GgaINT1009992 @ galGal4
Intron Retention
Gene
ENSGALG00000016155 | COL19A1
Description
collagen, type XIX, alpha 1 [Source:HGNC Symbol;Acc:HGNC:2196]
Coordinates
chr3:82314220-82316089:-
Coord C1 exon
chr3:82316027-82316089
Coord A exon
chr3:82314256-82316026
Coord C2 exon
chr3:82314220-82314255
Length
1771 bp
Sequences
Splice sites
5' ss Seq
CCAGTAAGC
5' ss Score
5.34
3' ss Seq
TGGTTGTTTTTTTTTAATAGGGA
3' ss Score
8.55
Exon sequences
Seq C1 exon
GGTGAAAGAGGACCTATAGGAGATACAGGCTTCCCAGGGCCAGAAGGACCACAGGGAAAACCA
Seq A exon
GTAAGCAATTTTATCTACTTTCATTAAGAAAACATGCATCTTAATTTATGAGAAGTTTCAAAAGAAATTAGTTCACATCCTGCTTTGTATTGGGCTTGATAACTTAAGAAGAACATTCCAGAGAAACAGTGCTCAATATAACCATCCAGTCAAGAATTCTTTTCATATAGAAGTGTGATGTGTTTATGTTTTAATAGCCGATGTTACTGTGATCCTTCGGAGGTAACTGAGATCATTTTGAATGTCACTTGGATCCTGTTGATTTGAAGGTGCCTTTAGTAGTTTTTCAGAATGAGAGTATTAACCCAGGAGCTCAGCACAGTCTCTTGAGTATAGGGCAACAAAACTCATTCATGGTTTCAATTATGCAGAGAACTATTGGCTTCATGACTCTGTATACACATTACTGTTCTGTGTTCCTCTACTGGTAATGCAACATGATGTCTGAAGCACATACTATTCTCTGAGGATATGTTTGATCTGACCTCTTTATCTAAAATGCCATGTTGTCAGCAGTGTATTGTAGCACTGTCCGAGCTAGTTTAAAACAGCCTCGTTCATATTCTAGAAATAGTTCAGCTAGGATAGCTCAAAACTATCTCCCCCTGAGCGCGGTGCTGCATTGACAAGCATGAGAAGTACACCATTCTGGTTTATTACCATATCTCCACACAATTCTTCCATCTTGAAAGAGACAATTTCTGTAATTTCTGCAGCAAACTGGCCCAATTTAAGGAACAACTTGAAAATCTGTATCACTAATAAAATTTTAAAGTGCCTACTTTCATGAGCTCTGTCAGGATGCTACAAGAGTAAGCTGCTCTGCAAGAGAAAGTGACTGAGCTGAGGGCAGGAACAAGATGGGGCCATGGACTCACCAGCAAGGGATGCGGGTCCACAGTGACCTTAATCATGCAAAACCATGCTTTGCAGTATGAAAGGGAATAAAATATTGCTGATTCCTTTGCTTATCCAAGTCTTCTTTTTCACTCTGCAAAATAGCACTAAGTTTTCTGTGTATGCAGGTTCTGGCCTTGTATATCCCAGGAAAATAAATAGTGACAGAGCATTTATCTTGCACTTACCTGGTGTTGAGCAATTGTTAAATTACACTGTGATGTTATTTGGCCCATGCCACCCAGCACATTCTGAGACATATGTCATGTTCCAGGCTGGAGAAAAACATGAGCCTGAGACTACTTCCAGTGGGCATTATGATTAAGACCACTCTCTTTAGGGCAGGAAAAAATGCTTTGACCACAGGTGGAAGCTGTGGCATGTCACAAGTCCTAATGACCAATGAATAGATCTGGACACTTACTGTTGAGGTCTAATCTCTGTATAACAGCAGGGGCTAATAGGGCATTTAGGGCTAATGCCTACCATACGATGAATCTCTTCTGTGGTTGTATAATGAACTAGGACTTGTAGAGTACCTGTACAGCTCCATATTCCACATGTTTGCAGAATTTCACTGTATCTGGTAATTTAAAGTTGCACGTTCATTATAATTGATACACATCTTGTCACTGAAGATATTTTTTGCACTGCACTCTCAGTTCAAATGTAATCTGCTTGCAGTCCAGCATGGCCCCAAGCTTTTTTGTTGCACATTCCTGAAGACTGTGGGTGTTTCAACACTGTAACCATGCAAACTTCTGACTGCAGCTTTAGAATGTTTACTGATACCATCTCTAACCAGTGAGCTTTACACTTTGTTTTCAAAATGCATGTAAATAATTATTAAAATATGGTTGTTTTTTTTTAATAG
Seq C2 exon
GGAATCAATGGAAAAGATGGACTGCCAGGTCCTCCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000016155:ENSGALT00000026059:44
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(28.6=100)
A:
NA
C2:
PF0139113=Collagen=FE(15.7=100),PF0139113=Collagen=PU(9.3=66.7)
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]