HsaINT0037940 @ hg38
Intron Retention
Gene
ENSG00000060718 | COL11A1
Description
collagen type XI alpha 1 chain [Source:HGNC Symbol;Acc:HGNC:2186]
Coordinates
chr1:102879683-102881765:-
Coord C1 exon
chr1:102881697-102881765
Coord A exon
chr1:102879917-102881696
Coord C2 exon
chr1:102879683-102879916
Length
1780 bp
Sequences
Splice sites
5' ss Seq
CTGGTATGT
5' ss Score
8.14
3' ss Seq
TTTTATTCCTTTATTCCTAGCTT
3' ss Score
6.54
Exon sequences
Seq C1 exon
GTAAGAATTTCATCATGGCCAAAGGAGAAACCAGGAAGTTGGTTTAGTGAATTTAAGAGGGGAAAACTG
Seq A exon
GTATGTTATTACCTCAACATGAAACGATTTTTCACGAACTCAAGAAGTGACATTCTGATTATGTATTTCTGGACTTTAACAGTGAAAGTCTAAATTATGCTAAATGAGGATTCCCTGTGGTCTCTAGTTTGTTCCACTTAATATCTCTTAGACCACTGTGGTATCTTAAAGCAACCTAACATTTTTGTATAAAAGTAAATGGAAATATGCTAAATTTATGGAAAACAAGGATCAAATCATGCATACAATTTATTAAGTACCTGAGATAGACATCATAAAAATTGATTATGTTAGAAATATCAGGTATAAAGAATATAATATCTACTTAATATCTTCCTATTATTTCACTTTCTGTCTGCTTGAAACCTAATTCCTTCTTTATTCTTCATATCAATAAGTTGGAATGTGCAACTTTTTCTGATTGTTCTGGCACAAATTTAAAGATTTCCATACAATTACCAGTTCATTTCAATAATTTTCTAAAGATATTTTAAGATTAGATGTCAAAATTAAATTAATCTTTAAAAGGTGTTTAATCATATACATGTGTTTAAAGTATTTTATTTAGAAGTTATTGAATTTAAAGTGTTTTCCAGTTATCCAGATAATTATTCAGTTGTTTAATTTTCTTTGAAAAGCTATTATTTTCCATTTATGATTATTTATACAGTTATTATTTCTATACAAACTCATGCATATTAACCACTTTTATTGACACTCTCCACTGGAGTTATAATTCTCTATTACAGTCTTCAAGTTGCATATTAAATATCCATATTACATTATTATCTTTGTATAAGTTTAAAAATATATACAGATAGAACTCTATGTGTGTGGATTGAATTTTCCCAGTAGATTTTTTTCTTCAACCCCCAAGAATACTCATGATCTGACCTACTATTCAGTAAGAACTAAGTAAAATCTGTTTTAAGGAAGAAAGTAACAAATAACTGCCTTTACATTGACCTAATCTATAATCTAGGTGAACATCTTAACCTTTTTTTTTTCAAATTTAAGTGTATATGTTACAGCTGAACTCAGATATTTTTATTACCAAAAATAAGACAATTTATAAAGATGATATGAGACAGTTGCTAATAAATTACAACTGAGACTATTTTCCTGCTATAATTTCAGAATAAGTATTGACTCAACAAATATTAACTTGCCTTGTCTTGCACATTATGCCTGCTGCTGGCAATACAATGTTGAATACACACATCATCTAAAAATAGATAAACAGGCATTTCTGAAAATATTAATAACCTTTGAGGACTATAGCCCCAAAATGAAAAGTGTAGGAACATGTTTACAGATTTGGGTAAAGTTGATACATTTTGAAATGTTTGAAAGGAATAGTCAAAATCAAACAACATAAAACCAGCTAATCTTTGCATTATTCTGAGATTCCTTGGTTTTCATTGTTCCATTATTTTACCAATTTTTTTTTCAAAAAGATACAGAAATATATTGAAACATTTCTTGGAAACTAAAGCATTTTTTATAGTGTTTACTGTTTAGGAAACTAAGACTTAGAGATAAAGTGGTTTTTTCAAAGATAAGCAGTGGCTACAGTAACTTAGGTGGGATACAATTCATAAAATCTTGTCTCTGGGTCTTCTGACCCTCAATGTACACTTTTTTTCATTAGGTTAAGGTGGGTCTTTTGATTCATCTACATGCTTCTGGCATCACAGTTCACTGTCTGCAGTGATTTAATTCTTTGTAGCATAAAAGAGGAAAAGAGTCATTAGGTGTCTTTTTATTCCTTTATTCCTAG
Seq C2 exon
CTTTCATACTTAGATGTTGAAGGAAATTCCATCAATATGGTGCAAATGACATTCCTGAAACTTCTGACTGCCTCTGCTCGGCAAAATTTCACCTACCACTGTCATCAGTCAGCAGCCTGGTATGATGTGTCATCAGGAAGTTATGACAAAGCACTTCGCTTCCTGGGATCAAATGATGAGGAGATGTCCTATGACAATAATCCTTTTATCAAAACACTGTATGATGGTTGTGCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000060718:ENST00000370096:65
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.087 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0141013=COLFI=FE(10.4=100)
A:
NA
C2:
PF0141013=COLFI=FE(36.3=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:
GTAAGAATTTCATCATGGCCAAAGGA
R:
CGCACAACCATCATACAGTGT
Band lengths:
303-2083
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