HsaINT0146146 @ hg19
Intron Retention
Gene
ENSG00000144306 | SCRN3
Description
secernin 3 [Source:HGNC Symbol;Acc:30382]
Coordinates
chr2:175263094-175264831:+
Coord C1 exon
chr2:175263094-175263170
Coord A exon
chr2:175263171-175264649
Coord C2 exon
chr2:175264650-175264831
Length
1479 bp
Sequences
Splice sites
5' ss Seq
AAGGTAGGT
5' ss Score
10.29
3' ss Seq
TTTTTTTTTTTTTTTTACAGTGT
3' ss Score
10.95
Exon sequences
Seq C1 exon
ATAGACTCTATGATGAAGTACAAGAGGTGGTTTATTTTCCTGCTGTAGTTCATGATAACCTGGGAGAACGTCTTAAG
Seq A exon
GTAGGTGAAATAAATGTTTTGTTAGCAATATGCCTTTTAAAAATATCATAAAGTTATTTCTATACATAGCAATTTGGAAGAAACTGTAGAAGTTAAAATTGAGGAGTTTACATTTGAAAAATAAATGAGTCAGAAATAAACTGTGATCTTTTATTTCAGTGATTCGGAGGACGTTGAAATAACAATAATAAAATTATCCATTGTTTGAATAAATATTTGAATGCTTTCCATATGCAAGCATGTTAGATAGGGCAAGAGATTTAAAGTCAGCTGTCAAGACTCTGTTCCAGGAGCTTAGAGTCTAGTATAGCAATAAGATGTGTATGCATTATACCCCATTATAAAATAGGATGGTTTAAATGCTAAATTTAAGTAACAGTAGCATGCTGTGGCAGCGGAAGAGAATGAACATTTAATTCAGCTTGGAGTTAGCTGGAATTTGATGGACAAAAAGGATTCTGATTCTGAATTGGCTTAGGTTCTACTTGATGTAGAATAGGAAAGTCATCCCAGACTTTAGGAATGACAGTTTTATGACACATCAAAAAAGGTTTATTAGGCCCTATGTTAACACTATCAATATACATTTTATGCAGTCACTTGGTAGTATACACATTAATTAAAGGATCCTTTAAAAACTTATTTTAAAAACCCATTTAATGTGGAACTTAAAATGAGAGCTTCAAATTATGCTATTGTTGCTAATTCATACTTTTTAGATTTTATTTTATTGATATTCTAATATTAAAACATATTAAATATTAGACTTTTTTCTGTATCCTATGCCATATTTTTTTCTTTTGCTAAGACCACTTATTCATCTGTGATACCACTTCCACTTTATTTCTTCATATTTAAATATAGCCTGTCCTGTAAACCAGTGGTTCTCATTCTTTTCATTGCTGTGGGCATACCTAATGGTTGACTTCAAAATGTGATGTGAGATTCCTATGACAAAACTCTTGTATTCGAAGGCTACCATGTGAGTAATTATATCACTAATCAAGAAACACTGGATATTGAGGTTGAGAACTACTTCCTTAAGCTTCAACTCACACATCTACAAAAATGTTTCAAGATATTACAGCTAGAGACCATCTTTCTCCTGAGCTCCAATAGCACCTTGTCTTCACTTCATGACCCTAATACTTTATACTTTATTTTATCTTAATGTAGAAGTTTTAGTTTCTCAAAAGTGAGATCTTTATCTGATTCATCTTTGTAACTAACATATCTCTTGGCAGAATGTTTTATAATAGGAAATGCTCAGCAAATATTTGAATGAATAAATATTTTAGGGTTATTCTGAATATGTTTTAAGGGTAATGCCTTTATTATTGAAAATTTCAATTTACTTATATTTCCTTTACCTCTTTCATAACAGTTTTGTCTTCTGACTGATTTTTTTAAATTCTGGATTTTGATAACTTTTCTGGTTTTGTGGTTCTTGCTATGACTTTTTTTTTTTTTTTTTTACAG
Seq C2 exon
TGTACATATATAGAAATTGATCAAGTTCCTGAAACATATGCTGTTGTCCTGAGTCGCCCAGCGTGGTTGTGGGGGGCAGAAATGGGAGCCAATGAGCATGGAGTTTGCATTGGGAATGAAGCTGTATGGGGAAGAGAAGAAGTTTGTGATGAAGAAGCACTATTAGGAATGGACCTTGTCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000144306-SCRN3:NM_001193528:2
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0357710=Peptidase_C69=PU(21.2=70.5)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ACTCTATGATGAAGTACAAGAGGTGG
R:
TGACAAGGTCCATTCCTAATAGTGC
Band lengths:
254-1733
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)