DreINT0002384 @ danRer10
Intron Retention
Gene
ENSDARG00000087544 | BX510934.1
Description
Uncharacterized protein [Source:UniProtKB/TrEMBL;Acc:F1QMM8]
Coordinates
chr4:55439551-55440634:+
Coord C1 exon
chr4:55439551-55440236
Coord A exon
chr4:55440237-55440549
Coord C2 exon
chr4:55440550-55440634
Length
313 bp
Sequences
Splice sites
5' ss Seq
TTGAGCCAC
5' ss Score
-26.57
3' ss Seq
CTAGTGTGACCGCAGCTTTGGTG
3' ss Score
-10.35
Exon sequences
Seq C1 exon
TTCACCTGCACTCAGTGTGGGAAGAGCTTTGGAAAAAAACACATTCTTAATATTCACATGAGGATCCACACTGGAGAGAAACTATTCACATGCACTCAGTGTGGGAAGAGTTTCAGCCGCTTATCATCCCTTAACCTACACATGATGATTCACACTGGAGAGAAACCATTCACATGCAGTCAGTGTGGGAAGAGTTTTTACTGCTCATCAAACCTTTATAGACACATGAGGATCCACACTGGAGAGAAACCATTCAAAAGCACTCAGTGTGGGAAGAGTTTCAGCCTGTCATCAAACTTTAATCCACACATGAGGATTCACGCTAGAAAGAAACTATTCACATGCACTCAGTGTGGGAAGAGTTTGAGCAAACCATCATCCCTTAATCTACACATGATGAGCCACACCGGAGAGAAACCATTCACATGCACTCCATGTGGGAAGAGTTTCAGCCGCTCATCATCCCTTAATCTACACATGATGATTCACACTGGAGAGAAACCATTCACATGCACACAGTGTGGGAAAAGTTTTTACTGCTCATCAAACCTTTATAGACACATGAAGATCCACAATGGAGAAAAACCATTCACATGCACTCAGTGTGGGAAGAGTTTCAGCCGATCATCATCCCTTAATAAACACATGAGGATCCACACTGGAGAAAAACCATTCACATGCACTTG
Seq A exon
AGCCACGGTCACACTGGACTTTTCTCCCCATAGACTTCCTTTCATACGCATGTGAATGCATCAGACATGAAACGCAAGTTCGTGTATCAAGTTTTGCAGTTCACTGCGTTGCAAAGTTCAAGTTTGGTGAACTCTGACCTGCAAAATCATATCACTTGACTCGAAGATCAAAACATGACCTCTCTGGACAGAAATGTATATTATGGACCAATCGCTCACTTTATATCTAATCATCTTGTTTAATCCTGCCCCTTTTCACAGTGCCGTACAACAGAATGTTGCATGCTCAAACTCTAGTGTGACCGCAGCTTTG
Seq C2 exon
GTGTGGGAAGAGTTTTAGTAACTCATCAAACCTTAATAAACACATGAAGACCCACACTGGAGAGAACTCATTCACATGCACTCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000087544:ENSDART00000127643:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.017 A=NA C2=0.069
Domain overlap (PFAM):
C1:
PF134651=zf-H2C2_2=WD(100=10.9),PF134651=zf-H2C2_2=WD(100=11.4),PF134651=zf-H2C2_2=WD(100=10.9),PF134651=zf-H2C2_2=WD(100=11.4),PF134651=zf-H2C2_2=WD(100=11.4),PF134651=zf-H2C2_2=WD(100=11.4),PF134651=zf-H2C2_2=WD(100=11.4),PF0013017=C1_1=PU(82.7=18.8),PF051298=Elf1=PU(32.4=9.6),PF134651=zf-H2C2_2=PU(69.2=7.9)
A:
NA
C2:
PF0013017=C1_1=PD(15.4=27.6),PF051298=Elf1=FE(41.2=100),PF134651=zf-H2C2_2=PD(26.9=24.1),PF134651=zf-H2C2_2=PU(72.0=62.1)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
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:
ATGAGCCACACCGGAGAGAAA
R:
CCAGTGTGGGTCTTCATGTGT
Band lengths:
350-663
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]