HsaINT0038520 @ hg38
Intron Retention
Gene
ENSG00000124749 | COL21A1
Description
collagen type XXI alpha 1 chain [Source:HGNC Symbol;Acc:HGNC:17025]
Coordinates
chr6:56060891-56061681:-
Coord C1 exon
chr6:56061649-56061681
Coord A exon
chr6:56061038-56061648
Coord C2 exon
chr6:56060891-56061037
Length
611 bp
Sequences
Splice sites
5' ss Seq
GAGGTATGT
5' ss Score
9.81
3' ss Seq
AAGATTTCTTTTGCTTTTAGAGA
3' ss Score
6.44
Exon sequences
Seq C1 exon
GGAATTCAAGGCCATCATGGTGCAAAAGGAGAG
Seq A exon
GTATGTTTCTTCATATATTATGCTCTCTTGCTCTCTTTCTTCGGTCCTTTTTGCTTGGGTTTCAATACTATATAAATCTAGCTTTTGAGTAAAAACCAGAAAACGAAATGTTTTTCATCTTCTTCAGTAGAAGTTCCCAATTAATTGTTTTCAGAATATGTACATTTATACTGAATTTGATATGAAATGTGAATTGTCAATATTATTGGTTTTTCTTCCAGACTTGGAGCTGAATTTTTTCTCCATATTTTTGAATAAAGAATATTGTACATTTCTGTATCTGTCGGACCCACTAAAATGCAAGCTCCTTGTGAATAGGACTGTGTTATGCCCATTGTTTTATCTCTGGCAGTATGCGTATTACCTATACAATATACTCAATCAGTTGTGGATACTTGTAGGTCTGGCTGGTTGGATGGATGGATAAATGACAGTTTAATATGACATGAAATTTCCCTTCTGGTCAATGACAATATTTCCGGCTATTCCTTACATACCTTACATATTTACATATGTATACATGCATATTCACATCCTTAACGAGCTTCATGATGCAATTATACCTCCTGAAATATTTAAATAGAACTTGTAAAGATTTCTTTTGCTTTTAG
Seq C2 exon
AGAGGTGAAAAGGGAGAACCTGGTGTCCGAGGTGCCATTGGATCAAAAGGAGAATCTGGGGTGGATGGCTTGATGGGGCCCGCAGGTCCTAAGGGGCAACCTGGGGATCCAGGTCCTCAGGGACCCCCAGGTTTGGATGGGAAGCCC
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000124749:ENST00000244728:25
Average complexity
IR
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=FE(14.3=100),PF0139113=Collagen=PU(11.1=63.6)
A:
NA
C2:
PF0139113=Collagen=PD(18.6=26.5),PF0139113=Collagen=FE(76.2=100)
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
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
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