HsaINT0037909 @ hg38
Intron Retention
Gene
ENSG00000060718 | COL11A1
Description
collagen type XI alpha 1 chain [Source:HGNC Symbol;Acc:HGNC:2186]
Coordinates
chr1:102965487-102970272:-
Coord C1 exon
chr1:102970219-102970272
Coord A exon
chr1:102965541-102970218
Coord C2 exon
chr1:102965487-102965540
Length
4678 bp
Sequences
Splice sites
5' ss Seq
ACTGTAAGT
5' ss Score
8.59
3' ss Seq
ATAATACTTTGCCTCCTTAGGGA
3' ss Score
8.92
Exon sequences
Seq C1 exon
GGACCACCTGGGAAGGATGGGCTGCCAGGACACCCTGGGCAACGTGGGGAGACT
Seq A exon
GTAAGTGACCTTGTTACTCTTATTAAAAATTTCCATCTCTAGCACCTCATCAGTTCATACATAGAAAGCTACTTTATTATGAACATTTCAATTACTAGGTTGAGAAAAATGGAAAAATTAATTCCATTAAGCCTTTTATTGAAATATACATATATATATAAATACAAAAATAGATACAAGAAATATACTTCAGGAAATAGGATGTTAGTTGATATGATTGTTTTTATTGTCAATAGCAGCATTTTAAGGATGAGCTGATGGAGAAGACACCATTATTTTTTGGACATCTCCTCAAGATTTTCCCTCTCACTCTTTTCACTGAAGACTGTTTATAGATACATTCCACTCAAACCCATCATCTCTCCACTCTAAAGGCAACAGATTACGAATAGCCATGATCATAATACCACATTCTTTTATCTAGAACTAAGGGATTAAATACTTGCTGATATTGGACCCATCGGCTATAACTGGTTGGGAACTATGTCAAAAGCATCTTTCCATGTGAAATAGGAAAAAGTAAATCAAAAACGGTCACTAAATTTTACTTAAAACCTATAAAGAATATAACAGTAAACAAATTGACTGAACAACTTACCATGTGTATAACAATTTGGGCAGAGAGGAAACTGGCAGCTCAGTGATGGTTTAAGAATCCTGGTGAGTTTATTTATTTTGCCCCTTTCAAAATCAGACATCTGGCTATCCCAGTGGATTGTCATTCTAATCAGAAATCATCATGGATTGGCATATTTCCATGGAATCAATTCTTGCTTCTCACCAATGATTACTTTTATCCAGACTTCTCAAGGAAACCACAAATGCAGACTACCTTTGACTATGTGGTTGAAAATCATGTTAGGGTAGGGGGCACCCTGAATACATATTGGAGTTGCATAGCAATGTACTATAATAAATCTGAAATCTGAAAAAAATATGATTTTTCTGCTATGGAGGAAACAATTTGTCAGCAGCCACCCAATTTTGCCTTGCTTACCATGTGGCAATTCTTAGTTTCACCATTTCTTAGTTTTAGCCAGATGAGAAACTTTGGAGTCTTGGATTTCAAAAGCAAAATTGAAATATGATTTAGTGAGACAAAAGAAAAAACTGTTTGGATATCCTCTTGGGAAAGATATCTGTATGAGGAGCAGAAATAAACTTTCTAAAGGAGAGTCAACACTCAATTTGCAAATGCATTATCATTCAAATCTTTCAGCCAAATCATTTTTAATGAAGTCATTGTATAACTTTCTGGGAATAACTATAGAATATTCCAAAATGTCTTGTGGGGAAAGGATACCCAGAGAATTACTGTTATAAAGTCCTTTATGTCTATGATTTAATCTGGAGCTTCCACTTCTAACAAAAATAATTATATCACATATAACATTGAGATTTAAACATAGAAGAAAAACAGCATAATGTTTCTAGAATGAATGTTTCTGTTTTGTAGCTTTTCACAGATAAAAGCCAGGATTATTTCTGAAAAAATTATATTCCCGATTTCACATCCACTTTAAGGGAATAGTGAATCGTCCTATAGCCTCAAAGCTTTCTTTCTCACTTTGTTCTCTGCTGACCCAGATTCAAAGGATCACCTTGTACAGGAGTCACAATCTAGAGTGGGCATTCTTTGCCATATATTTATTATCTTATTTAAATGGATAAATTTTTGAATTATATTTGAGATTTGTCTCCAGCCAGAAATCCATTAATTAAATGTTTGTTCTGACATCTTACATTCATTTGGGTTGTTTCAGTATAATAGAAACTATTCCCAATTTTTCCTGGTGGCCTTAAACAGCTTCAGAAATGGTTTCTATTATATTGAAATGACCCAAATTTGTCTCAGAAACATAGTGCCAAATGCTGTATTGGTCCTAAAATTGGCTTAGTCTTTTAAAGATTATCAGAATAGGAATCACATTTCTGTTGGATTGTAACAGCATATTTTTCAAACTACCCATGAATATGTCCAATTAATTTCCATTTTCAGCAACTTTGAAAAACATAATTTGACTAGCTACTCTGAAATTAAGTGGCAAGTGTAGTCTTATTACATGACAATATTGAACAAGCACAACTTGTTGTGAACTGTAAAAGTTTTCCTGTGTAGTTTGTTTGTAAGATCCCCAAGATCAAATGTATTAGATACTTGCAAACACTCTGAATGGATTGAATGAGCAGACATATGGGCAATGCTGTCTTCCAGCTTTCCCAAATCCATCACTCACACAAATGGGCTAGCAGCCAAGACTTCCTCTCTCCCCTTAGGATGTATGAGTGCAAGTCTATGTTGTAATTTTGTCGAGACTTTCTGCAATTAAGTATTGATTTTTAATCTATTACATTTAATTATTATTGCAATATTTTGTGTGTGATTCTTGCTCTCACAGTTAGTAAGACAAAATGCTTTATAAGACTTTTTTAAAAAGTTTGGAATTGCCTTTATATCTTCCTGTTGAATTTAATGATTAAAAATTGGAGGAAGAATAACCCAGACAGAGGAAACAGGTCATACAAATATATGGTGTGTGGCTATTCAGAAAAAGGTAGGAAGATCAGCATGGCTAGAATTTAGGATACATTATCAAAGCAAAGGAAGTAACTGAATTTGCATACTGGGCCCCTATTGGCTAGAACTTTGTCATCTATATGTTTAAAAATGAATTTATTGGCTGGGCGTGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGAGGCGGGCGGATCACGAAGTCAGGAGATCGAGACCATCCTTTCTAACACGGTGAAACCCCGTCTCTACTAAAACTACAAAAAATTAGCCGGGCTTGGTGGCGGGTGCCTGTAGTCCCAGCTACTCTGGAGGCTGAAGCAGGAGAATGGCGTGAACCTGGGAGGCGGAGCTTGCAGTGAGCCGAGATCGCGCCACTGCACTCCAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGAATTTATTATGTTTGGTTTTGTGGGTGATGATTCTGCCTAATGTAAACAAGTTAGTAAACCTTATTTGAAAACTCAACAATGGTGAAGGAAAGAGATGATTATAGTTTGAATAAGACAGGTCTACTAGGATAAGAGAGAAGAAGCTGTATTTGAGGGACCTTCTCACGTGACACATTCAGATAAAATAACTGATTAAGCATGGGCACTGAAGAAAAGTCTGGAATCTGAAGACACGCCATTAAAAAGGGGAAGAACATAGAAGGAAAATCAAAGGAGAAGATACATTCAGCAAGTTCCATGTTAGGAATGTTGAAGAGAGAGCATGATATACAACTGGAAATTTCTAGTAGGCACTTACTGAGAGAGTTTTAGGGCTCATACTGATTAGAGGTTTATAAATAGTTGGGAATGGAGGAGTTCATCAGCATAGAGATGGCAATTGTGGTGATGGAGGTTGTTGAGATAATCCAGGGACACACATACACATATGCACACATGTATATATGTGTTTAGGTATGTGTGTATGTAAATCTGACAACAGATTTCCAAACCAACTGGTTGATGAAAAAATTAAGCGACTAATATGCTTATAAAATGCTAAATAAATTTTATGACATTTCCCCCCAGAAATGATTGCTTTTGCTATTCATAATGATAGCTCAAATAGAACCCTGAAAGTCTGAATTAATAGATTTTTAAAATAGAACTCTATTTTCTTTCCCTGTAGCATCAATTGCAATAATTACAGACTCTTTACCTACTTATACAATTTTATTATTGTAAATAATTCATTCATAGTTATTGGGAACATTGTGATACTAACGTGAGACTGCTAGTTCCTACCCATTTTTTTTCTAATCTTATTATTTTCAGTCTGACCAGATGTTGTAGGGAATAAAATATTCAGTTCTTTCGAAACTTCTCCCAATATTTTCTATCTACTTCTCCAGCTGTTAAAAGTAACTTAACTCTCATGGGTAAGAAATTTACCTATATTCACACAATTATGTGGAATGAATAACCCACAGCCTAGAGAAAAATAAATACCAGAATATATGCCCAGAAGTTTTATTTAGTGAGTATATTCTGCTCAAATCAACCAGATGATATTTTAATGACTGAATTATTTTCAAAATGCATTTATGACTATATCTCTTGAGTTTCTTACAAGAAAGAATATTGATAAACGCTAAAATAATTACTAACTATGCAAAGCATTATTTTAGTAGATCTATTTTTATATCTTGTTTTATGAGATTTTTGGAATACAATAGAGAGAAATGTATTAATATCACAGGCTGTGAATTTACCTTTGTATAAACAATCAGTAAACTGTTTCAAAGAATGTCTAAATCATCATTTACTTCATCCATAAACATTACTGGGTTAAAATTCTGTATGTTGTTTGACCTAGTGGAATGGGGCTAAGAACACATTTTTACTCTAGCTTCATTTATTAAAGGTAATTATTGCCCTACCATGTGAAATATTGAAATGGCAAGTTTTGAATTTTAATGAAAACTGAAATAAGTTTAACATATTAAACATATTTAAGCATTTGAAAATAAATATTTTTAGTCAATAGGTGACTTTCTTTTAATGTGACTTATTCAGCTATCTCATAGAATTTTGATTTATGCTTTGTGTTGTATGTAGCTTTTACAAATAATACTTTGCCTCCTTAG
Seq C2 exon
GGATTTCAAGGCAAGACCGGCCCTCCTGGGCCAGGGGGAGTGGTTGGACCACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000060718:ENST00000370096:37
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(22.1=100),PF0139113=Collagen=PU(13.9=61.1)
A:
NA
C2:
PF0139113=Collagen=FE(22.1=100),PF0139113=Collagen=FE(21.5=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:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
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