HsaINT0138828 @ hg19
Intron Retention
Gene
ENSG00000056586 | RC3H2
Description
ring finger and CCCH-type domains 2 [Source:HGNC Symbol;Acc:21461]
Coordinates
chr9:125611732-125613508:-
Coord C1 exon
chr9:125613360-125613508
Coord A exon
chr9:125612102-125613359
Coord C2 exon
chr9:125611732-125612101
Length
1258 bp
Sequences
Splice sites
5' ss Seq
TCTGTGAGT
5' ss Score
7
3' ss Seq
TGTCATTTCTTTTTTCTCAGGGA
3' ss Score
10.09
Exon sequences
Seq C1 exon
GAGATCTTGGACATACAGCTTGGTATCAGTTCTCAAAATGATCAGTTGCTAAATGGAATGGCAGTGGAAAATGGGCATCCAGTACAGCAGCACCAAAAGGAGCCACCAAAGCAGAAGAAACAGAGTTTAGGTGAAGACCATGTGATTCT
Seq A exon
GTGAGTGTTAGACAGAAAATTCATAAACAGTGGGCATAGGACATAATAAAGAGAAAAAAATGCGAAATTAATTTTTGGCTTTATGCTGTGAGGGGAAGACCTTATATGGGCAATGATTTGGTCAATCTGGATTTTTAGGGAAGAAAAAGTAAAATTGAACTAACAAAGCAGTCCATTTTGGTAGCCTGAAACTTGCTTTTTGTTGAGATAAAGTTAATCTGTGTTCCAGCATCAGGTTATGCTTCTTTAATCTGGTTGCCAAATTTCTAGACTACAAAATGGAGAATGACAACCTAGATTAATGGTTTCTCTTTTTGAAAATCATGTTAAGATTTTCTTGGCTAGGCTGGGCGTAGTGGCTCATGGCTGTAATCCCAGCACTTTGGAAGGCTGAGGCGGGTGGATCACAAGGAGTTCAAGAGCAGCCTGGCCAACATAGTGAAACCCTGTCTCTACAAAAATACAAAAAAATTAGCTGGGCATAGTGGCGGGCACCTGTATTCTCAGCTGCCTGGGAGGCTGAGGCAGGAGAATCGCTTGAACCCGGGAGGCGGAGACAGTGAGCCAAGATCGTGACACTGCACTCCAGCCTGGGCGACAGACTGAGACTCCATCTCAAAATTATCTATCTATCTATCTATCTATAGATAGATAGCATATAATATAGTATATTTTCTTGGCTATAATACTGCCATTTTGAATAATTACTGCCAAAAATATGGGCTTAATCTTCAACTTGGTAGTTTGGCCTTAAACTAACTAGTATTTTAATTTTTATCATAACTTTTGGAAAACAGGACTTTTCAAGCCAGGAGTGGTGGCTCACACCTGTAATCCCAGCACTTTGGGAGGCCGAGGCGGGTGGATCATTTGAGGTCAGGAGTTCTAGACCAGCCTGGCCAACATGGTGAAACCCCATCTCTACTAAAAATACAAAATAGCTGGGCGTGGTGGCACATGCCTGTAATCCCAGCTACTTGGGAGGCTGAGGCAGGAGAATTGCTTGAATCCAGGAGGCAGAGGTTGCATTGAGCCGAGATCATGCCACTGCACTCCAGCCTGGGCGACGGAGGGAGACTCTGTCTCAAAAATAGGAAAACAGGACTTTTCTAGTTACTTCTGATACTTCTAGTGATAAAGACATGTCTTTGCTAGAGACTCCTAAAGTTTGCTGTAGCTTTCATTAAATATGTATAGTCACCCTTAACAGTTTGCACTTAAAGCTAATTTGTTTTTAATGTCATTTCTTTTTTCTCAG
Seq C2 exon
GGAGGAGCAAAAAACAATTCTGCCGGTAACTTCTTGCTTTAGCCAGCCACTCCCAGTGTCTATTAGCAATGCAAGTTGCCTCCCCATCACCACATCTGTCAGTGCTGGCAACCTCATTCTGAAAACTCATGTTATGTCTGAAGATAAAAACGACTTTTTAAAACCTGTTGCAAATGGGAAGATGGTTAACAGCTGAAAGGAGGTTCATCTTTCAAATTTGTGACCACACCATGGAAGCATTTACACTAGCTTTTTATATATATAATATATATTATATAATGTATATTTTTTTTAAAAAAAAGATATTACTGGGGGCATCCATTTCCTGTGGACTCTTTGATACTTCAAGCCCTCTTGCATTAGCATTATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000056586-RC3H2:NM_001100588:20
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.753 A=NA C2=0.226
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Rat
(rn6)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ATGGCAGTGGAAAATGGGCAT
R:
AGCTAGTGTAAATGCTTCCATGGT
Band lengths:
343-1601
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)