HsaINT0037934 @ hg38
Intron Retention
Gene
ENSG00000060718 | COL11A1
Description
collagen type XI alpha 1 chain [Source:HGNC Symbol;Acc:HGNC:2186]
Coordinates
chr1:102888723-102888919:-
Coord C1 exon
chr1:102888866-102888919
Coord A exon
chr1:102888759-102888865
Coord C2 exon
chr1:102888723-102888758
Length
107 bp
Sequences
Splice sites
5' ss Seq
CCAGTAAGT
5' ss Score
9.09
3' ss Seq
TTTGCATTTGCATTTTGTAGGGT
3' ss Score
7.38
Exon sequences
Seq C1 exon
GGAATTCCTGGTCCTGCTGGTCCCTTAGGTCCACCTGGTCCTCCAGGTTTACCA
Seq A exon
GTAAGTACAAGACAAAATAACCTTATAAGGTAGGGTTAAGTTACAAATATAACAGAGACACAAATGCTCCAGATTTTTATCTGTGCTTTTGCATTTGCATTTTGTAG
Seq C2 exon
GGTCCTCAAGGCCCAAAGGGTAACAAAGGCTCTACT
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000060718:ENST00000370096:60
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=PD(20.8=88.9),PF0139113=Collagen=FE(27.0=100)
A:
NA
C2:
PF0139113=Collagen=PD(0.1=0.0),PF0139113=Collagen=FE(17.5=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:
GGAATTCCTGGTCCTGCTGGT
R:
AGTAGAGCCTTTGTTACCCTTTGG
Band lengths:
90-197
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