HsaINT0037957 @ hg19
Intron Retention
Gene
ENSG00000111799 | COL12A1
Description
collagen, type XII, alpha 1 [Source:HGNC Symbol;Acc:2188]
Coordinates
chr6:75864132-75865570:-
Coord C1 exon
chr6:75865378-75865570
Coord A exon
chr6:75864254-75865377
Coord C2 exon
chr6:75864132-75864253
Length
1124 bp
Sequences
Splice sites
5' ss Seq
TAGGTAGGA
5' ss Score
7
3' ss Seq
TATATACTTTAACATTTTAGGGC
3' ss Score
8.04
Exon sequences
Seq C1 exon
CTTCTCGGTTTAAGTCTCCTAGAAACCTCAAAACATCTGACCCAACCATGTCAAGCTTCCGAGTGACTTGGGAGCCTGCCCCTGGGGAAGTGAAGGGTTATAAAGTCACATTCCACCCTACGGGGGATGACAGAAGACTGGGGGAGTTAGTGGTTGGACCCTATGACAACACAGTTGTTTTGGAGGAACTTAG
Seq A exon
GTAGGAATTAACTACGTTTGTATCAAAGGATGAAATTAATTTGTTTACAAGGTTGAATAGCTTTTGTAAATTAGTAGGCTTTACACAAATATCACTTATATGTCTGTTTGCCAGCAAAGTATTTAAAATCAGCTAAAGCTGTTTTCTTATGCTTGGTGCTGCTGGAGTTGAAGTTAGGATTCAGGGGTCAGCAACAGAATTTAGGCCTGAGCAGGATTTTTTTGTAATGTTTAATAATTTTTGTTTGTTTTTAAGGGATCAGAATTGGTGTTTTCAATAACACCCTGCTTTTAAGAAATTAATGTTCTTATTACACAATGTCACCGAAATTGTAGCCATGTGGAAGCATGGGGGTTCCTGTACCTTTTGGCAAGGTTTGAGGGACTCATGCTGAGATCTTGAGTGTGAATCCCCCTCCAGTGTGCCATACAGGAGAAAGAAGGCAGGACCTTGTGGGTGCCAGCTGGCAGGAAAGGGCAAGGCTGGGCTCATGAAAGGTCCAGCTCCAGGCTGTGCAGTGAAAAACAAGGAAGTTTCAGTTTGAACAGCACCCTACATTCATTACAGTAAAAAGAATGAACTACTGTGTGTAGTCTTTTGGGAAGTTTGTTTTTCAATCATTCATTCAAGACTATTGAAATCTATATAAATGCTTGTGATTTACTTTTACCAGAGTAGGGAGTATAAAATTTATTGAGCTTACTATGTGTCAGGCATTGTGTTAGGCATTGTCTTATGTTACCTTGCAAGGTACAGCACTTCAATTATTTTCTTAAAGCCCATTGCTTAGAAACAGTAAGATTAAAGAGTCTGACCCTTCCTGACATGCTGAAAGGCAGGGTAGAGACTCTGCATCTGCTAGAAAGGCAAGACAGAAACCAGTGCTGTGAATTCCTAGTGTTCTCTGGAATGATTGCTGTCTAGTTTCTCTTGACACCTCACAGGGTAAGCGTAAGTGAGAAAGAGGCGGAAATTATTTTTCTTCTCTTATAATGTTGTACACTATAAACTCTTCATAGTGTAAGCTTGTAAATCAAGAAAAATGTCTTTAACAAAGCAAAAAAAAAGTGCTACCACTTGAGCCTATGGTTCTCACAGGCTATATATATACTTTAACATTTTAG
Seq C2 exon
GGCTGGTACCACCTATAAAGTAAATGTTTTTGGAATGTTTGATGGAGGAGAAAGCTCACCACTTGTTGGACAAGAAATGACAACCCTTTCCGACACAACTGTTATGCCAATTTTATCTTCTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000111799-COL12A1:NM_004370:16
Average complexity
IR-C
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.400 A=NA C2=0.119
Domain overlap (PFAM):
C1:
PF0004116=fn3=PU(74.1=92.3)
A:
NA
C2:
PF0004116=fn3=PD(24.7=47.6)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TTCTCGGTTTAAGTCTCCTAGAAACC
R:
AGATAAAATTGGCATAACAGTTGTGT
Band lengths:
310-1434
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)