HsaINT0037958 @ hg19
Intron Retention
Gene
ENSG00000111799 | COL12A1
Description
collagen, type XII, alpha 1 [Source:HGNC Symbol;Acc:2188]
Coordinates
chr6:75862049-75864253:-
Coord C1 exon
chr6:75864132-75864253
Coord A exon
chr6:75862199-75864131
Coord C2 exon
chr6:75862049-75862198
Length
1933 bp
Sequences
Splice sites
5' ss Seq
CTGGTAAGA
5' ss Score
9.45
3' ss Seq
TCTCATGATTGCCATGTCAGGGA
3' ss Score
3.65
Exon sequences
Seq C1 exon
GGCTGGTACCACCTATAAAGTAAATGTTTTTGGAATGTTTGATGGAGGAGAAAGCTCACCACTTGTTGGACAAGAAATGACAACCCTTTCCGACACAACTGTTATGCCAATTTTATCTTCTG
Seq A exon
GTAAGAAATTGAGTTACATTCCTTGAGGAAAACAACTTAGGAAACTATTTCAAATGTGAACTGTTAGGGTATCATACAATGGAAAACAATGATACAAATTTTACACTAAAATTTATTTCAATAATTTACATACTTAGCAAAAAAATTCTTCAAACATCCAGTCAAGCATGCTTTTTGACAGTATTTTTTTATACTTCTTTTATCAGCATTGCATTATTTCATACTTAAATTATTACATAAATCTATTTTTAAGAGTAATATATAATTATTAATGTATTAATAATTATTAGTGATGTAATTAATGTAGTAATTTTAAATTATGTAATAACGCATAATTTAAAATTGTGCATTAAATTTATTAATGCATTTAAATATTAAATTTAAAATTATGCATTATTGCATAATTAAGCTCTATTATTTAAAGAGTTTTTACTAAATGTAGATATTGTACCGTTTTCTATTTTTAATGACTAAGATGCAGTTTTCTTTTGTTAAAGTAATTGCAGAAATGTTTTATTTGGGCTGGGTAAGCAGTGTTAGGTTACATAAATGGGTGGGCAACTATGACTTGGGAAGGAAAATGGTAACATAAGCCCCTTAGATTTTCTGTCCCTGCCACAATTACAGCCTTTATGAACATAAAGCTAGTTTTTAACATTCTTAGAGACGGAGGTGGTGGACAGAGTTTACTTCTGATAGTTTTCATTATTGCTAAAAAAGAGTAGATCTGGGCAGAGCAGGAGCAGGCTTGTAAGGGCTTATTTCCTTGGGATAGTATTTGGGAATCCTTAATCCTGATATAGTATATAATATATGAGTGACACATTTGTATTCTGTAGTGTGATGAGCATTATTTAATTTTTTCCAATGATTTCTTTTGTAATATAAAGACCAAATGCTAACCTTGTAATAAACTGGAAAATTTATAGCTGGTAATATAAGCTTTTGGAAAGGAGAACATTAAAAAAATGGATGTGGACAAAATCAAGTGTCAAATCTTGCTGTTTTGCATTAATGTTCTATTGTTTCTCTTATGATGATATTAACTGACTTATATTTTTATTTTGTAGCTTGTACACTGAGGATGTTGGGATTATTTTCTCTTTCCAAAGCTTTTCCTATGTATCAATGTTTGTGCTTATCTTTACAGCTCTCAATTTGTATATTTGTTTGCATACTTTTCTAAATTGTCTTCCTTCTTTCTTGATTCTTTAAATGTGCAAACTTCACCATCTATATTTACATGATTTTTATTCACAGTAGATCATAAATTTAAATGATTAATAGCTAGATAATAATATATCAGGGTTTAAAAAATATATCTTTACCTCAAAAAGGTATAATTTTAAAAGTTATGTGTCTAATCCTTCATATATATGTGGTAGTTACCTAACAGCTTAGCTATTTGAAAAGATAATTTTTGGCTCACAAAAACCTTTTTTTAGTTTACATATTTTATCAGTCCATCTCATTCTTGTCTGCTATGACCATTAAATATTGCAGAAGAATGCAATATCTAATGATTTGACTACATTACAATTTTATTAAAGTTATTAGTACTTCATAGTTAGACAGCTATACATTCTCATTTATTTATTTCAGCCTTTGAATTTGTGAGCCCATCAAATTTTCAACAATGGCTTAATTCAAGTCTCCAGGTTCTATGAAAGAGGGCAGGAAATCGAGTCAAAGATAAAGGAAAGATTGGCCACTGAAATAATCTTTGGAGGAACTGCTGACTCTTAAGACTGTTAATTGAGGTTAATAAATCAGATGGACATATTTTCAGAGTCTTATACTCCACATCACTGAGCTAGACCATAGTACTGAGACAGGCAACACTGAGGATCCAGGGAGTGGTAGAGGTGTGACAAGGAAGTACCCTTGCCAACAATTTGCTTCTTACTGTCTTGTCTCATGATTGCCATGTCAG
Seq C2 exon
GGATGGAGTGTCTCACCAGAGCTGAGGCAGACATTGTGTTGCTGGTGGATGGATCATGGAGCATCGGCCGGGCAAATTTTAGAACCGTGAGGAGTTTCATTTCTCGTATTGTGGAAGTCTTTGACATTGGCCCCAAAAGAGTACAAATTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000111799-COL12A1:NM_004370:17
Average complexity
IR-C
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.119 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0004116=fn3=PD(24.7=47.6)
A:
NA
C2:
PF0009223=VWA=PU(23.1=78.4)
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:
GGCTGGTACCACCTATAAAGTAA
R:
ATTTGTACTCTTTTGGGGCCA
Band lengths:
270-2203
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)