HsaINT0038341 @ hg19
Intron Retention
Gene
ENSG00000082293 | COL19A1
Description
collagen, type XIX, alpha 1 [Source:HGNC Symbol;Acc:2196]
Coordinates
chr6:70861289-70866123:+
Coord C1 exon
chr6:70861289-70861330
Coord A exon
chr6:70861331-70866018
Coord C2 exon
chr6:70866019-70866123
Length
4688 bp
Sequences
Splice sites
5' ss Seq
AAGGTACTC
5' ss Score
7.46
3' ss Seq
CTTATCTTTATACTCATTAGAAT
3' ss Score
4.52
Exon sequences
Seq C1 exon
ATTGCACTTCCTCTCTTGGGAGACATCGGTGCTTTGCTCAAG
Seq A exon
GTACTCTATTGCTATGTAAGAAATTATGTGTTAATTTCCAGGAAAAATTAGAAAGAAAAATATTTAGCAGAAATTGAGTCAATTGCTTAGCTGGAACTAAAATTCAATTTTTAAATGGCAGGACATCTTTAAGATAGGAAAATAAACATGTATCTTATATATCTTGTGCCATTTATCCTAATTCTTTCACTCTCTTCTTCTTTACCAGCCTCTCATTTTGGGTGGGGCAGGGGTGGAGGGCAGCTGGTAGGATAGTTATGAATTGGCTACAGGGAAGGAATTATGTCATTAGCACTCTGGAGTAGATTATTCTCTCCTCTGGAGGAACATCTTTCTCTTAATGGGTGTTGACTCACCCTGGCTCACTACTGTGAAACCTAATCTTTCTCGCTATATCTGGCCTGGTCAGTCCCAAGATGAAAATCAGTGCTGCTCTATAAATAGCCACTTACAAGGCTGAATTTTGATGTCATAGGATTTTACAAAATTCCACAGTTGACAAGTGCCCTAATACCTGTTACTCTGTTCAATAAAAATCACCTCTACCTATTATCGTCTCAGGGAATTAATCTTGCTACCTCTTTTTTTTTTTTATCTCTAACACTTCCCTGTATTTTATCAGTAAAACAGGTAGGGGGGGATGATAATGGCACATATGTAAGGGTATGTATTTGCATGTTTCTGCCTGATATGCTAAGATTGAGTGAGGCCACATGAAAATCAGGCCCTTGACTTCATACTCAAACACAGTGTGTTGTATCTGTCTTTGTATGAATGGACGTTGTGTATGTGTACACACACACACGCACACACACACAGACTACAGTTATATATATATAATTTAGTTTGTATTTCTAGCATTTAGCCCAGTGATTTACACAATTATTTGCACAATAGTAAGCAGGCAGAAATATTTGTTTAATTGAATTCAAAAGACTCGAGTTCCGGCATATACATTTGTAAGGTAGAGTTTTGAGAATAGATATATAAACATAAGTGTAAATATGAATATAAATATAAAAATATATTAAAGGAGTTTCTAAGACCTCCAAAACCAGCAGTTTTTATAAGCCAGAGAAGAATATTTGTGGGGATTTCAGGAAAATCTTATATTTATTGAGTTAAAATTACATGCCACTCAATATGCCACTTTACTTATATCATCTTATTTAATTTCCTTAATAATCTTATGAGTTCAGGCTGTTGCGCATTCCCACTCTATAGATGAGAGACCAGAAGTTCTCAGCAGTTAAGTAACTTTTTCAGTCATAGAGCAAGTAAATGTAACATTAACACAGGAACATAGGTCCTCAGACATTAAGTCCTAGATTCTTTACAAGACAGTGGTGCTGGAAATAGCAGGATTGCCGGAGTTATATCATTTCAGAATACTTAGGGTTCTTTAAGGATGAGAAACTTGTATGCTTTAGTAGAAATGAATATACTGGTAGAATATGGGATCTCACAGAACAGATAAAAGGACCATGAATAGGCTCTGACGGGAAGTGGAACCAGGGCTCTCAGAAGTGGAACTAATTGACAATCTCGCCCGGGAATCATCCCTCTAATGAGTGTGCTCTGCCATTGCACCAATCCCTGCATCATTTCACTAAGGTTCTGAGTCCATAACGAGCAGGACATCTTGACTGATAGTCTCCACAAACTGTATACAATAGAAGAAAGGGGAGGTATGTAGTTCCCCGAACAAAATCCAAATACAGGAATTTAGACTGTGGGTTGGATCTGTCATGCCAATGTAATAACATCATGTTAAATCCTGATCTTGTTACCCTATATGTTAACACTATCTCTCTCTGCCTTGAGTCTTTAGACAATTTGATCATCCTGCTTTCTGTTCGCAAAAATATCTTTGATTAAAGTATTAAAAAGAACTGGCATAATTACAGGCACCTTCAAAGGCCTTCTTCTAGATTAATCAGCATATCAATCCCTCTTTGAACGACTTTGTGTATTGGTTAATAATTGATGCATCTTTATTCTTTCCATGAGAAAATCTTAAGACATTTTTCCAAGAATGTTAACAAAACTCAGTTATTTAAATTTGCCATTCTGGTAACCCTAACCCAAAGAAAATGAAGTCAGTTTCAAATGACTCTTAAAAATTATGTTTATCATAATGATTATCATTTTTTAATGTTTCACTTAAACAGTCTATTGAATAATCTATTCTAAAATGTTGCTCCATATTGATATGCCAAGGTTTTGCTCCATATTGAGATGCCATGTTTGTGTCTGCAGATAATTATCTTTTTCATACTTTTTGAAATATGGAAATCATTTTGTTTTTCTTAAGTTCTCAAGTGTCTCTTTATCTTCATAGTTTTTCAGGTGTCAGTAATAGTTCTATAAATATATATATTTAACTCCCCTGCCAACACATTACCACCTGTGAAATAATCCAGGTGGTAAAATTCATCTGGGAAACATTGCATATAACCCTAGTTCCCTTTTATATATTCAGACTCTAAGAAAGACCACCATGAAGAGAGCTTTTTCACCCAGCATTTTTTTTATGTACTTTAAGTTCTGGGGTACATGTGCAGAACGTGCAGCTTTGTTACATAGTTATACACGTGCCATGGTGGTTTGCTGCACCCATCAACCCGTCATCTACATTAGGTATTTCTCCTAATGCTATCCCTCCCCTACCCCCCCCAACCCCCCACAGGCCCCAGTGTGTGATGTTCCCCTCCCTGTGTCCATGTGTTCTCATTGTTCAGCTCCCACTTATGAGTGAGAACATACGGTGTTTGGTTTTCTATTCTTGTCTTAGTTTGCTGAGAATGATGGTTTCCAGCTTCATCCATGTCCCTGCAAAGGACATGAACTCATCCTTTTTTATGGCTGCATAGTTTTCCATGGTGTATATGTGCCACATTTTCTTTATCCAGTCTATCATTGATGGGCTTTTGGGTTGGTTCCAAGTCTTTGCTGTTGTGAACAGTGCTGCAATAAACATACGTGTGCATGTGTCTTTATAGTAGAATGATTTATAATCCTTTGGGTATATACCCAGTAATGGGATTGCTGTAACCCAGCATTTTTGAGATGATTTGCCTCATGTATTCATCAGGGTTCTCTAGAGGGACAGAACTAATAGTATATATGTATATATGAAAGGAAGCTTATTAAGGAGAATTGACTCATGTGATTACAAGGTAAAGTCTGACAATAGGCTGTCTGCAAGTCGAAGAGCAAGGAAGCCAGTAGCAGATCAGTCCAAGTCTCAAAACCTCAAAAGTAGGGAAGCTGACAGCGCAGCCTTCAGTCTGTGGCCGAAGGCCTGAGAGCCCCTGGCAAACCACTAGTGTAAGTCTGAGAGTCCAAAGCTGAAGAATTTGGAGTCTTATGTTTGAGGGCAGGAAGCATCCAGCACAGGAGAAAGATGAAAGCCAGAAGACTCAGCAAGTCAACCCCTTCCACCTTCTGCCTGCTTTATTCTAGCCGAGCTGGCACCTGATTAGATGGTGCTCACCCAGATTGAGGGTAGGTCTGCCTCTCCCAGTCCACCAACTCAAATGTTAATCTCCTTTGGCAACACCCTCACAGATGCACCTGGGAACAATACTTTGCATCCTTCAATCCAATCAAGTTGACACTCAGTATTAACCATCACACCTTGTAAGCTTTTCAGTATCGTGCAAAATTAGTGTTCCAAGGAGCCCATGTTTGAAAATCAGATTTACATTGCTATTCATTAGGTCAAAAATATTGAATTTGAATAGCCATGGGCTTTCTTGCCAGCTTCTTATCAATAACAAGCTTCACTTCTTTTTCATGTTTAAAGATTCTTCCCTTTAGGGAAAAGGATGGAAGAATGGAAACTTAAGTTGTCCTACCTTCTGTCAACTGTTAAACTATCTCCCCCACTCAGTGGCCCTTATTCTGTGCCTTTCTTGGTCATATTCTTATTCCAACAATTTATTTAAAAATAAGCCTATATAGAGCTTTTCACACACACTTTCTTTAGCTGTGTGATGAGAGTTATGTTTATCTTATGAGCTCAGACACTTGAAGTCAAGCCTTCCCAGATCAACTAAAGGTTGCAGAGAAGGCAATGGAAAGGTCATTTCACTTAGATTTCCTATTGTCACTTGGATATGACCTAGGAGTCAAGTTTATGTCAGTCAAGTAATTATTTCTCTCGAGTGCCTCCACTGACAAAATGTTAGTAAACTGTATGTAGTTGGAGAACTAATTTTGCTCCCAGAAGAACAAATCCTTTCTTCACAATTTTTTCTGTTGTTTTTAAAATGGTTTATGCTATAGGTTGTTTGAATTCTGTAATCTTGCTGGGTTTTCTAAACTTTATTACCACTCCCTTTTAAAACATTCTGCTAAACAATTGAGCCTCAGTTTTTGTTCTTGACTTATGTGTCTTTTCCTTATTTATTTGGAATTTTCTATTTAAGTGTCATTGGAGACCTGTTTTAAAAATAAAAGTTCATCAATATCATAAACAGATATCACTGATGAGCTTTGTAAACAGTTTTTGCCTCACAAAAATTAATGTTTTTAAATTGGATACATCAAGTGTCTGAAAGCAGAATGACCTATCTATATCACTCATCTCCAGAGGTTCCAAAAAAACTTCACATCACATGAAACCTCACCTTTATAGACGGCTTTTATGACTCCCTCAGTAACCTTATCTTTATACTCATTAG
Seq C2 exon
AATTTCTGTGGCAACTGCCAAGCCAGTGTCCCAGGGCTGAAAAGCAACAAAGGAGAAGAAGGAGGTGCTGGTGAGCCTGGAAAGTATGATTCCATGGCCCGGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000082293-COL19A1:NM_001858:31
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.500 A=NA C2=0.829
Domain overlap (PFAM):
C1:
PF0139113=Collagen=PD(1.8=7.1)
A:
NA
C2:
PF0139113=Collagen=PU(34.6=80.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Rat
(rn6)
No conservation detected
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)