HsaINT0037964 @ hg19
Intron Retention
Gene
ENSG00000111799 | COL12A1
Description
collagen, type XII, alpha 1 [Source:HGNC Symbol;Acc:2188]
Coordinates
chr6:75857391-75858213:-
Coord C1 exon
chr6:75858074-75858213
Coord A exon
chr6:75857521-75858073
Coord C2 exon
chr6:75857391-75857520
Length
553 bp
Sequences
Splice sites
5' ss Seq
GAAGTGAGT
5' ss Score
7.97
3' ss Seq
TGTTTAATTTTTCCCCCTAGTTT
3' ss Score
10.11
Exon sequences
Seq C1 exon
GTGATTTGGAAGCACCTTCTAACTTAGTTATTTCTGAGCGAACCCATCGTTCTTTTAGAGTGAGCTGGACACCACCTTCTGACAGTGTGGATCGATATAAGGTGGAATACTATCCAGTTTCTGGAGGGAAACGTCAAGAA
Seq A exon
GTGAGTAGGAACACCTATAACTTACTTCTTCCTGATGTTGAGATTGGGTCCTCCTCATTAGGACTCTGAGAATAATGTTAGGTGAGGGGCAAGAGGGATGAAGAGGGGCCAGAAATGAGTCAAGAATAGTGCTTTCTATTCTTGACTTTGCTAGGCAGGCATTTCCGTCTGGCTTTAATTAAAGGGAAAGAGCTTTGCTTAAATTCTTACGGTTTCTAAGAATTGTAGAATATCACTATGTTTTTTTCATTAAAATCTAATTAGAAGATGCTTGATTTATTTATGAATTTGTAGTAGAATCAGAGAGTTAGCAAGGAACATTGAAGATGATCTATTTTTACCCATTCATTTTACAAATAAATAACAGCTGGGAGAAAAATTATATGAATTGTCCAAGATCTCATTGTAATCTGATAGTTTCCAAATACAAAAGACAATGGCCTAATTGAAATATAGATTCTAAGCTCACTGCAGTTAACTACTTTGTAAGTATAGTAGGAAAAAGGGAACTGATTATACATACGTTGTTGCTCTGTTTAATTTTTCCCCCTAG
Seq C2 exon
TTTTATGTGAGTCGAATGGAAACTAGCACAGTGCTGAAAGATCTGAAACCTGAAACTGAATATGTTGTCAATGTGTATTCTGTGGTAGAAGATGAATATAGTGAGCCTCTGAAGGGGACAGAAAAAACCT
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000111799-COL12A1:NM_004370:22
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.106 A=NA C2=0.063
Domain overlap (PFAM):
C1:
PF0004116=fn3=PU(53.8=91.5)
A:
NA
C2:
PF0004116=fn3=PD(43.8=79.5)
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:
GTGATTTGGAAGCACCTTCTAACT
R:
TTCTGTCCCCTTCAGAGGCTC
Band lengths:
263-816
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)