HsaINT0035043 @ hg19
Intron Retention
Gene
ENSG00000128656 | CHN1
Description
chimerin (chimaerin) 1 [Source:HGNC Symbol;Acc:1943]
Coordinates
chr2:175676239-175677210:-
Coord C1 exon
chr2:175677037-175677210
Coord A exon
chr2:175676317-175677036
Coord C2 exon
chr2:175676239-175676316
Length
720 bp
Sequences
Splice sites
5' ss Seq
GAGGTGAGC
5' ss Score
8.7
3' ss Seq
TAACTAGTTTTATTTTTCAGGTC
3' ss Score
9.39
Exon sequences
Seq C1 exon
ATTGTGGTTTGAATGTTCATAAGCAGTGTTCCAAGATGGTCCCAAATGACTGTAAGCCAGACTTGAAGCATGTCAAAAAGGTGTACAGCTGTGACCTTACGACGCTCGTGAAAGCACATACCACTAAGCGGCCAATGGTGGTAGACATGTGCATCAGGGAGATTGAGTCTAGAG
Seq A exon
GTGAGCCATTTGCAGTGCGGGTTGCAGTGGTCTCCGTTCACTACCAGTACCAATCCTGATGCCTTTTGGGTACCTCATTGCACAATACGGTTGTCTTCTGTAATTTGGAGGGGAATGGTTTCATATGTCAAATGATCTCAAAGACTGAAATGAATTAATTTAACAATTAAATAGCTTGATTTCAAGGTACATTTAACTAAGTGTAGCCAATGTGCTTGTATAAAAATATATTTATAGATGATGCTTCCAGTCTGCAAAAGTTGACAGGTAAAGACAAATTCATTTTTCAGTTTTTAAATTTTTCTTTGGTTCAAAAAGCAAAAGTATAAATGCTCTACTAAAACTATCTATAAAGCCAAAAACAGAGCTGCATCCTAATTATTCTTTCCCACTTGAGAAAAACAGGCCTATATTTTATCTTAGTCTTCTGTTATGTAAAAGAATTTATGATGTAATTGGGGTGATGAATTATTTCCCTTAAGACTTAACATATTTCACTTAATTAGACCAAATGATGAGCCAGATGATATTCAGGTGACAATAGGTAAGAGTTAAAGAACTGTGTGTGAAATCGTTTTATTCTAGGAGAAGAGTGTGAAAAGATTTCTAAACATGTATATTTTATTTCTTCTGACACATTACCTCCCAGCTTAAAGTGTGAGGAGTTAAAATCTGAAGAAAAGGCATAATTCAAAGAAACTAACTAGTTTTATTTTTCAG
Seq C2 exon
GTCTTAATTCTGAAGGACTATACCGAGTATCAGGATTTAGTGACCTAATTGAAGATGTCAAGATGGCTTTCGACAGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000128656-CHN1:NM_001822:9
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0013017=C1_1=PD(37.7=33.9),PF0231811=FYVE_2=PD(42.3=74.6),PF087466=zf-RING-like=PD(55.6=42.4),PF0062022=RhoGAP=PU(17.7=23.7)
A:
NA
C2:
PF0062022=RhoGAP=FE(16.9=100)
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:
GTGGTTTGAATGTTCATAAGCAGTGT
R:
TCTGTCGAAAGCCATCTTGACA
Band lengths:
248-968
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)