTCGCGTATTAACATGTCTCTGTAATAACACGTAAAATCATAACAACACAGGACATGTGCAAAGCAACTGGGATTAAAAGATCTGTTCAGCACTCTGTGATCATCAATCACCATCAAATGTGATTAAAAGTTTAAAACATTTTTAAAAGCAGGTTTGTAATGAATTACAGCGAATTTACCGTCTTTATCACCACAACCGCGTGTCAGCACAATTCATGAAGACGCTTCAACCACGGTTTGTGAGTGTTAAATCAGGTTTATTTTGTACATTAACATAACGGATGTCCATACAGCAGTGGATATTAACGTGTATCTTGTCACAACTGCCGTGCAAAAACAGTGCAAAGTTAAACGCGTGCTGTGTGTGTGTTTGTCTGCTGTGTGTGTGCGCGTGAACTTTGTGACGACATTGTGTGTGACTCATCATTGCAGAAAGGTTTGAATTAACTCCACAACAAATACATCAAATAATCATTGGGAAAGTTCTTACTGTAGTGTTTCTCACAAATGTTAAGTGTGATCTGCTTCCTTTATGTCTTTCACTGTACTGTTTATCTGACGGAGATGGAGACGGAAACACTCTGACAGGCATGGAGGAATGATGGGCACAGGCCACCAAAACAAAATCCGATATTTTGAAAGCTATAATAAATAATCTGATGGGTGTTTTGAGCTGAAACTTGACAGACACATTCTGAAGACACAAAAGACGCATCCTAAATCTTGAAAAAGGGGTAAAATAGGTGCCCTTTAACTGAAATCATTATACTTAGTGAAACATACAATGCAGTTCAATGGCTATCAACACTGAGTAAAAAAAAACATACAGGCCAAACTAATTTAATGCCATGTTTTATGCACGACTGATGATTTTGTCTCGTATTTATCATCAGTGTATGTATTGTCTAGAGTTATTGTCGCCTACTGTACATAATGTGTAAAATAATTCAATGCTCAAAATAGCTCAATATTCTGCCCTGTGGATATTCCGCTCAAGTACACGTCTACTTATCTATGCATGAACTGCACATGCTCACTGGAAAAAAAAAGTCTTCTCAAATATTGGCTTGACAGGAGGACATTGTATGTAGTATACTTGTTCTTGCTGCTTGCAGTAGATCAACTGTTGTCATGGTAACGCTGGTAAAATGATGCCTCTTGCTGTCAATAAAATGTTACTGTCAGTGCAGTTTGGTTATTTTTTATTGATATAAATTAAGTTGAGGTAAATTAAAAAACTTTTATTTATTAAAGTAATACATAATTGCCATAGTTTATTCTTAAAACAACAAGAATGGGATTTCTATTGGTTTCTAAGATGATTTTGAACTGTGAATTAATAATTGCCATTTTTAAACACTTTAACGCAAATTAACTACTTTATTGTTATTTGTTTGGAAG
Seq C2 exon
GTTGAGTTCCTGAACTCGGTCATTGTGGAACTGCAACGGAAGAATGAAGACCTAAAATCTAAGCTAGAGAAGATGGCCGAAGCAGCGCTCAATGGAAACGGTGCAGCTGAAATGGACAGCCGTAACAACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000078722:ENSDART00000145122:11
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.784 A=NA C2=0.716
Domain overlap (PFAM):
C1:
PF079267=TPR_MLP1_2=FE(11.2=100),PF089465=Osmo_CC=PU(39.5=78.9)
A:
NA
C2:
PF079267=TPR_MLP1_2=PD(16.2=59.1),PF089465=Osmo_CC=PD(57.9=50.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGATTCTGCCTTAAGAATGTGGA
R:
TGTTGTTACGGCTGTCCATTTCA
Band lengths:
182-1984
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]