HsaINT0037962 @ hg38
Intron Retention
Gene
ENSG00000111799 | COL12A1
Description
collagen type XII alpha 1 chain [Source:HGNC Symbol;Acc:HGNC:2188]
Coordinates
chr6:75151141-75152031:-
Coord C1 exon
chr6:75151867-75152031
Coord A exon
chr6:75151288-75151866
Coord C2 exon
chr6:75151141-75151287
Length
579 bp
Sequences
Splice sites
5' ss Seq
TTGGTACGC
5' ss Score
6.8
3' ss Seq
GTATATATCCGTTTTTGAAGGTA
3' ss Score
6.4
Exon sequences
Seq C1 exon
GCATGGCTTTGAATTTCATTCGCCAACAGAACTTCAGGACCCAAGCTGGCATGAGACCTCGAGCTCGAAAAATTGGTGTGCTCATTACTGATGGAAAATCACAAGACGATGTTGAAGCACCTTCAAAGAAACTCAAGGATGAGGGAGTGGAGCTGTTTGCTATTG
Seq A exon
GTACGCACTGAAAAGGACAGTGATGCCCCTGGGGTTACAAATGTGCTGAGGATATTTTTCGTAGTTAGAAGTTTTATCTGAAGCATGAAAAAAAATACCCATTTTTTTCTATCACATAATTTATCAAAATAATGTTCCAGGAAGTTAATTCACTTTTTTCTTCTTTTTTTGGGGACAAAACTACATGGTTTCTTAAACGAAAATTAATAGATCAAGAAGAAAAATGTGGTATTAATAGGATTCATAAAAACTCCTACTTGGTTTTCCACAGAACCGTGTTTATTTTTGATATCCATTATTTTACATTCCAGAAAAAACACTGAAGAGAGTCTTTTTGGCGGGAAATTGGTGCTATATACATTTAGAAGAAGCCAATTTAAAAGAGCTTTCAGTTTGTATTATCCTTTGTTTCTGTTTTATTATTGAGAAAAATAATATGTATGTTTTAGTTAACTAATTATTAAACCTTCATAGTTGGCCAAAAGCAGCCATGAATTAAGAAAGCCGTAAATCATTTGCTTCATTCCATTAATTTTTTTCTGAGAAGTGCTTTTAATTTGTATATATCCGTTTTTGAAG
Seq C2 exon
GTATTAAAAATGCTGATGAAGTCGAATTAAAGATGATTGCAACTGATCCTGATGATACCCATGCATACAATGTGGCAGATTTTGAGTCACTCTCCAGGATAGTGGATGATCTCACCATTAATTTGTGTAACAGTGTCAAAGGTCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000111799:ENST00000322507:20
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.088 A=NA C2=0.057
Domain overlap (PFAM):
C1:
PF0009223=VWA=FE(31.8=100)
A:
NA
C2:
PF0009223=VWA=PD(21.4=74.0)
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:
GCATGGCTTTGAATTTCATTCGC
R:
TGGACCTTTGACACTGTTACACA
Band lengths:
311-890
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