GgaINT1009988 @ galGal4
Intron Retention
Gene
ENSGALG00000016155 | COL19A1
Description
collagen, type XIX, alpha 1 [Source:HGNC Symbol;Acc:HGNC:2196]
Coordinates
chr3:82322246-82323544:-
Coord C1 exon
chr3:82323518-82323544
Coord A exon
chr3:82322300-82323517
Coord C2 exon
chr3:82322246-82322299
Length
1218 bp
Sequences
Splice sites
5' ss Seq
GTGGTACGT
5' ss Score
8.61
3' ss Seq
TTTAATTTAAAAAAAATCAGGGC
3' ss Score
2.2
Exon sequences
Seq C1 exon
GGTCCAAAAGGAGATCCTGGCACAGTG
Seq A exon
GTACGTACTTTTGGTCATAATAGAGATTCCCTAAGTATGATTCCCTCTGATTTATCAGTGAAGATCAGGAAACTCTGAGAAGTATTGGAGAGATCATTTTCTAAGAAAAATCACATCCCTTTCACCAGACAAAGTGAGAAAACAGCTATGTCTGCTACTAATGAAACAAGTTACATCTTCAAGTGGAACATCTACAGTTCCTTAGGGCTTTCAGGAGTTGATTCAGCCTCTAAGAAGCTGACTCTTTACCTCTCTAGCTGTTGTCCTGTCTTCAGGTTGTCAGTCCTGAGTAAAATACATAGAGTTAACTGCTGACCTCCAAGAGTATCTGGCTTCACTCACAAAAATAGCTGCAGTGTTAACCACAGCTAGCTCAGACTAACTCAGACAAGCCCAAAGAGATGAGGCAGTTAACATTTTGAAGAGTTAGCTAAGACTTAATCTATCATGAAGGCACATAATCTCCACTCAGCCAGCCTACACAGGGCCTACAGTTGCTCTTAATGCCCACAAGCTGAATATGTCTTTCTATACCAGCAACCACTTCCTACTCAGGAAGTACTTTCTCCCATAAAGGGTTTGGAAAGTGAAATCTGTCAAAGAATTCATAACATCTGCAAGAGGAATTTGCTGTAGTTTTAGATAGCTGAAATATTGGAATTGTTAACAGTAGCTCAGATGTCTATGATAAATTATCTGTTGATTGCCTTTAAAAAAGAAAAAAAGAAAGAGTAATAGAACCTTCCCGGTTTAACTGATTTCTCCAGTGTAGAAATTTTCTGCTTTTCATTCAAAACCTGAAGACTTGCACAGGGACTTTGCCTGTGTGCCCCTTGTTGCAGAGAAAGCTTTGTGCAAGGAATAGAGCCGTGCTCCAATACAGTAAATTGGAAGTTGAACAGAATTGCTTGGATGTTAGTTCTGTGGTGGATAGAATATTCTCACAACCTGTGGCTCTGCTGCTGGAAAGTGGTGACTTAGAGCTTGAAAGTGGTAACTCAGATCTGACTTAGGCTTGAAAAAAACACGAGGACAGTCTTCCAGATTACATTCTTAGTCAAAATTAAAGCAGTATAGCAAAATCTGTTCACCTAACACCTGTTAGCTATTTTGGTAATCTCGAGTTAAATATTCTGCTTTTGCTTGCTCTTCCACGTTTCTCTTGAACAGTTCAGAGTTTCTAATCTATGTAATCCATTTTAATTTAAAAAAAATCAG
Seq C2 exon
GGCGACCCAGGACCAATGGGATTACCAGGACTAGAAGGACTCCCAGGGGAAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000016155:ENSGALT00000026059:40
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(13.1=100)
A:
NA
C2:
PF0139113=Collagen=FE(27.9=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
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]