HsaINT0031237 @ hg19
Intron Retention
Gene
ENSG00000013725 | CD6
Description
CD6 molecule [Source:HGNC Symbol;Acc:1691]
Coordinates
chr11:60781391-60783307:+
Coord C1 exon
chr11:60781391-60781486
Coord A exon
chr11:60781487-60783184
Coord C2 exon
chr11:60783185-60783307
Length
1698 bp
Sequences
Splice sites
5' ss Seq
AAGGTAGGA
5' ss Score
9.45
3' ss Seq
CGACTCTGTTCTCTCCCCAGTTT
3' ss Score
10.19
Exon sequences
Seq C1 exon
CCCTCCCCGTAATGGTGAACCACCAGCACCTACCCACCACCATCCCGGCAGGGAGCAATAGCTATCAACCGGTCCCCATCACCATCCCCAAAGAAG
Seq A exon
GTAGGATGTCCCCCATCCTGGGTGTGGGAGGGCTGGGGAGGACAAGAAGGGTGAGCTTTCTGGAAGGTCAGCACCACTTAGGTCCAAGACGTACACACAGCTGGAGATGAGATCTGGGCCAGCCCACTCCCGGCCCTGGGACCTTGAGCAGGCTCAAGTCGTCCCTGGACATTGAAGGGCAGATGACCTTCCAGTTCAGTCATGCTAGGACTCTATAGAGTTTTGAGTTCTGGACAAATACAGGCAAAGCACGTTTTAGATCTTGGTTCTCAGAGGAAAGCTCTGTTCTGCTTTGCTCTGCTAGTTGGCTAGTAGGCTTGTGATATCATCATCCCTATCAATGTCCTGCCCAATTGGCCTTGCGAAGCCCCATCAAGATTCTCCTAGAATGTGGTTTTATTTCATAGTTCATATTTTCTAAACAAAAAAACAAATTGGGGCTGGGTACAGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAACCTGAGGTGGGCAGATCACTTGAGGTCAGGAGTTGGAGACCAGCCTGGCCAACATGGTGAAACCCTGTCTCTACAAAAAATGCAAAAATTAGACAGGTGTGGTGGCGTGCACCTGTAATCCCAGCTACTTGGGAAGCTGAGGCAGGAGAATCGCTTGAACCTGGGAGGCGGAGGTTGCAGTGAGCCGAGATCACGCCACTGCACTCCAGCCTGGGCGACAGAGCAAGACTCTGTCTCAAAAAAAAAAAAAAAGAAAAGGTTCAGTCATTCATCCTTTATGATATATGGATTTATACCTCTTGCAGAGGAATTTGAGCTTAATCACCTTGCATTATGAATGTATTCAATCACCTTTATCGGAAAGAGTTCAATGACATAAAAACCAATACAAAACTCAGCCAAATATTATAAATATCCTTTGCACAGAGAGTCCATATATATGAAAAGAGAATGTGAATACAGCATCTAGCATAAGGCTTAGCATAAGGCAGCTGCTCACTGAATAGCACAGTCTAGAGGTTTAGAGCCAGACTGCCGGCTCTGGGCCAGGTAAGAACCTGTCTGTGCCTCAGTTCCCTCCAAGGCAAAATGGGGATAATAATGTACCCACTTCACAGAGTTATCATGAGGGTTAAATGAGGTAATACTTGTAAGTGTTAGAATAGTGCCTCACATATAGTAAGTGCTGTGTTAAGCGTTTGCTAAATAAATGTTTAGTTCTCCATATTGGAAATGAACGAAGGCAGCCTAGAAACTTCAGACTGGGTGGCTTGTACAAGATGGGCTACCCAGGTTGGGCACACTGGTGGATGCCTGTAGTCCCCGCATTTTGGGAGGCCGAGGGGGATGGATCGCTTGAGCCCAGGAGTTTGAGAACAGCCTGGGCAACATGGTGAAAACCTGTCTCTACAAAAAATTCAAAAATTAGCTGGGCGTGATGGTGCATGCCTGTGGTCCCAGCTACTCGGGAGGCTGAGGTGGGAGGATCGCCTGAGCCCAGGAGGTCAATGCTGCAGTGAGCTGTGATGGCACCACTGTACTCCAGCCTGGACAACAGAGTGAGACCCTGTCCCAGAAAAGAAAGAAAAAAAAAGGGGGCTACTTGGTGCTCCCCTGCTACTCTGCCTCTCACCTCTGCCGTTCATACTCTACCATCCCTCCCTACACCTTTCCGCCCACCACTTTGCCATGCCCTCGACTCTGTTCTCTCCCCAG
Seq C2 exon
TTTTCATGCTGCCCATCCAGGTCCAGGCCCCGCCCCCTGAGGACTCAGACTCTGGCTCGGACTCAGACTATGAGCACTATGACTTCAGCGCCCAGCCTCCTGTGGCCCTGACCACCTTCTACA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000013725-CD6:NM_006725:8
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.404 A=NA C2=0.460
Domain overlap (PFAM):
C1:
PF151021=TMEM154=PD(5.4=15.2)
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCCTCCCCGTAATGGTGAACC
R:
GTAGAAGGTGGTCAGGGCCA
Band lengths:
218-1916
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Genotype-Tissue Expression Project (GTEx)
- 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)