HsaINT0037937 @ hg38
Intron Retention
Gene
ENSG00000060718 | COL11A1
Description
collagen type XI alpha 1 chain [Source:HGNC Symbol;Acc:HGNC:2186]
Coordinates
chr1:102886807-102888630:-
Coord C1 exon
chr1:102888577-102888630
Coord A exon
chr1:102887057-102888576
Coord C2 exon
chr1:102886807-102887056
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:ENST00000370096:62
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=0.833
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