HsaINT0038332 @ hg19
Intron Retention
Gene
ENSG00000082293 | COL19A1
Description
collagen, type XIX, alpha 1 [Source:HGNC Symbol;Acc:2196]
Coordinates
chr6:70852659-70854155:+
Coord C1 exon
chr6:70852659-70852712
Coord A exon
chr6:70852713-70854101
Coord C2 exon
chr6:70854102-70854155
Length
1389 bp
Sequences
Splice sites
5' ss Seq
GTTGTATGT
5' ss Score
4.04
3' ss Seq
ATTAACTCTGAGTTTTCTAGGGA
3' ss Score
2.34
Exon sequences
Seq C1 exon
GGTCAGCAAGGATCTGCAGGCTCCATGGGACCCAGAGGACCGCCAGGAGATGTT
Seq A exon
GTATGTATAATGTCTTTGATATTTCTGGAATTGAAATTGAGACTAGGACATGTTTTTAAAAACATCAACATGTGTTCAAGTAACTGAGTTATCCCTCATTTCCCAAAGACATGGGTCATCTATGCCACAAAAACTGATCATACCTAATGTCAGGAGCTATTGGGAAGACTAGACCCTTCATATAATCATGTGAGGTCCTTTTGAGTATCATTAGCCTAATAAATTGGTTTTTGGAGCTCAAGTTAATCAAATTGTCATTTTGGACATGCTTGTCAGTGCTGTACCAGCAGTAGAGGAGATTGGAAATGTCAAAAGAAATAAAGAACACCAAAAGAGAAAGCAAACATTTTCAATATTCACAGTTTTTAGTTCAAGTCTCCATCTAAGGAAGACATTTCGAAAGCTTCTATCATTTTCTAGCAAAAGCCTTCCAAAAAAAGCAAGTCTTTTGGCTAAAAGTATGTCTGGAGGAAGATCGACAGATTGCATTATAACCTAGCTTTAGTGGACTTAAAATACTCAATACACCTTTCTATTCATTATCCGGATCAGCTTTTTGTTCCTTGGACAACTTTCTAGCCTTCTGACAACTTGGGAGCTGCGAGCTCTCCATCAGTTCACACTTGAGCAAAATAAGAAAAATCCTTGGCCATAACTCCTTGGAGACTGATCACTATCTGACTATGATTAGAGTTCCCTCCAGGCAACTCTTAGGATCTCTCCTTTTTTCATGCCCTGGGAACAGCCCCTTAACCTCACATTCTATTCTCCATGCTCACCGCTTGAGCCTCTCCTGTCTACTAGTCGGTGCACATATTCTGCTTGGTACTTTGAACACCCAGTTTATAGAGCAAAGCTTTTGATCACTCCCCTATGCCAAGTAATGGGCCACTGTAGATAAACCTAGTGGACAGATCTTATGAAAAGAGAGATAATCCTGGTGGCACAAGTGGAGCCACAATGCTCAAAAACTGAGACTAAGTGATAGTGGCCAGAGCTATAAAAAGAACAAAATCTAAAGGGAAAGAGCCACTGTTTCTAAAACATAGTAAAAATATATTTTTCTAGTTGCCCTAGAGTTCTTTGGAATCATTATGTGATGCTGCCAACCACCATCCTTCCTCGATGGCAATAATATGGGTGAGACGTTCGGTTCAATTCGACTTTAGTTTCTTTCCTATGGCATCCAGGTGGCTTCACTTGAAACAACAAACCACGTAGAATCACTAATATTTTTCCAGGTCTTAAAGGCCAAAATCAATCCAACTCCTTCTATTAATAGGTTATATGTTAAAATTCTGTTCTCTTGACAGAGATTCACAGATATAGGGAAATGTTATTGTAAGAGATGTTCTCATTACTCTTTCCTATTAACTCTGAGTTTTCTAG
Seq C2 exon
GGATTGCCAGGAGAACATGGTATCCCAGGAAAACAAGGCATTAAAGGAGAAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000082293-COL19A1:NM_001858:23
Average complexity
IR-S
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=PD(24.6=88.9),PF0139113=Collagen=FE(27.9=100),PF0139113=Collagen=PU(27.4=94.4)
A:
NA
C2:
PF0139113=Collagen=FE(27.9=100),PF0139113=Collagen=FE(27.4=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:
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
Other AS DBs:
FasterDB (Includes CLIP-seq data)
AS-ALPS (AS-induced ALteration of Protein Structure, links to PINs)
APPRIS (Selection of principal isoform)
DEU primates (Only for human)