HsaINT0069720 @ hg38
Intron Retention
Gene
ENSG00000198756 | COLGALT2
Description
collagen beta(1-O)galactosyltransferase 2 [Source:HGNC Symbol;Acc:HGNC:16790]
Coordinates
chr1:183944196-183945564:-
Coord C1 exon
chr1:183945432-183945564
Coord A exon
chr1:183944324-183945431
Coord C2 exon
chr1:183944196-183944323
Length
1108 bp
Sequences
Splice sites
5' ss Seq
GAGGTAAAT
5' ss Score
8.39
3' ss Seq
CCTACTGATGACTTTTGCAGGTA
3' ss Score
7.3
Exon sequences
Seq C1 exon
GGCACTCAACACAAGCCAGCTGAAGGCACTGAATATTGAAATGCTGCCTGGCTATCGAGATCCCTATTCCTCCAGGCCTCTAACAAGGGGTGAAATCGGCTGCTTTCTCAGCCACTACTCAGTCTGGAAAGAG
Seq A exon
GTAAATAATGCTTTATTCAGATTGCAGTTTTATGATGAGGAGAAAGGAAAGCAGGCTATCGTAGGTGAGTTAGGGCCAGATGTAAAGTGAGCCCGCAACTGTTCTGGAAATGTGCATGAGAGCTGCTCCTGCCTTGTGTCTCCCTCTGACCCAAGACCAGCAACAAAGGGGCAAGGAGGAGTAGCTTTGGTGCCACTTGGGGTGGTGACGGGGGAGACACCCATGTCCTGTGTGCCACACTCTTATTAATTCATTATCATCATTAGCAGGAATGCCTTCTATTATACCTATTATGACATCACTTATTAAGTGATTTTATACAAGAAATCACACAGAAGTCATGTGAGGTGGGTTGGGAAGGACAGACCACCTTTACCGAAGAAGAAATTATTAAGTAGCTTGACCCGGTAAGAAGTGGCAGAGCCAGAAGTGGAACCCCTGTCTTACAGATCAAGACATATCTGGAGCAGATATTGGTGTGTGGGGTTCCTGATAAACAGTCAGTTTCCACAACCAAAAAGAAAGTCCCTGAAGAAAGGCCCCTTGAACACTTTCTCTTTTAATGATCCAGTCTATGCCTGCCTTTGTTTTCTTTAAACTTTAAGTGAAATGTGATAAATAGGTATAAAAAGATATAGATCAAAAGATACAGCTCAGGGAAATTTCACAAACCAAACAACACACCCATGTTAATCAGTACACAGATCCAGAAGCAGGTAACCAGCATCCCACAAGCACCCCCCCACCCCGTACTGCCTTCTGGTCATCAGTCCCCAAGGGCAGTCACCATCCTGACTTCTAAAGGCATTGAATAGCTTTACCTTTGTTTGTACTTTCCCTTATATGAATGGAATCATGCAGTATGTGTACTCTCCTAACATGACATTTAGGAGATTCACCTATAACGTTGCGTTTAATTGTGATCATATATCCTCACTGCTGTGAATATTCCAAAGTTTATTATCTATTCTACTGTTGATGGCCATTTGCTTAGATTCCAGTTATGAATCTGTGCTACTAGACTCGTGACTTTTTAATACTTATTTATCTAATAAAAATTGGGTTTCAAACTTTTCATAGGGTATCTTCCTACTGATGACTTTTGCAG
Seq C2 exon
GTAATTGATCGAGAGCTAGAGAAGACTCTTGTAATTGAAGACGATGTGCGTTTTGAGCATCAGTTTAAGAAGAAGCTGATGAAGCTGATGGATAACATTGACCAGGCTCAGCTGGACTGGGAACTGAT
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000198756:ENST00000361927:9
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0175512=Glyco_transf_25=PU(22.4=96.8)
A:
NA
C2:
PF0175512=Glyco_transf_25=FE(22.6=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CACTCAACACAAGCCAGCTGA
R:
ATCAGTTCCCAGTCCAGCTG
Band lengths:
259-1367
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