GgaINT0090134 @ galGal3
Intron Retention
Gene
ENSGALG00000015908 | COL12A1
Description
NA
Coordinates
chr3:83645632-83646641:+
Coord C1 exon
chr3:83645632-83645802
Coord A exon
chr3:83645803-83646169
Coord C2 exon
chr3:83646170-83646641
Length
367 bp
Sequences
Splice sites
5' ss Seq
CAGGTAGGT
5' ss Score
10.28
3' ss Seq
CCCCTTCCAATCTTCTTCAGAAC
3' ss Score
9.99
Exon sequences
Seq C1 exon
GTCCACAGGGAGAATCCAGAACAGGTCCACCAGGCTCCACAGGATCACGAGGACCACCCGGGCCTCCAGGTCGTCCTGGAAATGCGGGTATTCGAGGTCCTCCAGGGCCACCAGGATATTGTGATTCATCCCAGTGTGCTAGCATTCCTTACAATGGCCAAGGATTCCCAG
Seq A exon
GTAGGTTATGAACAACAAAATTGCTCTTTGTCAAAAATAGCCTTCACAAATGTGGCTGTTCATATTGAGTTGCTTTACATGAGACAGTCCTGCTGGCCTGGACATACTGAGTAGGGGAAAAAGCTGCAATGAGCAGGCCTGCCTCACTGTAACACGCAGGCGTATGAGCAGCCATGTGTATTTGGATGCAGGTTTAACTGATGTTATGTGTGATTCACTTTAAATAGGAAGTAGAAACAAAGTATTTCAGTTTTTTTTTTCATTAGCATAGAAGGTTAATAGTTGAAAATGTTGCACATAGGATTTAAGTGACCATTTTCTCTTCTTCTTTTTCCCCCCTCTCCCCACCCCTTCCAATCTTCTTCAG
Seq C2 exon
AACAAGGTTGAATTCTCCATGTTTCTCTTGAAAAATAAAAAGAATGCTGTGGCTGGCAATTTCCGTGTGTCTCTTTTTGAGCAATGTCAGGATTATTTATACCAAATTTCTACCTGAAATCAAAATTTCCCACAAAGGAAATCCATTTGGTGGTACAGTGCAACTGAAAAATACCACTGTCCTGCAATTTCTGCTGAGTTAAACACCATGGAGTCTCTGACTAACCCTGGGTCATACCAGCCTTCTACTCTGTGTTGAATCTTAAAACAGTAGGCTGCTTCTGGAACCAAATACAGGGTCACCAGTTCTGACTGAAAAGATTCCAGTATGTTTTAATGTGGGGATCCTGCAGGAACACACTATTGTTAACAAATTAATAAGTATGCATTGCAACATCTCAAAATTAGTGTATGTGATACTACTATTGAATATGGTTTGCTGTTAGTATATTGTGCATGTACTCATGGGAAAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000015908:ENSGALT00000037087:67
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=NA
Domain overlap (PFAM):
C1:
PF0139113=Collagen=PD(73.2=70.7)
A:
NA
C2:
NA
Main Inclusion Isoform:
NA
Main Skipping 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:
AGGGCCACCAGGATATTGTGA
R:
TGGTTCCAGAAGCAGCCTACT
Band lengths:
357-724
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]