DreINT0153705 @ danRer10
Intron Retention
Gene
ENSDARG00000067673 | snapc4
Description
small nuclear RNA activating complex, polypeptide 4 [Source:ZFIN;Acc:ZDB-GENE-030131-5794]
Coordinates
chr5:50536152-50537518:-
Coord C1 exon
chr5:50537368-50537518
Coord A exon
chr5:50536259-50537367
Coord C2 exon
chr5:50536152-50536258
Length
1109 bp
Sequences
Splice sites
5' ss Seq
AGAGTGAGT
5' ss Score
7.36
3' ss Seq
TGTGTTTATGTTCTCCGTAGTGT
3' ss Score
9.39
Exon sequences
Seq C1 exon
ACCAACAGAACAGCTTTCATGTGCTTCCAGACCTACCAGCGCTACATTTCAAAGACATTCAGAAGGACTCATTGGACAGAAGAGGAAGACGATCTCCTCAGAGAACTTGTTGAAAAAATGAGGATCGGGAACTTCATTCCTTACATACAGA
Seq A exon
GTGAGTGAACTGGATCTTGTACTGAATGTGGCATATTTTGTTTCTAAAGTGTGTGTTTATAGTTTATTTCTTGTTTCATTTTTGACCCTGGATCACAAAGCTAGTCATAAGTGTAAATTTTAAGAAACTCAAATTTATTAACCGTCTAAAAGCTTTAATTGATGTATGGCTTATGAATGGACAATATCTAGCCAATATACCACCTTTTTGAAAATCTGCAATCAGTGGTGTAACAGATCACAAATCTTACGGTTCGGTTCACATCATGGTTTTTTAGTCACGGATCAGATTTTTTCGGATCAGCTAAAAAGGGAAGGAGACAAATGTCATTTGCTTGCCATTTATGACAAATAAGCACTGCAAGACACTTTTGGTTTTAACAAAGAGAGCATAGAACCTGTAATTTTATTAAAAATAAAATGAAGAAAAAATCAGCTAATTAAAAAATAAATTGTAAATTATTCTGTATATACTGTGAAAAATTCACTGTTACTACTACTGTTGCTGATAACACTAAATGTAGAAATTATTATAATCATTATAAAAAACATATAATTGGTACAACTCATATTTATTTTTAGTCTCCTTTTCAATAAATGATTCAGTCATTCACTCAAAAACTTAGTTTCATTGCTTGATGGATGCTTTTTAAAGAATTATTTAATGGCCTGTTTTTGATGGCTGGTTGTCGCCACCTTTTGGTAAAATAATGTAATTGCTGCCTACAACTTTCATTTTTGAGCGTCATTAAATGCATATGGCTGTGATTTTAATCTTTACCATAAATATCAGTGGTTATGTCTAAACTATAAACTGTTATCCAAGTATATTTGTGTTATTTGACTGTTTGTAACTTTATAACTAACTCAAAACACTAAAGACTGAATCTCTTCCTTGATTTTTGCATTTTTCAAACATATAAATGCAGCGATTCGAAGGATTAATAAACATATGCAAATCACCATTATTTATAGTTTGTTGAGTGGGGGTTGAGATCCCAATCTTTTTATGATTAATCTTGCAGCTTAATTTGCCAATAGCTTTACTTAAATTCGATAACAAGTGTGTATCATTGTGGCTATATATATTTGTGTTTATGTTCTCCGTAG
Seq C2 exon
TGTCACATTTTATGGTGGGTCGTGATGGATCTCAGTTGGCATATCGCTGGACATCTGTCCTGGATCCCTCATTAAAGAAAGGCCCTTGGTCCAAAGAGGAGGACCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000067673:ENSDART00000141424:9
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF139211=Myb_DNA-bind_6=PD(50.0=58.8)
A:
NA
C2:
PF0024926=Myb_DNA-binding=PU(19.1=25.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCAACAGAACAGCTTTCATGTGC
R:
GTCCTCCTCTTTGGACCAAGG
Band lengths:
254-1363
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]