GgaINT0087749 @ galGal4
Intron Retention
Gene
ENSGALG00000016155 | COL19A1
Description
collagen, type XIX, alpha 1 [Source:HGNC Symbol;Acc:HGNC:2196]
Coordinates
chr3:82449240-82451104:-
Coord C1 exon
chr3:82451024-82451104
Coord A exon
chr3:82449366-82451023
Coord C2 exon
chr3:82449240-82449365
Length
1658 bp
Sequences
Splice sites
5' ss Seq
CTGGTAAGT
5' ss Score
10.65
3' ss Seq
AAATCTTGTTTTTATTTTAGTGC
3' ss Score
7.21
Exon sequences
Seq C1 exon
ATTGAACTTTACCGCATAACAGTTTATTGTAATCCAAAAGTTGCAACAGAAGATACGTGTTGTGAAATATCTGCGGACCTG
Seq A exon
GTAAGTTATTTGTTAAACTAAAAATGGTATTAGAAAATGTTTCATTTTCTCTTACTACAGAGTTATAAAGAAATTTCAGTGGAAGCGTCAGTGTTCAACCTCTGAAAATGAGTCCTGTATCTGGAGTTGTGGTGCAGTGGTGCATTTTTTCTTGTCACCGAAACAAATGGCTTAGTGGAACTTCAGTAAAAGGCACTAGGTGCTGCTAGTGCTTTTTAAATGCCTATCTTAACATTGATTAGTGTTTAATTAGTAATTGAGGAAGTGTCAGAGAGCAGGAAACAAATTCACCGCCATCACCTTCACGTAATATAGGCTAATTTAATAACTATTATCTGCTCTAGAATTATAACTGGTAAGCAAAGAAAGCCCATGAAAGACTTTGTGTGACAGTGGAAGAGAAGAAAAGTAGGATGGTGTTAAAGGCATATCCCTTATTTTAGTATAATAACATGGGAAAATGGATGTTTTGTGATTGGCAAAACTTCATTATAGTGCATAATGGAAGATGTTCTTTAGTCTGTAGAAATGTTAGAAGTTATATATGTGACTGTTTTGCTAAATTAAGCCTGTTTGGAAGGGGGGAAGGAAGAAAAGCAAATCCCTCGGGGGGGGGGAACAACAAAACACCAAACAGGCTAAAATATTGGTTTATTAGTTATGAACAGTCTCCCAGAAAAGGCTTCTCTGAGACCATGAGTACTGCGATCATCACTCATTGAGAATACTTTGTGGGAACTGACAACTGATTGGTGATCAGAAGCCTAAGAGACTGAATCTAAATTATCAAAGGAAATCTCAATTTTAAATAATAACTTCTTGTTCAAATATACTTCAAAATATATTCCTGATCATAACACAGGCTTTCTTTTGAATTTATAAGCTCATGGCTAATTGAAATGAATGATTTTTTTTTCTGTAAGTTTCACTTTGTACATGGAAAAAAATATCTGCTGTTATGACACAGAAACAGACAAGAAAAATAAACCCTAACTATACACAAACACAAAAAGATCAGGGATATGCTTTACTGATAGCATCCTAAATGTTCTTTGAGCTATGAAGACAAAAGCACTTTGTTTCAATTGCATGTCTTATATTGAAGGTATAAAAAAAATGGAGTACTTGTTAATGACTTTCATATTGAATTCGGCATCACATTTTTTTTTAATTTTTTCATTACCTCCCTTACCAATCATATCCGTAATCATATACCAATCATATCATAGAGCTACATTTTCAGTAATTTAGGGAAAGGGATTATTCCTTAATCACAGATTTCTACACTGAGAAGTAAGTCATGTCAGAATTTCTTTGACAAGAAGGCTCACAGGAGACTATTGTATCTTAATGAGAGCCTCTGAATATTATTTTTCCCGTCATCTTTTGCTTTCACTTTTTATAGCTCCTGGAGGCTTTCTTCCTATGTCTGGCTCTTTAGGAAGAAAGAACTGGGACAGTCAGTTCTGTTTTAACCAGTACTGTTTTCAGTACAGAAGGATCATAATGTCTAGACTTCATTTTGCTACATCTTTTTCCTCTGTTTGGCAGCAGTGGCTTTTCTGTAAAACAGAAAGTAAGTTAAAATAGCATTTGGCTGGTATTTATCTATTAACAAAAGTGGATCAAAAATGAGACAAATCTTGTTTTTATTTTAG
Seq C2 exon
TGCCCACATGAGGACAGATTACTTGCTACTACTTCATCACCAGTGTCTGCTCATGCCAGCAAAATATACACTCTTCCAGGAACACAGCAAGAATCTACGGACAGATGCCACTGCTTTCCAACTAAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000016155:ENSGALT00000026059:7
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.476
Domain overlap (PFAM):
C1:
PF133851=Laminin_G_3=PD(6.5=37.0)
A:
NA
C2:
PF0139113=Collagen=PU(1.7=2.4)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TTGAACTTTACCGCATAACAGTTT
R:
TTTAGTTGGAAAGCAGTGGCA
Band lengths:
206-1864
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]