GgaINT0125648 @ galGal3
Intron Retention
Gene
ENSGALG00000003509 | C9orf9
Description
NA
Coordinates
chr17:7368058-7369483:+
Coord C1 exon
chr17:7368058-7368205
Coord A exon
chr17:7368206-7369418
Coord C2 exon
chr17:7369419-7369483
Length
1213 bp
Sequences
Splice sites
5' ss Seq
AATGTGAGT
5' ss Score
7.8
3' ss Seq
GCTCTTTTCCCCTCCCACAGGCA
3' ss Score
11.3
Exon sequences
Seq C1 exon
ATACCCCCACGATGTTGTGAATCACCTGAGCTGTGACGAAGCAAAGAATCACTTTGGAGGTGTGGTGAGCCTCATCCCCATTGTCCTAGATGGTGTGAAGGAGTGGCTATCCCACACTGAGAAGCTGCCGCGACGCATGCTGTGTAAT
Seq A exon
GTGAGTGGTGGAAGTGCTGTCACTGAGAAGAGGGCACCCCAGGATGCAGCAGCTAGGGCAGCTATTTCCCCCAAAATACCTTCCGTCCACCCTGAAGCTCAGACCTCAGTTAGTAACAAAGATTGCATACAAGTGCAGGGGAATAAGCATGTCAGAAAGAAGCACATGACTGACAGAGAAAATCACAATGGGAAACTTAAAGGCCCCTGGAAACCACCTGGCAGACATGCCTTTTAAAGGATCAAAGTTCGTGCGTCTTCCACTTAACCGCCTTTAATCAGGTGGCTGATTAAAGATAGTGAAATGAACACTAGAGATCCAAGATCTGAAGAGTTAGTCCTGCCAGATACACCCTCCTCTTCCTTGCTGCTATTTCCACTGTCCTCTTGAAAGTCAGACCTCAACAGAAGCAGCTTTATCTCTCATGGTCCCTTTGGCAAGTATTCTGGTGAGAGTAACAGTGAGGAGCAATCCGATTCTAATCACACTGGGCTTATCCCTAAGATTTCCCCACCCCAGCTGATCCCATGGAAATCACCTGCTTTTTGGACCAAAGAATCAGCGTTGACAGGACTGTAATGCCATTGGCTATAGGAAAGGTCAGCATGGTTTAGCTGCACTGCCTAGGTTCTGCTGGTCCTTGCAGATCCTCACACCATCACCAGTAACACCACCCAGCACATCTTCCTTATGCCCATTTTGACTTCTCTGCTGTCAGCAGAGCTGGGGATATAAAGGATTTCTTCCCAGATCTCTGCAAAGCTAATGGGAGGTCCTTTTCATTAAGGGTGATTAATGGGAATCTTAGGGAAGCAGAGACTGAGAAAGCTGTGGCCATTTTCAGATGGTTCCTTTCTTCACAAACTACAAGTTAAAAAAAAGTCTCTCCCCCTTTTCAAGGAAAGAACCCACCTTCCTTCATTTTCAAGGGTGTTATGACACCTCGTTCATTGAAACTGAAAGGCACTGGAAATAGTCTCACACTGCTTTTATAACAGCGCTTTGCAATTCCAGCACAATACCTTTCCACCATTGCTGAGAGCAGCTTTCTTCCCAGCCCGCTTAGGGGGCTCAGCAGTCACAGAGCCCCCACTCCCTGCAGCCGACACGCATCTGTGGTGGTGCTTTTATTCAAATGCAGTTAGCTACAAACTTAGGATCTCACTAATGCTATGTCTTCCCTGTATCTGACTGCTCTTTTCCCCTCCCACAG
Seq C2 exon
GCAAATTAGCTCCTGTTCTTTGCTTCCTGCTGGAAGACACTCCTGAATAAACAATTTCCCCTTGC
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000003509:ENSGALT00000005551:3
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF151201=DUF4561=FE(29.3=100),PF0114712=Crust_neurohorm=PD(2.9=4.0)
A:
NA
C2:
PF151201=DUF4561=PD(0.6=33.3)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Human
(hg38)
No conservation detected
Cow
(bosTau6)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ACCCCCACGATGTTGTGAATC
R:
GCAAGGGGAAATTGTTTATTCAGGA
Band lengths:
211-1424
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]