HsaINT0037925 @ hg38
Intron Retention
Gene
ENSG00000060718 | COL11A1
Description
collagen type XI alpha 1 chain [Source:HGNC Symbol;Acc:HGNC:2186]
Coordinates
chr1:102914352-102914811:-
Coord C1 exon
chr1:102914704-102914811
Coord A exon
chr1:102914406-102914703
Coord C2 exon
chr1:102914352-102914405
Length
298 bp
Sequences
Splice sites
5' ss Seq
CCGGTAAGT
5' ss Score
10.91
3' ss Seq
CTTTCAAAACGTCATTCTAGGGT
3' ss Score
6.04
Exon sequences
Seq C1 exon
GGTCCCAAAGGAGAAAGAGGAGAGAAAGGGGAAGCTGGTCCACCTGGAGCTGCTGGACCTCCAGGTGCCAAGGGGCCACCAGGTGATGATGGCCCTAAGGGTAACCCG
Seq A exon
GTAAGTGAGTTTGGTCCCCTCTAATGTGGCATTTATGCCAAACTCACCTTGGAGCTTTTCTTAGAAAGATTTGAAATCCTGAGACTCTGGAACATAGATGGTAAATCTGACTTTTCATCATTTCATATATTCGTAAGCATTCTCAATTGAATTAATTCTTTAGAAATTTTTTGGCGGGAGAAGAGAAATATTCTCAGCAGGTTTTGTCATGACTTTAACCTCTTCACCTCCAGAATGTCATAATTTTATAAAAATTTATTTTTCATTTATTTCTTTTTCTTTCAAAACGTCATTCTAG
Seq C2 exon
GGTCCTGTTGGTTTTCCTGGAGATCCTGGTCCTCCTGGGGAACCTGGCCCTGCA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000060718:ENST00000370096:51
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(41.7=100),PF0139113=Collagen=PU(34.5=55.6)
A:
NA
C2:
PF0139113=Collagen=PD(4.8=22.2),PF0139113=Collagen=FE(29.3=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGTCCCAAAGGAGAAAGAGGAG
R:
GCCAGGTTCCCCAGGAGG
Band lengths:
156-454
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