HsaINT0059730 @ hg19
Intron Retention
Gene
ENSG00000141971 | FAM125A
Description
family with sequence similarity 125, member A [Source:HGNC Symbol;Acc:25153]
Coordinates
chr19:17535430-17536140:+
Coord C1 exon
chr19:17535430-17535486
Coord A exon
chr19:17535487-17535739
Coord C2 exon
chr19:17535740-17536140
Length
253 bp
Sequences
Splice sites
5' ss Seq
GAGGTGGGT
5' ss Score
7.07
3' ss Seq
TCTCTCTCCCCATCCCCCAGTAT
3' ss Score
8.29
Exon sequences
Seq C1 exon
GCCTTCTCTGCTTTTGGGGACCTGACCATCAAGTCTCTGGCGGACATTGAGGAGGAG
Seq A exon
GTGGGTGCAGGGCTAGGGAGGAGGTGGGTGCAGGGCTAGGGAGGAGGTGCCTGAGGGGCCGGCACCCGCCCCTCGTCCGCCCCAGGCTGTCCCAGTTTTCCCCATCCCCGCTTTGCCCCAGACACACACCATCTCTCCAGGGCAGAAGACCACTCAAGTCCCTAAGTACCCACTCTGCCATTCCTCAGTCACTCCCCCTTTGGCCCTCTCTTTACTCTGGCACCTGTTCACTCTCTCTCTCCCCATCCCCCAG
Seq C2 exon
TATAACTACGGCTTCGTGGTGGAGAAGACCGCGGCTGCCCGCCTGCCCCCCAGCGTCTCATAGTCCCTCACCCTTCCGCGGAAAGAGCCCCCTTACTCCACCTCCCCGCCAGCCTGGGGCCACCCCCCCTCACTGCATCCTGGGGCCACCCCCACTCACTGCATCCTGGGAACCTTCGCCCTGCAAGGCGTTTGCTATCTTCAGCCACTGGGCGGAGCTGCAGCCCTGGAGGAGGGGGCGGGTCGAGGCTGCGTGGTGATGGGGTCTCCGCCCCCACGCCCTGCCGGGCAGGGCTGGAGCTGGACAGAAGCCAGTGCCTTTAAGTCATTTGTGTCAAAACCCTCTGGGGTCCGGAGGCTGTGCGGGTGTCCTCCTGGCAATAAACACTACCCGGTTCTCGC
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000141971-FAM125A:NM_138401:8
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.050
Domain overlap (PFAM):
C1:
PF102404=DUF2464=FE(21.7=100)
A:
NA
C2:
PF102404=DUF2464=PD(12.8=68.2)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Chicken
(galGal4)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTGACCATCAAGTCTCTGGCG
R:
GAGACCCCATCACCACGCAG
Band lengths:
304-557
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Autistic and control brains
- Pre-implantation embryo development
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)