HsaINT1008090 @ hg38
Intron Retention
Gene
ENSG00000204248 | COL11A2
Description
collagen type XI alpha 2 chain [Source:HGNC Symbol;Acc:HGNC:2187]
Coordinates
chr6:33184992-33186818:-
Coord C1 exon
chr6:33186627-33186818
Coord A exon
chr6:33185055-33186626
Coord C2 exon
chr6:33184992-33185054
Length
1572 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGG
5' ss Score
10.07
3' ss Seq
CCTTCTCTCCTTGGGGTCAGGAC
3' ss Score
7.14
Exon sequences
Seq C1 exon
GGTGATGTCCAGGAGCTGGCCATTGTCCCAGGGGTCCAGGCAGCCTATGAATCATGTGAACAGAAGGAGCTGGAATGCGAGGGGGGCCAGAGGGAAAGACCCCAAAACCAACAGCCTCACAGAGCCCAGAGATCTCCACAGCAGCAACCATCAAGACTTCACAGGCCACAAAATCAGGAACCCCAGAGCCAG
Seq A exon
GTGAGGGAGCTGGGAGAACCCCCAAGTGCAGCACACCCCAGAGAGGGAAGACACCCAGGCATCTCTCCTCCTTAGTTGTCCTCCCCACCCTCATCTCCCTATTCCCATCACCCCCTCCTCCTAGTCCTCATTCATCAGCCTTTTTATTTTCATCTAAAAATAAAAAGAGTTGTTATGAAGAATTTGTGGCTGGGAGCTGTGTTCCCTGCTCTGCGTCTCCTCTTCCAGTCTTCCTGGAACTGTGTCCCTGGGTTTTCCCTTCCTTCTTTGAATTAAGAGATTGGGAGACAGTGGGAGAGGGGTGAGAGCTGGGGAGGCAGGTAGGAGAGGGGACTGAAGCCAGGAGAAAGCAGTCGGGATGGTGAGACCAAGGAGGAGGAATGGGAAGGAGTAGGGATGGAGGGAATATCAAAGGAGGGGTGGGTCTGCAGAAGTGTGGGAGTGGGGAACCCAGTCTCTGGCCCCCACCTACCTGGAGGGGCAGGAAAAGGGGAGGTAGTAGGGGGAAGGGAAGGGAAGGGAAGGGAAGGGAGCCTGGGTTGGATGGGGTCTGGAGAGTTAGAATACAGATAGGCTCTGGGGTCAGTGGTCTAAAGATCAGAGGGTCAATCTCTTAATCATGTCTGCTTCTGCCCCACATGTGGAACCCCTTCCCTCTGTTCCACCTCTCCCCACCTCCCTCCTGACCCTCAACCTCTCCTTTCATCTTCAACTCTCTGTTTCCCAACTCCACACCTCCCCCGTTTCCCAACTCCCACACCATCTTTATATCTCCCTCTCCCGCCCTTCACCCCACACCTTCCAATTACCCCATCCCCTTCCTGTCTATGCCCACCCCCCAATCCCAGCCCACTGAGTCTCTCTACTATGACTACGAGCCCCCCTATTATGATGTGATGACTACGGGGACAACCCCTGATTATCAGGTAAACTCAAGGGACCCCTTCATTTCTTCCCTTTCTCCCAGCACCCCCAGCAATCATCTCCTAGGACACCTTCCTCCCCTCCCCCATGCCGTGGGGAGAGGCACAGTGTGTTTAGATTATGGGGATTTACTTAGTTCCTGCCCCCTCCCTGTCTCTCTGCTGCAGCGCCCTGGGAGCCCCCACCACAGGCCTCCCCCTTCCCCTAGGGGGCATCGGACCCCTCCCTGAAAGCCTACCCCACCTGCCAAGAGGTCAATGACCTGGCAGGCGTCCCCCTCACCAGGCCGGAGGCCCTCTCCAACTGCAGGCTTTGACCCAGCATGGGAGCAGCCTCCCCTTTCCCGATGCCCAGCTCGGAGGGCAGCTTCCCCCACTGCCTGGCCCCGCCCCAGGACCAGAGGCAGCAGTTACCGGCAGGTAGAGCCGGGGCATCCAGATCTCTGCCCCCAAACCTCTATGACCTTGGAGGTTCACTCTCCCCAAACTATCCCCCTCCAAAGGGGCTGCAAGATCTGAGATTTCCCCCATCCCCCAGCACAGACAGACCCTGCCCTCGGGGGACAGGTGCTGCTTTGCCTCCCTTCTGCTAACCTTTCTCCTTCCTTCCCACCCCGTGCTACTCTTCTCCTTCTCTCCTTGGGGTCAG
Seq C2 exon
GACCCCACCCCAGGTGAAGAGGAAGAAATCCTGGAGTCGAGCCTCTTGCCACCCCTTGAGGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000204248:ENST00000374708:5
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.723 A=NA C2=1.000
Domain overlap (PFAM):
C1:
PF0221019=Laminin_G_2=PD(7.3=14.1)
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Rat
(rn6)
No conservation detected
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGTGATGTCCAGGAGCTG
R:
CTCCTCAAGGGGTGGCAAGAG
Band lengths:
255-1827
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Autistic and control brains