HsaINT0038522 @ hg38
Intron Retention
Gene
ENSG00000124749 | COL21A1
Description
collagen type XXI alpha 1 chain [Source:HGNC Symbol;Acc:HGNC:17025]
Coordinates
chr6:56060018-56060795:-
Coord C1 exon
chr6:56060741-56060795
Coord A exon
chr6:56060219-56060740
Coord C2 exon
chr6:56060018-56060218
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:ENST00000244728:27
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.632 A=NA C2=0.897
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