HsaINT0038522 @ hg19
Intron Retention
Gene
ENSG00000124749 | COL21A1
Description
collagen, type XXI, alpha 1 [Source:HGNC Symbol;Acc:17025]
Coordinates
chr6:55924816-55925593:-
Coord C1 exon
chr6:55925539-55925593
Coord A exon
chr6:55925017-55925538
Coord C2 exon
chr6:55924816-55925016
Length
522 bp
Sequences
Splice sites
5' ss Seq
GAGGTAGGT
5' ss Score
9.65
3' ss Seq
GGTTTCTTTGTTTTTGAAAGCCC
3' ss Score
4.09
Exon sequences
Seq C1 exon
GGAAGAGAGTTTTCAGAACAATTTATTCGACAAGTTTGCACAGATGTAATAAGAG
Seq A exon
GTAGGTATCAAATATAGCATTTTAATAACTTTTCTCAAATTACAAAAGTAATACAAATTCTTAGGACATATTGTAGAGGATATAAGTGAGGTGAAGAAGAAAACAGATAACATTTATAAGCCTCATCTACTTTTCTTCAATGAGTATTTTTATAAAGATTTATCATATATACTCTTTTATAATCTTTTTAATAAAGACATTTATTATTTTGCCATTATTTGAATTTTCTTTTGTAGCATATTTTTTGATAATTTAGTTCATAAATATGAATATAGTCCACCAATTTCTTTTGGGGGCACTTTCACTTTTTCCCCTATTTTAAGCAATTGCTCTAATAAAATTACCGCACAGAGCAATGAATATTTCCATAGTCAAATTCCTAGAAGTGAAATTATTGGCCAAGAAATATGCACATATTCAATGTTCGTAGTTTTTTCTCTGTAAACTGAAAAAAATTAAAAATATAATTAACACCAACTCACCATTTAAACATAAGGGATGGGGTTTCTTTGTTTTTGAAAG
Seq C2 exon
CCCAGCTACCAGTCTTACTTCAGAGTGGAAGAATTAGAAATTGTGATCATTGCCTGTCCCAACATGGCTCCCCGGGTATTCCTGGGCCACCTGGTCCGATAGGCCCAGAGGGTCCCAGAGGATTACCTGGTTTGCCAGGAAGAGATGGTGTTCCTGGATTAGTGGGTGTCCCTGGACGTCCAGGTGTCAGAGGATTAAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000124749-COL21A1:NM_030820:27
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.724 A=NA C2=0.902
Domain overlap (PFAM):
C1:
PF0139113=Collagen=PD(8.2=26.3)
A:
NA
C2:
PF0139113=Collagen=PU(75.4=67.6)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Mouse
(mm10)
No conservation detected
Mouse
(mm9)
No conservation detected
Rat
(rn6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CAGAACAATTTATTCGACAAGTTTGC
R:
AATCCTCTGACACCTGGACGT
Band lengths:
238-760
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)