HsaINT0030823 @ hg19
Intron Retention
Gene
ENSG00000177675 | CD163L1
Description
CD163 molecule-like 1 [Source:HGNC Symbol;Acc:30375]
Coordinates
chr12:7519832-7520793:-
Coord C1 exon
chr12:7520683-7520793
Coord A exon
chr12:7519928-7520682
Coord C2 exon
chr12:7519832-7519927
Length
755 bp
Sequences
Splice sites
5' ss Seq
GAGGTGAGA
5' ss Score
7.66
3' ss Seq
CATGAAGCATCCATTCTCAGTTT
3' ss Score
2.11
Exon sequences
Seq C1 exon
GTCATTTAGCACTTATTTTATCCAGTATCTTTGGGCTCCTTCTCCTGGTTCTGTTTATTCTATTTCTCACGTGGTGCCGAGTTCAGAAACAAAAACATCTGCCCCTCAGAG
Seq A exon
GTGAGAGCCCCACTAGGATTGTATAAAATGTGAGTTACCTGCCACCAAGGGCACACAGGATGGGGGATTCTTGCAGAATGGAAGAAATGCACTTGCCACTTTGAGTGAGATGGATTGGAAAGTGCCAGGCCAAATGCAGAAACATGTGGAATGATCAAGAATCAGCCAATCCACAATTTCCATTTACACAAATGTAATCTTTTAGAAGCTGTAGCTTGCCATACAGACGATGAGTCAGATAGGCAAATATCTTAGCTGATAGAAGGAAGGTAATTGTATGTTTTGGTTCAGAATCTAGACTGCAGAAATAGCCAATAGAAAATGTAGAAGCATGGTGGAGGATTAAGAACAAGAGTTTCCTGGGTTTGAACACCACTTATATAACTTACTAGCTGTGTGGCCTTTGGCTAGAAACTACCTTTCCAAACTCCAATTTCCTAATTTGTAAAGATAATAATAGTCTTACCTCATCAGGTTAAGATAGTTAAATAAATTAATCATCTGTATGAAAAATGGCCAGCACATAGTAAATACTATGTAAAGAACTTGGTAATAAAAGTGGAAGAATATCAAGGGAGAAAAAGGAGGATAAATTTTAAAAATGTAAAAAATTCACTAGCAGGGGTAGGTGCTGAAAGAGCCATTGGATTTTAGCTCAGAGGGATTAATATGTGTCAAACCTTAGCATTAAGTGTCCTAATATAAGGGATAGGCCATTTGAATTTGAATCCTAACCATGAAGCATCCATTCTCAG
Seq C2 exon
TTTCAACCAGAAGGAGGGGTTCTCTCGAGGAGAATTTATTCCATGAGATGGAGACCTGCCTCAAGAGAGAGGACCCACATGGGACAAGAACCTCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000177675-CD163L1:NM_174941:17
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=0.333
Domain overlap (PFAM):
C1:
PF151641=WBS28=FE(52.9=100),PF153301=SIT=PU(61.5=84.2)
A:
NA
C2:
PF151641=WBS28=PD(35.7=75.8),PF153301=SIT=PD(36.5=57.6)
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Mouse
(mm10)
No conservation detected
Rat
(rn6)
No conservation detected
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:
TTATCCAGTATCTTTGGGCTCCT
R:
CTGAGGTTCTTGTCCCATGTGG
Band lengths:
190-945
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)