HsaINT0037994 @ hg19
Intron Retention
Gene
ENSG00000111799 | COL12A1
Description
collagen, type XII, alpha 1 [Source:HGNC Symbol;Acc:2188]
Coordinates
chr6:75899268-75901476:-
Coord C1 exon
chr6:75901417-75901476
Coord A exon
chr6:75899532-75901416
Coord C2 exon
chr6:75899268-75899531
Length
1885 bp
Sequences
Splice sites
5' ss Seq
AAAGTGAGT
5' ss Score
8.4
3' ss Seq
AGATATCAAATGTATTTCAGAAT
3' ss Score
5.02
Exon sequences
Seq C1 exon
TTCAAACAGGTAGTTCGACAAAGCCAGTGGAGAAGAAACCTGGAAAAACCGAGATACAAA
Seq A exon
GTGAGTGTTTCTCTTACTATTTTTGCTTAGATTCATGGAAGTCATAAATGTAGGATAGAACAGATGTTCCAATTATATACATAGATTGATCTTATTCCTATATTAATTTATATAAGCTTTATCTGGAAGGAGCACAGACAATATAAGAATAATGTATAACTAAGTCATTATAACCTAAGTTCTGACATTCTAGCTAGTTTTTCATTCTATTTACTAGATATTCTTTTCAATGGGAGTGTTTTGAAATTGTGTGTGTCCAACCTTTCCTGCAGGATTTTGGCAATAGGTGAAAACAAAGCACATCTCAGGACTCAACTCATTTCTCAAAGACAAACTGATAGCAGTAGGTGGTACTTAGGAATATATGAGAAATACAGGGCTGGAACATGAGAGGGATGCCCTCAGCTAGTGTTCAAAGTAATACAATTGCCATGAAAATACTTTTCTAAGTCTGTGTGTATGTTATGCTCTTCTCTAGGTTATTTACATGGCCTTAGTTGATGGTAGTTGTAACCTTTTTGAGAGTCTCTGTAACACACCTCTTATAAATTGGTGCATTTGTAATCAGATGAAAGCAATTTTATTTAGTCTAGATCTTGCAGTTATTAGCCTCCTTTTGTCTTATATTGCTTTTCTGACTTATGGGGATAGATCCTTAAGGGGTTTCTTGGACTTCTAATTTTGTCATCTCGTAAAACTTGGATTTATGACCCAGAATGACAATAAAAAGATTATAAACACAAAGGTCTCTTTATCTGGAAGTATCCCCTCCAGATCACTGTTTATCATTATTTCAGATGCTAATATTTTCAACAATTATTATTTATTTTAAATTGAGGTATTATGCCAAGTATTGACTTTTTAATAGGCTTAAATTCACCTATTAAATAGTGTGCAAAACTTATTTAAGCATACAACTTGTATTTATTTGGCTTGCAAAATTTTTCAGCACCCTCTCCTTCTCTTCCTAGCCAAATACTTCTTTTATTACCTATCAGCTGACTGCAAGAACAAAATCATCATCAGAAAATTCACTTGGTATTGCATTACAAATACAGATTTTCATAAAACCAACCTGACCTCCACCATAGAGAGAAGGAAAGATAACATATTCAGTTACAAAAGCTGATCATTGTATTTTGATAATTTCAGGATACCACATGGATTTTTAACTTTTGAATAAAAATAATTGTTTACCCTCTTTGTTCACTAAAAGTAGGTTTTAATTGTCAAATTTAAATATATTGATAATTAGGACTATATATTTTGGCTATTTTGCATAATTTTATGCTTGTTTTTACTTCTATCAGGCTCCCTTAGCCCTCTAGACTAACCCTAATGCAAACTTTAGACAATTATATTGAAAAGTGCAAGAGTATATTAACAAATTAGGTCTTCAACTCAACTGCACTTCCTTGAATGGTACAGCAATTATTTTGTATTTATTTGTTGATAAATACCAAGGAATAAAAACCCTTTGCTTATATTTCTTTTGTATGACTCCTAAATGTTTTATAAAATTTGTACTTGTAAAGAAGAGTGAGGGTATAGTTTATAAAAATGGATAGGTTGATAGCACGAATACTTGGACTTTATGCTCCCGGAGAGCAGATTATAGATCTATTTATCTCTTTTTGTATAATGTCTTATAAAGCAATTTAAAGACATCTAGTTCCATGAATTCATCTTGATAAAGGCATTGAAAATGCTTCTATGTGTTGTTAGTAAAATTGTATATTTCTTTGTGCATGTGGGTGAAGAACAATTGGTGAATATGTTCTAATGAACAGAATGATTTAAGGAGCCAACATTTTTGCAATGTTAACATGTATTGATGAGTTGATTTAATAAAGCATCATTTAAAAAGATATCAAATGTATTTCAG
Seq C2 exon
AATGCTCTGTCAGTGCCTGGACTGATTTGGTTTTCCTCGTGGATGGCTCTTGGAGTGTGGGAAGAAATAATTTCAAGTACATTTTAGACTTCATTGCTGCTCTTGTGTCTGCTTTTGACATTGGGGAAGAGAAGACAAGAGTTGGAGTTGTTCAATACAGCTCTGATACCAGGACTGAATTTAACTTAAATCAGTACTACCAAAGGGATGAACTTCTTGCTGCAATAAAAAAAATTCCATATAAAGGTGGCAACACAATGACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000111799-COL12A1:NM_004370:5
Average complexity
IR-C
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.476 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0009223=VWA=PU(46.2=89.9)
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:
ACAGGTAGTTCGACAAAGCCA
R:
CTGTCATTGTGTTGCCACCTT
Band lengths:
319-2204
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)