GgaINT1009973 @ galGal4
Intron Retention
Gene
ENSGALG00000016155 | COL19A1
Description
collagen, type XIX, alpha 1 [Source:HGNC Symbol;Acc:HGNC:2196]
Coordinates
chr3:82338543-82339043:-
Coord C1 exon
chr3:82338954-82339043
Coord A exon
chr3:82338588-82338953
Coord C2 exon
chr3:82338543-82338587
Length
366 bp
Sequences
Splice sites
5' ss Seq
CCAGTAAGT
5' ss Score
9.09
3' ss Seq
TTTTTTTTTTTTTTCACTAGGGT
3' ss Score
11.44
Exon sequences
Seq C1 exon
GGTGACCCTGGCGGGATCATGGGACCTCCTGGACACCCAGGTCCAAAAGGTGAGGTGGGGCCACCTGGACCAAGTCTGCCTGGAAGACCA
Seq A exon
GTAAGTCTGTGATTTGAAAAAGTTTTTATGACTTTATTTCTTGTAGGGATAATGTGAAAGGATTTTCATTGTGCAGTGAAAGTAATGCAGTAAGAACAAGTAATTTTCAGATGTGATTTCAAACTTGAAATATATATTATAGTGTTATTGTAAGCACATTAAAATATATAGTATTGCTAGCAGAAGACCTACAAGTGATCCTAGTGACAGTACTATTAGCAAGGAAGGCATATGTAAATCTACCGTAGCTTACTCATAAAGGCTGACTAGTTTTCACAATAAAATTCACCTGGTCTCTTTCATTTCAAAACATAATTTGTGTTTTCTTGTTTTTATTTCTGTGTTGTTTTTTTTTTTTTTCACTAG
Seq C2 exon
GGTTCCGCTGGTATTCCTGGAAACCCAGGTCCACGAGGACCAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000016155:ENSGALT00000026059:25
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=PD(7.9=16.7),PF0139113=Collagen=PU(40.3=83.3)
A:
NA
C2:
PF0139113=Collagen=FE(22.6=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]