DreINT0154658 @ danRer10
Intron Retention
Gene
ENSDARG00000005186 | sp4
Description
sp4 transcription factor [Source:ZFIN;Acc:ZDB-GENE-031202-3]
Coordinates
chr19:2615891-2616798:+
Coord C1 exon
chr19:2615891-2616403
Coord A exon
chr19:2616404-2616712
Coord C2 exon
chr19:2616713-2616798
Length
309 bp
Sequences
Splice sites
5' ss Seq
GTGGTACGT
5' ss Score
8.61
3' ss Seq
CTTTTTTGTTGTTGTTGCAGATC
3' ss Score
10.65
Exon sequences
Seq C1 exon
AAAAAAGTGAATTTCGGAGAAATGTCGTGTGAGTGAATTCCCGACGAATATCCTCACACGCACAAAAAAGAGCGGAGAGAAAGGGAGAGCGAACACTGAACATGATGGTTTTGGCATTCATAGATATTTAAATGGGAGTGGGTGGGCCTTCGCGCAGACGGAGATCTCTGACAGACCTGCACATATTTCCGCGGAGGAACATTATTTAATTCCGGATTCAGCAGCACATTTGGGCCCGCTTTGAACGCGTACGGGACCGCCGCTCTTCAAGCCGACCTGCTCGGACCCTCTTGGCATTTTGTGCTCCGTTATTGAAGGGTGTTTTTGCATTGGCACCGCCCTTCCTGGCGGGGTGGGTCCGTGCGTCAGAGCTGCGCCACAGTCCGCGGCCGCTGGAGAAAATAGGCCGTCCTTCTTCTGGGCTTTTGCCTGCCTTCTGCCTGCCTTCCACGGCGTCCGGCCTTTTTTCTCTTAAACAACTCCTCTCCGGGTTTTATTAATGCGGAATGAGTG
Seq A exon
GTACGTACCCTCCCCTCCTTATGCGTCTCCACCCCTTAATTCTCCATGCGTGCGTCTGTGCCATCTATCCATCGCTGTCCCCCCACTTTCATATGCGATCTGCTGTTTATTTGCGCCCATTGATCACTTTTGGCTCTTGTGCAATGCCTGTGAGCGACAGGAAGCCCTGCTTGATGTGTTTAGACTCTTTTGCATTACAAAACCCGACCCTTGTGTGTGTGTGTGTGTGTGTGTTTGTGGTGCAAGTGTAATGTGTGGCATTAAATTCATCCAGATGTTTTAGGGTTGACTTTTTTGTTGTTGTTGCAG
Seq C2 exon
ATCAAAAGAAGGAAGCCATGGCCACTGATGGGGGGAAAGCCAGTGGAGGTGATGGGGGTACGAAAGGGAAAACTTCTGGATCACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000005186:ENSDART00000097528:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.952 A=NA C2=1.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
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:
GATTCAGCAGCACATTTGGGC
R:
CATCACCTCCACTGGCTTTCC
Band lengths:
353-662
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]