GgaINT0105268 @ galGal4
Intron Retention
Gene
ENSGALG00000016843 | COL4A2
Description
collagen, type IV, alpha 2 precursor [Source:RefSeq peptide;Acc:NP_001155862]
Coordinates
chr1:138382070-138382909:+
Coord C1 exon
chr1:138382070-138382216
Coord A exon
chr1:138382217-138382792
Coord C2 exon
chr1:138382793-138382909
Length
576 bp
Sequences
Splice sites
5' ss Seq
CAGGTAGGA
5' ss Score
9.79
3' ss Seq
ATCACTGTTGTTGGTGCAAGGTC
3' ss Score
4.71
Exon sequences
Seq C1 exon
GCTTTCAGGGCCCTCCAGGCTCTCCTGGGTTGCCACCAATTCCTCCAAGGCTGGTTGCTGAGCAAGGTTCACCAGGTCCCCGTGGAAATGCAGGGCCTCGGGGAAGTCCGGGTGATGCAGGACCTCAAGGTCCACCAGGAGAACCAG
Seq A exon
GTAGGAACTGCACACTTAGAGCAACAGCTCAGTTGCCGTGAGCAGTGAGGCCACCAGTGCACTGCTTTGGCTCTCTTCAACTCAAAGTCATATGAGTCAGAAAGGAGAGTCAAACTTGGGCTTTTCAAAGCTAGAGGCCTGGCTTTCCTCTGCCTCCTAAGATTCAGACCTTAAGCAAAACAGGAGAGAATTGTTGACGACACTTGCACAACCAAAGCAACATCAGATATGGATACAGGCACTTAAATCAAGAACAAAAGTCACTGAAAAACTCATCTTTGTGGGTGTGCTTTTGGTGAAGGAAATGTAGTGACACACAGACCAGATGCAGCGCACCTCTTGCTGCTGGTCTTGTTACAGACGTGTGGTGGTAGCAAGAGTGAAAGATTAAGGTGGTGGGTGTCATGTAGTCTTGATCCTAGCAGTCTTTTCCAATGCTGTTTCCAGTGCTCTTTGAGCAGTAAGATCTTGCTCTCAGTGTAAATTGGTAAACCTGGCAGGCAGGACTGAACACATGCAAACAGAGTACACGTTAATGGAGTAAGTCATTGTGCTCATCACTGTTGTTGGTGCAAG
Seq C2 exon
GTCTCAGAGGCTTACCTGGAGAACCAGGACTCCAGGGCAGAGGTGGCATTCCAGCTCCTCCTGGATCCAGAGGTGAACAAGGAGCAATGGGGTTTCAAGGTCCAGTGGGATTTGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000016843:ENSGALT00000027208:43
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(19.7=24.0),PF0139113=Collagen=PU(57.4=62.0)
A:
NA
C2:
PF0139113=Collagen=PD(40.7=55.0),PF0139113=Collagen=PU(61.7=92.5)
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:
GCTTTCAGGGCCCTCCAGG
R:
TCAAATCCCACTGGACCTTGA
Band lengths:
262-838
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]