HsaINT0159199 @ hg19
Intron Retention
Gene
ENSG00000139767 | SRRM4
Description
serine/arginine repetitive matrix 4 [Source:HGNC Symbol;Acc:29389]
Coordinates
chr12:119591344-119592188:+
Coord C1 exon
chr12:119591344-119591454
Coord A exon
chr12:119591455-119592047
Coord C2 exon
chr12:119592048-119592188
Length
593 bp
Sequences
Splice sites
5' ss Seq
CAGGTACCG
5' ss Score
10.05
3' ss Seq
AACCCCCCGCGCCCCTTCAGGGA
3' ss Score
7.96
Exon sequences
Seq C1 exon
GTCCTACTCCCGCTCTCCCAGCTATTCCTCCAAGTCTGGCAAGAGGAGCCCGCCCAGCAGAAGCTCTAGGTCCCGCCGCAGCCCTAGCTACTCCCGCTACAGCCCCAGCAG
Seq A exon
GTACCGGCCCCGCCCCTCAAACTAGGCCCGTCCTAGGCCCCACCCCTTTGCTCTGATCCTCCTCTCTGGCCCCGCCTCCCCGTTCTCGGGCCTTCTTCCTCTTAGGTCTGACCCTGACTCAGCATTCTTACAGTTCCCTTTGTCCAATCAGGAGTGGCAGCGAGGCATCAAATACCCTTGTTTCCTAATGTCTCCAGCCCAAACAGTCCCGCAGACATACCCCAGAATTCACATCCCCAGCCCTCAGCCTCTACAGACCGTCCCCATATTCAGAGCCCCCAGTTCTTACCCACGCACCAGGGCCTGCGTAACATTCACGTCCTCACCCCTGCAGCACCTGCCCTGCTATGATGCCCACCTGCAAATGCTGACACCCCTGCACAAGCCCAGCCCCCACCCCTACGGTACTAACAACCCTCGCAGACTCTTACCGCAGCCCCGTCATCCTCCCTCCGGTCTCCCTTGCGGCAACGTGCAGACCCCATCCCGTGACCCAGTGGGGTGGGAAAGAAAGGGAGTGTCCCTCTCCCACGCGCTCACGCAGAAAATCCAGCCCAGCCCCAGCTCCCCAGTAACCCCCCGCGCCCCTTCAG
Seq C2 exon
GGAGCGGGATCCCAAATACAGTGAGAAGGACTCGCAGCAGCGGGAGCGCGAGCGAGCGCGTCGGAGACGTCGGTCCTACTCGCCTATGAGAAAGCGCCGGAGAGACTCCCCGAGCCACCTGGAGGCCCGGAGGATAACCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000139767-SRRM4:NM_194286:11
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=1.000
Domain overlap (PFAM):
C1:
PF152301=SRRM_C=PU(15.7=28.9)
A:
NA
C2:
PF152301=SRRM_C=FE(67.1=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCTACTCCCGCTCTCCCAG
R:
GTTATCCTCCGGGCCTCCAG
Band lengths:
247-840
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Autistic and control brains
Other AS DBs:
FasterDB (Includes CLIP-seq data)
AS-ALPS (AS-induced ALteration of Protein Structure, links to PINs)
APPRIS (Selection of principal isoform)
DEU primates (Only for human)