DreINT0139743 @ danRer10
Intron Retention
Gene
ENSDARG00000040067 | si:ch211-274j7.1
Description
si:ch211-274j7.1 [Source:ZFIN;Acc:ZDB-GENE-141212-344]
Coordinates
chr3:6161564-6163117:-
Coord C1 exon
chr3:6163049-6163117
Coord A exon
chr3:6162216-6163048
Coord C2 exon
chr3:6161564-6162215
Length
833 bp
Sequences
Splice sites
5' ss Seq
GATGTGAGT
5' ss Score
7.77
3' ss Seq
AGTTTCTTGCTCTTTTACAGCAA
3' ss Score
8.49
Exon sequences
Seq C1 exon
AACAGTAGATCTGAAATCTGAGCAGCAGATGTTCCCGTTTATCTGAAAGGTCTTTACAAACCTGTTGAT
Seq A exon
GTGAGTATATATTTGTTTCTGTTTAAGCCCTTAACTAAGATGATTTTATCAGTTTTCTTGTCAAGACATTTAAAAAATGTCATTGCTTTCGTCAGGCAGGGGAGGAGATCTTTGGCTTTGGCTTTGGATTGCTTCATTCCTTAACTGAGGGTGCTTTCACACCTGTGAATCGATTCAGTTGTTCCGAAACAGAGATTACAATTGTTACATTGTTGCTCTTGGAGCGGTTCGCTTTCACACTGCAAAGTTTCTAATCGGACCAAAAGAGCTAAAACAAGTCACGTGCGAGTAAACTCTCCTCACATTAGTCAGTGTGTCAGGGTTTTTTTTGCAGCATCCCGCTAAGCTGTCAGGAGAGGTGGTGGTTTGGTAGTGATTGACAGGGTGCGCGAGCGCGCGACGTGTCTGAGGAGAGACGTGGTGGGGAGAAGGGTGCGCGACGATGCCTATTTAAGGACTGGGAGGGAGACACGAGATTACCGGGAGATCATCATTCGTTTGCGGGCATCCGGAGACTCGCGAAACTTCCCGCCCTACTCATAATTCTCTCTTCAAATAGTTGTAAGCCTATTACATATCTATAAAACACTGTGATATAACCGCGCTCAGATCGGATCGCTTTCTCACTGCAATCGAACCGCTCCAGGGTTCGTTTGAATCGAGCCGAGACCACCTCATTCAAGCGATCTCGGAGCGATTACTTTGGAGCGGAACAGAGCGCGATTGCCCTGTTCACATATGCCAAACGAACCGCGCTAACTGGGCAAATAAGACACGTTCCCAAACAAAAGTGTAGGTGTGAAACTCACCCTGAGTTTCTTGCTCTTTTACAG
Seq C2 exon
CAACATGAGTTCAAACAACCAGCAACGATCTGGTGGAAACGGTAAAACCACTCTTGAGAAGCATGGAAATGACCCACCTGATGTCACTTTAGAAGAAATAGCAGAGGATTTGCTTTCTTATATTGGAGGATCTCCTCACCTAAAGAAGACAGAGAAACAGATTGAAAGGAAATACAGCATTGAAAAGAAGGATGGTGATTACTGGTCAGCCGATGACATCAAGAAAGCTTGGGGGAAAACACAGAGGATGAGAAAAACTGATTTAAAACGAAAACGCTGGGCTCTTGCACTATTGTTCCAGCTAATAAATCGAAAGGCAGTCAAAACAACGACACAGTGCGATGATGACAACACTGGAAATGTATCCCAGCCGATTGTGGGAAACACACCTGACCAAACGAAAGCTGAAGGAGAGAGCGTAAGAGACAAAGCATCAGCCTTAAAACTTCTAAATTCCAATGAAAAAGAAAACCAAGCACAGAAAGAAGAAGGCTCAACAAAACAGACTGTCTACATACGCATCCCATTATCGGACATGGTTAGCAATGAGTCTACCTCTGGAGGGAAAGATGAGGAAAAAGGAAAAACAGGAAACAAACCAACATATAAATTAATTGACAGATATCCTAAACTTCCTCAAATACAGAAAAAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000040067:ENSDART00000161031:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
5' UTR
No structure available
Features
Disorder rate (Iupred):
C1=NA A=NA C2=NA
Domain overlap (PFAM):
C1:
NA
A:
NA
C2:
PF0119217=RNA_pol_Rpb6=WD(100=16.7)
Main Skipping Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Human
(hg38)
No conservation detected
Human
(hg19)
No conservation detected
Mouse
(mm10)
No conservation detected
Mouse
(mm9)
No conservation detected
Rat
(rn6)
No conservation detected
Cow
(bosTau6)
No conservation detected
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GAGCAGCAGATGTTCCCGTTT
R:
ACAATAGTGCAAGAGCCCAGC
Band lengths:
346-1179
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]