DreINT0179127 @ danRer10
Intron Retention
Gene
ENSDARG00000104436 | zgc:153426
Description
zgc:153426 [Source:ZFIN;Acc:ZDB-GENE-060929-220]
Coordinates
chr3:45419743-45420953:-
Coord C1 exon
chr3:45420813-45420953
Coord A exon
chr3:45419852-45420812
Coord C2 exon
chr3:45419743-45419851
Length
961 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAAA
5' ss Score
8.38
3' ss Seq
CTTCTCCATCTCTCTCTCAGTTC
3' ss Score
9.71
Exon sequences
Seq C1 exon
AAAAAAAGCGGCTCAGCCCGTTAGCGAGCAGAAGAAGCAGCCCCTCGACTCCTGCATCCCCGCCGTCATCCTTCCTGCAGCACCATGCGCGAGATTGTGCACCTGCAAGCCGGCCAGTGCGGCAACCAGATCGGAGCCAAG
Seq A exon
GTAAAAGCTAAAACCAAAAATGTTGCTTGGTTGGATGGGGGGTTTAACGTGCACGAGGGTGTCCTTCAGGGCGACTAATCTGGTCCTTAAAGAATCCACTAGAAGTGCATTGCAGATAATTGATTCTGCAGGTTTTATTTGCATGATGCACGATTTAAAGGGGATTTTGAGTTCTGGTTTGCAGCTGTGCATAATCGGTTCATTGTGGGTTGAGATGTGCTTCCATTGGGCGTGGAAACATCCATCCATTGTACGACGGGGAATGATGAATTAAACGTTCCTTTAATGTTTCTTTTGCTGGCTCTATTACTTATACCCATGCGTTTATGGCACATTTATTAGATTTAAACCTTATAGACAGTACACAGCCAATGTTTTTGAAGCTTGTGTGGTACTTGGGATCGACTGTTCCTGTATACGATAATGACCTACTTTATGAGTAATTAGCATATTGGGAAAAGGATTGTGTTTTGTTATGTAATATAGAGCAAATATATCCATATAGATTAGTATGCATGTAATATCTTGCAAATGGATCCTAGTCTGACCTATATCTCATCAATCGATGAAAGAAAATAATGTCACATTGATGCATTTGTTCTGATTCACTAAAATCCATATAATTTGCATAATCTACAAGATTCCAACATTATGTAGTGAATCGTTCTTTTAAACCACCATGTACATTTGAACTGTAAAAATATTTTTTTTCTAAATGTATGTATTATTATTATTACTATTGTTGTTTACAATCATCATCCTACATTAAAACCAGATATTCACATTGTTGATGCCTATTGCATTTTTTATAATAATTATATATATATATATATATATATATATATATATATATATATATAGTAGTGTTGAGCTTATTCTTACTTGGCCTCCGTTTATTTCTCCCTCTCCTCTCTCTGGCATCCGCCCTGTTGTTTCTCCTCCTTCTCCATCTCTCTCTCAG
Seq C2 exon
TTCTGGGAGGTTATTAGTGACGAACATGGGATTGATCCAACTGGAACATATCATGGAGACAGCGACCTTCAGCTAGACAGGATCAGTGTTTACTACAATGAGGCCACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000104436:ENSDART00000161507:1
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=0.135
Domain overlap (PFAM):
C1:
PF0009120=Tubulin=PU(7.2=84.2)
A:
NA
C2:
PF0009120=Tubulin=FE(16.2=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Mouse
(mm9)
No conservation detected
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTCAGCCCGTTAGCGAGCA
R:
TGTGGCCTCATTGTAGTAAACACT
Band lengths:
238-1199
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]