HsaINT0038425 @ hg19
Intron Retention
Gene
ENSG00000164692 | COL1A2
Description
collagen, type I, alpha 2 [Source:HGNC Symbol;Acc:2198]
Coordinates
chr7:94038634-94038920:+
Coord C1 exon
chr7:94038634-94038732
Coord A exon
chr7:94038733-94038875
Coord C2 exon
chr7:94038876-94038920
Length
143 bp
Sequences
Splice sites
5' ss Seq
CCTGTAAGT
5' ss Score
7.52
3' ss Seq
TCCTTTCCTTTTCCTCATAGGGT
3' ss Score
11.22
Exon sequences
Seq C1 exon
GGTGAAATTGGAGCTGTTGGTAACGCTGGTCCTGCTGGTCCCGCCGGTCCCCGTGGTGAAGTGGGTCTTCCAGGCCTCTCCGGCCCCGTTGGACCTCCT
Seq A exon
GTAAGTAGCCACTGTCTTTAAACTTTATTGAGTAAAAGAAAACAAAGGTGGAGTATGGGGAAGAAGAAGAATGAAGATGGGGTCAAAGAAGAACCGAAATATTCCAATTAACTGATATCCTTCTCCTTTCCTTTTCCTCATAG
Seq C2 exon
GGTAATCCTGGAGCAAACGGCCTTACTGGTGCCAAGGGTGCTGCT
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000164692-COL1A2:NM_000089:17
Average complexity
IR-S
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=PD(1.2=3.0),PF0139113=Collagen=FE(37.6=100)
A:
NA
C2:
PF0139113=Collagen=FE(16.5=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:
GGTGAAATTGGAGCTGTTGGT
R:
GCACCCTTGGCACCAGTAAG
Band lengths:
140-283
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)