GgaINT0010855 @ galGal4
Intron Retention
Gene
ENSGALG00000005628 | COL9A3
Description
collagen alpha-3(IX) chain precursor [Source:RefSeq peptide;Acc:NP_990636]
Coordinates
chr20:8712938-8715152:+
Coord C1 exon
chr20:8712938-8713009
Coord A exon
chr20:8713010-8715116
Coord C2 exon
chr20:8715117-8715152
Length
2107 bp
Sequences
Splice sites
5' ss Seq
AGGGTAAGG
5' ss Score
9.16
3' ss Seq
CTCCTTTTGCTTATTCTCAGGGT
3' ss Score
9.02
Exon sequences
Seq C1 exon
GGTCCCAAAGGTGCCAGTGGGGAACCTGGCCTTCCTGGTCCGACTGGAATTCGTGGAGAGTCTGGTGACAGG
Seq A exon
GTAAGGAGAAGATGATGTTTGTAACACCATCCTGTTTGGGAGATGTGAAATTAGAGCTGATGTCATCACAGCAAGCGGATGCAGTCTCAGTAGCAGGCTGGCACATGGGGTGTCCCCCCTTGTCCTGCTGCTGCTGCATGCCCAAGCTGGGCCCCAAGCAGGCAGCAGGATTCGTGCATCTGCTCCTATTCCTGCCCATGTCCCTTGCAGTGCAGGAGCTCCTGCTAGTTCCAGGCAGGATGGGATCCTATGTAAGCCAGAATAGACAACTCTCGTTTCCTGCTTTGCATGCCACACATGCACAGGAGAGCTGATTCGCGCTGTCATTCAGATGCCTTGATTAGCGTTTCAGGATTTTATTTTTAATTACAGTTTGTTCTGTGATTTCTTTCTGAACAGCCCCACAGGGCCCCACACCTCCGAACAAATCCAACTGTTTTTTTTTTTTTTATGTAAATGAATTCCTTCTCATTTAAAAGAAGGCAGCAGGGCAAAGTGAATGGCATTTGCTCAGGGCCTGCAGGAGAGCAGCAGCCGTGTGTTGGGCGGCTGCCCTGACTCCAGCTTTAAGGTGAACTTTCTGTGTCAGCGGTGGATTTCACAAAGGCCCCTCTGTGTGGGTTTAAAGAAGGCCCTCAGTGCAGCCTGAGGTGTGAGACAGGAGCGGCATTGTGGCCCTGCCCGTGTTCAGGGCTGTGCTGCCATGAGAAATGTGTGCTCCAGAGGGGGAAAGAGGCCGTGCGCGGAGCAGCGTTATCTGGGGAGCTGCTCTGGGGGAAAAAAATCGTGCTTAAAGCAAAAAGCAGAGCAAAAAAAGGGTTTATTTCTGGCTCTGAAGTTAAGCGTGGTTGCTCTGAGATGTAATTGTTGATTGTTTCGTAACCCCTGCTGCTCATTAGCAGGAGAACGTGCCATGTCAGGCCGGGGTACCCCCAGGAGCTTCCCACCTCCCTGTGCACAGCTGACACGTGCAGTGACTTCCCACAGTGCCACTGCTGTTGGTGACAGCCCCACGTGTGCCCACTGTGCGAGAGAACATGCAGCGTTAGTGCAGCTTACCTTCACTGTGCCTGCAGTCTGAGGCACCCATAGGCAAGTATTCCTTCACAGGATTCATGCCACAGATTCCTGGGGATCCTGTATGCAGCATCTCCCAGCAGTCCTTCCCTGAGAAATGTTGGCTGTGCTCAATGGATAGAGGCACCCACGTGAGCACAGCACCGGGTGTAGAACTGGCAGTCCTCAGGGCCACGGGGGTCACTTCTTCCTGCTGCTGGGAGTGGTGGCTGCAGGAAATCCCACCGTTTTGAATCCGAATCTTTTCCACCTGAGCTTTTTTTCCGAGGGAGTGTTCCTTACAGGGGTGTGTTTCATTGCTGTGAACTTCCGTGGAGCCTCAGGACCCCAAAAAGTTGGAGGTGTAGATCCAGGCGGTGATGTCCAGGAAAGAATATATTGCCTTTGCCACTGGCAAACATAAAACAGGAGTCATAGCTATAGTAATTTCTGCATTTCCACGTGCTAGTGCCTGTTTTGCCAAGAATTATTTCTTTCCTTAGTAGAAATCCTCCCCCTTCTTTTTTAAATGTATTCAGTGCTTGATTTGAGCACAATGGCGTGGCCTTATTCTGCGTCTGTCCGCCTCTCAGGTTCCTCCTGCTGAGCCATCTGCAGCTCTGGTTATTAAGGAACGGTCAGATTGCAGGTGCCAGCTTGATGAATGTGCTGTAGAAACCTCACATGAAGGGCAAAATGGTTCATCACTGCGATGTATTTTATCCCTGTGTCATTCTGTGAGCCTCCATGTGAGGAGCACCTGACTGAACCTCCGAGAGAACTGATGCTCTAAAGCCTTGAAATGCCTCCTGTTGCTCTTAGGGTATAAAATGCATGGGCTGAGGCCTGAGCTGCTGGCTGCAGAGTGCGCTGCAAGAGCAGCACGGATGCTTTAACTCTCTTGTTATGTCTGAGAAATGTGAATGAGCGTTGATCCCTCCTACCTGGCAGTTAGGGTGACTCACTGCTGTGTGAGTGCGTGTGTGATGCACCAGGAGTTCACAAGGGAAGAACAATTTGAGCTCATTGGCCTCCTTTTGCTTATTCTCAG
Seq C2 exon
GGTCCTGCTGGTGTTATTGGTGCCAAAGGTAGCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000005628:ENSGALT00000009029:24
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:
NO
A:
NA
C2:
NO
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:
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]