HsaINT0038441 @ hg19
Intron Retention
Gene
ENSG00000164692 | COL1A2
Description
collagen, type I, alpha 2 [Source:HGNC Symbol;Acc:2198]
Coordinates
chr7:94045717-94047143:+
Coord C1 exon
chr7:94045717-94045815
Coord A exon
chr7:94045816-94047035
Coord C2 exon
chr7:94047036-94047143
Length
1220 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAAA
5' ss Score
8.38
3' ss Seq
TCACATGTGTTTGACTCAAGGGT
3' ss Score
4.45
Exon sequences
Seq C1 exon
GGGGAACGCGGTCCCCCAGGTGAGAGTGGTGCTGCCGGTCCTACTGGTCCTATTGGAAGCCGAGGTCCTTCTGGACCCCCAGGGCCTGATGGAAACAAG
Seq A exon
GTAAAATCTTATGTTTTCTATATTGCTGGTTTGGCCCAGTCTGCCTGGAATAAGTAGACCCTTTACAATAGAAAGATAATTGTTTTTCAGATTTTTATTTATTTCCAGTTCTGTGATGACTTCCCTCTCAGTAAACAGCAATCCGATTCCAGTGGACCTGAATTATTCTAAACAAACAAACAATAGCAACAAACTGTGGGGGAAAATTCAGAGTTCCCAAAACATAAATGAATTAGTATGGGTTGTCACTCTTTTCTCCTCACGCTGTTTATGCTTTTGTTTTAATCTAGAAACATTGTATTCATTGGACATTATTTTCAGAGAAAATAACTTTTTATCTTAACATCTCATCCCATAGAGTAAAATTTCAACAAGTAGTCTGACTTTTAATAATAAGAGTTTATGATGATGAAAATTCATTGGGCAATACATTCACCCCCAAAAATTTGTCTGGAAACTTGTGTTCCAAAATAGAATCTGTGGTTTAGATTTTAAAATAGATTTAATATACATTCCTGAAAAAGAGATTACCTTAACCACAATAAAAAGAAGACAACACATATTATTTTCATTCTTAACTCTAGGGGAAAAAATGTAAACATTAGTTGCAAAAAGCTATTTTAGTGTATGGAAGGATGTTCTTGGGAAAAAAATAAAAACATAAAAGGGAGAGAGGAAATAAAGAAACCACGGTTTTGTGAGGTAGTACTTTCAAAGGGATCTATGTATCTCAGAAGCTAGTCAACAGGTTTTAAGTATGTGGAATTGTAGGGTTTTATATAAAAATGGAAGATACAGTCTCTACTCTTAAGGAGATTAAAACACAAACATCTCCTCAATTGACAAGGTCTCTTTCCATGCTTTCTATCTGGGCTAAGAGACTTATCCTTGAAAAATGTTTGTGGGTAAACATTTTTTACTCTCTGCTTCCCATTGTCCTATCCTCTTCTCCATGCCTGCCATCCTTAAGAGGACTGAAGCAGGTTATAGAGGAATCGCAGCTGTGCACTCCCACTACCCTCATCTCTTCAGTCACCATGTCATTAACAGCATCTCTCTCTGCTATATTCTCCCTCCTTTCAATAGCCCAGCCTTCTTTGTGTTTCAAAGCAGGCAAGAAGCCTGTCTAGCTAGCTGTTTAAATTGGAATTCTTCTAGAGTTTGATTCTTCATTTTCTTCTTTCTCCACTAAAATTGATTTCACATGTGTTTGACTCAAG
Seq C2 exon
GGTGAACCTGGTGTGGTTGGTGCTGTGGGCACTGCTGGTCCATCTGGTCCTAGTGGACTCCCAGGAGAGAGGGGTGCTGCTGGCATACCTGGAGGCAAGGGAGAAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000164692-COL1A2:NM_000089:31
Average complexity
IR-C
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=1.000
Domain overlap (PFAM):
C1:
PF0139113=Collagen=PU(30.8=60.6)
A:
NA
C2:
PF0139113=Collagen=FE(53.8=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGTCCCCCAGGTGAGAGTG
R:
CTTTTCTCCCTTGCCTCCAGG
Band lengths:
198-1418
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)