HsaINT0037937 @ hg19
Intron Retention
Gene
ENSG00000060718 | COL11A1
Description
collagen, type XI, alpha 1 [Source:HGNC Symbol;Acc:2186]
Coordinates
chr1:103352363-103354186:-
Coord C1 exon
chr1:103354133-103354186
Coord A exon
chr1:103352613-103354132
Coord C2 exon
chr1:103352363-103352612
Length
1520 bp
Sequences
Splice sites
5' ss Seq
CCAGTAAGT
5' ss Score
9.09
3' ss Seq
TCACATTATCTTCTTTACAGGGT
3' ss Score
9.47
Exon sequences
Seq C1 exon
GGACCCGCTGGCCAGAAAGGTGACAGTGGTCTTCCAGGGCCTCCTGGGTCTCCA
Seq A exon
GTAAGTATATGTTAACAAGAGTGATGTTCTGACAGTTTGCATCTGGAAGCTGCCAATGATTTCTCTGAACTTATAAGATAGACAAAAAGCACATTCTGCCAAAAGTGCTGATTTTATAGGAAACATTATATCATTTAAGTAATCAAATCTACATGCCAAGACTTAAATTTTAATTGATTTCACTCTTCAAATATAAATGCCTTAATTGTATATTATAGTCTTGTTTTTATTATTTTTTCAAGAGAATCATATACTATTTTGTCACGTTAATGAAACCAACTTATTTTATGCCGTAAAGATACATTTTTACTTGACTCTAGGAATAATGACAAAAATTCAGATGCTTCACATTTTTTCCTAGTGCATTATAAAGATACTAATAAAAACAATAGTAATAGCTACCACTTTATTAATACTAAAATGTTCTAGGCTTCACATAACTAATTAAATGGTAGAATTAAAATATAGGTCCATGTGAAAGAAATGTTATTCTTCTTTCTTGAGCTAAAATCTTTCCAACTATATGTATACTAGTTTGCTAGGGCTACCATAGCAAAGTACCACAGAGTCGGTGGCTCAAACCACAAAAATGTATTGTCTCCCAGTGTTGGAGGCTAGAAGTCCTAGAACAAGGTGTCAGCAGTGTTGGTTCCTTCTGAGGTCCATGGCGGAAGGGTCTGTTCTGCACTTCTCTTCTTGGCTTGTGGTGGCTGTCTTTCCCCTGTGTCTCTTCACATTATCTTCCCTCTTTGGGTGTATCTGTGTTTAAATTTCTCCTTTTTATAAGAATATCACTTATATTGGATTAGGGCCCACTCTAGCGATGTTATCTTAACTAATTATATTTTCAGTGACTGTATTTCCAAATGGGATTACATTCTGAGATACTGAGAATTAGGACTTCAACATTACAAATTTTTGTGGGATACAATTCAACCCATGACAATATGATAACTATTTGATATAGCTCTGCTCGTAATGTAAATTCAAGTCGGGTTGCATTGATTTTAAGTTTGTTAATTTATAATGATTTAAGTCACACATATTTGAAGCAAACTAATGTGTACATATTTTTTAAAGTTTAATGTTTTATAATATAAATTATCATCAAATATAATACACAGTTGATTAGATAGCGCAATAGCTTTAAAGTGCTGTTCTAATCCTCAGAGACTTTACAATCTAGTTGTGGAGTTAGGGCATATAAATGATGACTAATTAATAAACAAGAGACTAACATATATAACATATCTACACAAATCTGTGCTATATTATTGTATAGATAAAGGGTGAGAAATCATCTAACTTATTCACCTACCTCAATATCTCCACCAAGTTCATCATAGAAGAATCTATGACGTTTATATATTTATAAACTTATCCTATAGCATAAATTTTGTAGCTAATGAAAAGCTAAACCAACTCTAATTTCTTATAACAAAAACATAACCAGTAATAATTAATATCTGCAGAATATTCCACTTTATGAAACAATTGCACTCACATTATCTTCTTTACAG
Seq C2 exon
GGTCCACCTGGTGAAGTCATTCAGCCTTTACCAATCTTGTCCTCCAAAAAAACGAGAAGACATACTGAAGGCATGCAAGCAGATGCAGATGATAATATTCTTGATTACTCGGATGGAATGGAAGAAATATTTGGTTCCCTCAATTCCCTGAAACAAGACATTGAGCATATGAAATTTCCAATGGGTACTCAGACCAATCCAGCCCGAACTTGTAAAGACCTGCAACTCAGCCATCCTGACTTCCCAGATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000060718-COL11A1:NM_001190709:61
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=0.791
Domain overlap (PFAM):
C1:
PF0139113=Collagen=FE(27.0=100)
A:
NA
C2:
PF0139113=Collagen=PD(12.7=9.5),PF0141013=COLFI=PU(12.7=32.1)
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:
GACCCGCTGGCCAGAAAG
R:
ATCTGGGAAGTCAGGATGGCT
Band lengths:
302-1822
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)