HsaINT0038011 @ hg19
Intron Retention
Gene
ENSG00000111799 | COL12A1
Description
collagen, type XII, alpha 1 [Source:HGNC Symbol;Acc:2188]
Coordinates
chr6:75794042-75797463:-
Coord C1 exon
chr6:75797293-75797463
Coord A exon
chr6:75796274-75797292
Coord C2 exon
chr6:75794042-75796273
Length
1019 bp
Sequences
Splice sites
5' ss Seq
CAGGTACGT
5' ss Score
10.65
3' ss Seq
TCATCTTTGACCTGTTTCAGGTT
3' ss Score
9.34
Exon sequences
Seq C1 exon
GTCCACAAGGAGAATCCAGAACAGGTCCACCAGGGTCCACAGGTTCAAGAGGTCCCCCTGGCCCCCCTGGCCGTCCTGGAAACTCAGGTATCCGAGGACCCCCAGGTCCTCCTGGATACTGTGATTCTTCTCAGTGTGCCAGCATCCCATACAACGGGCAAGGCTATCCAG
Seq A exon
GTACGTTGTTGCCATTGTAGGAACCCCAACTCACCTGAAGTAAAGAACTTTACGGAAATGAAGTTCCTTAGGATTGAAGGAAGGCTGATTTGAAGATGTCTTGAAGATAACAACTCTTTCAGTTCTGATTATATAATAATAGTGTTTGCTATCATAGCACACAACATTATTTCACTGTTAGGATTGAATTATTTTCTTTTTTCCCCATGTTTCTGCATTTACCAAATCACATCATAAACCTCCCCTTACTTCTCTTGGGACTTCAAAGCATGCTAGTAATTGACTTTTTTTTTTTCTTTTCCCCAAGATTGGGAACAGGGATTTGTTAAATACAACTGTAAAATGCCAAGAATATGTATTTAAAAATTGTTTTGGGAATCTAATTTATGGGTAAACTATGTAATAATATGGTGTAGACAACTGAACATAGTTAACTGTCCCATACTAGCCATGGAATTAATATTTATAAAATCTGGGACTTAATAATTGTTTTTAAAGGATTTTTAATGAAATTCTAGTGTTTGACAATTGTAGAGGGCAGAAGTCTCCTATACTTGATTTTGTGGGATGTGAGGACTGGGTAGATATGCCAATCTGGAAATAAGATAGTCATGCTGTGGTCAATGGCGACCATTTCATTACTGCACCCTCAAGCATCTTGCAAATTTAAAAAATTATACTGCTGTTTGATATGATTTGCTACTTTCAAATAGTGCATGAGTAGTTGAATATCTAAATATCTATATATCTATATATTTATATGCATAATTACATATGACCAAAAGTAATAACAAATCTTAATGTATATTTCCATGCAACCCATTCAAAAAATTGCAATTTAATTCTTTATAAATTTAAATTACCACCTCCTTATGGGATGTGAGAATAACTAAAAATATATGGATATATATATATATATATATATATACTTTAACCATTACATACGTAGATGGATGTGTATTTATATTTTTTACTTAGTCATTCAACTTTTAAAAACTATCATCTTTGACCTGTTTCAG
Seq C2 exon
GTTCCGGCTAACACATTTTCTAAGTCGCCAGTGCTGCTTACAGTTTGAATACATGAAAATCCTGTTTCTGAGATGTTTGCGCACGTGCTTATTAGGAAATGAGTCTGTATGGAAATCTCACCACAGATAATGGTTAACGAACCGGGTCGACATCACAAAGGAGGGTGGAGACTCTTTTTACTAACTTGAATGAGACAAAAGCAGTGGTGTCAGTTTATAATCCTGATGCATTTCAGTAATAATGTAGAAAAACATTATTTTAAAAAAGTTCCAACACACAGCCATGAGGAGCCTCAGTTTTGAAAGAGGTGCATAATAAAACTACTAACCAGAGGAGTCTATGCCATTTTAAGAAAAACAATTAACCTGGTTAAAGAGAAATGTCTTATGTAAATAATAAACTAATTGTGGCTTGTAAATGATTTGTATGTGATCCTGTCGACTAAAATCACTTAACAATTCTACAATAAGCTTCTGCATCAAAGCCTGCCGCTTGCTCTATGCCGGAATAACACCAAATGGAATCTCCTCATCTCTTGCTTGTTAGCGATGTGTCTGATTCAGGGCATCTGTCTTTTTGTTACTTTTTTGTCCGTGTCCTCTCATTTGGGTTTTGTAACTGCAATTTTCAAACCAAAGTTTAAAATCACCTTTTCTTCCTGTTTTGCTGTAGTCACTGGTGTTCCTCACCCACCAGCTGTAACTCAGTTTGTGTGAGGTACAGCCACAGAAGATGTCATGTACTGTATATTACCTGGTGATAGTTGCTTTTCACCCCCCGAGTTCAGTTTCTAGGAGCCAATGAAACTTCCCCTCACCTCCTCATCTTTCCAAGTTGTTCTTTGAATTGAGGAGTTTGAAGGCATAAACAGTTACTTGGGGATTTGCGAAAATCCTACTTAGTTACTGCGTTTACAGTTCTTTGGCCCAGTCTCTGACCCTTCCCAAGTATTTGTGCAATGATTGTGTTTACTGCTGGATTTTTGAAGGTTTTTTTTTTTAAGAAAGTGCCATTTCATTATTTGATTATCACCAAATTATCTGGAAATAATTGGGACATTGTAACTTATCTATTTATAGTTATGAGATTAAGACTGGAGTGCCATCACCGCGGGTGATGATTTAGCTTTTGCTGTGTGTGTGTGTGTGTGCCTTCCAAATCATGCCATAATTGTAATGTTGAATCGGACAGAGCCTTACGTGCCCGAGGGCGGGGCCTACCTGCCTGAGCGCGAGCCCTTCATCGTGCCGGTGGAGCCCGAGCGGACAGCGGAATACGAGGACTACGGCGCAGACGAGCCTGCAGAGGAGCCTCCTGAGCCCCACCGGCGCTGGCGGCGCGCCCTGCCCCACGGACCCGGGCAGTGAACCAGAGATCACGCGCCGCGCCGCGAGGCTTGGGGGAGGTGTTGAAATTCTCATTTACAGGTCAGATAGAGCAGTGTACGTCTTTTCTGAGGTGTTTCTTCCAGCGTTGCTCATCCAGGAGTACCCTTTCTGATTGTAGAGAACCTTGTTTCTGCAGGAAGCCTAGCTCCAAGCACGCAGTCTGTAGACATTTTTGCCTTTGCCCTTGAAATGCTTGCAAAATACTTTGTTAACAAAAGCTGCAAAGAGAGAACATGCCGTGTGCCTTTAGTTAGCACAGCGGGCAGCCTCAGTGAAACTCTTAGGTTAAGCAGTTAAGTCCTGGAACCCAGAGCTGCTGTGTATTTCGAGCGGGCAGTTTATCTTTTGCTATACTTATTTTCAATTCAATTACACCACGATTCAAATAATTCCCCTCCTAAAACCAAAAAGGAGGGAAACGTCAACTCCATTGCAATTACTTATCTTCCTCTTCTATCTCTGTTATACGCCGGGGCATAGAATGCTCGTATACATCTCTTTAACAACCACAAACCTTAAGCCATGTAGATGAAGTTAGTGCATCAACGGGATACAGTTCCATATTGCCTTAAACCTCCTTGTTTTAGACACACTAACATTTATACCAAATTGCAGATTATTCTGCAGAGAGGGAATTGCATGTTTGTGTTGTATATTTAGTATGAACTTTTTTCAGAATATAATATTTCTTAGTTATCAAAAGTAGTTGGAAAACATTTGCAAGACTATGAACATAGAATTGCTGCTTTTATATTTTAACTGCAGATTGTGAATTTCACTGCCTTATATTATTTATTTCTGAAACAAAAGAGGCATTTTTCAATAAAACTACTGAAAATTTGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000111799-COL12A1:NM_004370:65
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=1.000
Domain overlap (PFAM):
C1:
PF0139113=Collagen=PD(73.7=72.4)
A:
NA
C2:
NO
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGTGCCAGCATCCCATACAAC
R:
GCACCTCTTTCAAAACTGAGGC
Band lengths:
349-1368
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)