GgaINT0099739 @ galGal3
Intron Retention
Gene
ENSGALG00000023195 | F1NCZ0_CHICK
Description
NA
Coordinates
chr2:24407053-24408212:+
Coord C1 exon
chr2:24407053-24407522
Coord A exon
chr2:24407523-24408018
Coord C2 exon
chr2:24408019-24408212
Length
496 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGC
5' ss Score
9.6
3' ss Seq
TGCGGCGTTTCGCTTTGCAGATC
3' ss Score
11.69
Exon sequences
Seq C1 exon
GCCTTAAAAAAATAAACCCGCCGCCTCCAGCGGTGCCGCGGCGGTGGCCGGGCAGGGCGGCCGGGCGCGGGGGGCGAGCCGGAGAGCCTCGCTCTCTGCCTCCCCGCCGTCGATGATGACCATGACCACGATGGCTGACGGGTTGGACGCGCAGGACTCCTCCAAATCCGCCTTCATGGAGTTCGGGCAGCAGCAGCCGCCGCCGCAGCCGCCGCCGCCGCCCCACTCGCAGCAGAGCTCGCCGGCCATGGCCGGAGCGCACTACCCGCTGCACTGCCTGCACTCCGCCGCCGGCTCGCACCCGCACCACCAGCACCACCACCACAGCTCGCCCTACTCCGGCACCGGCGGCTCCTACAACCACCGCTCGCTCGCCGCCTACCCCTACGTGAGCCACTCGCAGCACAGCCCCTACCTGCAGTCCTACCACACCAGCGGCGCGCCCAGCCAGACGCGGCCGGACGACGCAG
Seq A exon
GTGAGCGGGGCCCGGCGCTCCGGCCTCCCCCCTCGCCTCTCCCCTCCGCCGTACCAAACCCCCCCCCCCTCTCCCCACCCCCCCGAGGCCGGCAGCCCCCGGGCCGCGGGTCGCATCGCGCTGCGGGGCCGTCTCGTCGATGTCCGCGTAACGCCGTTTTTCGCAGGGATCCGATGTTTACGTTCTGCGTGCGGAGGGGCGAAGGGGGGGGAAAGCATTGTTGCGGGTCTCGGGCTGCCGCCTCCTGAGCGCCGGGCGATGAGCCGCGTGCTGCCGAAGGGCCCCGGCTCCCAAACCTTCCGCTTTCGTTTTGGTTTTTTTGTTTTGTTTTGTTTGTTTTCCTAATGATTTGGATCGGTAATTATTTTCCCCCGGGGGGGCCGCGCGGCGTTACGCGGCTGCCGCGGCCCGGGGGGACGGCCGAGTTGGGGGGTTGGGGGGGGGAGGGGGGGGAAATCTGCGGCCGAGCTCCCAGCTGCGGCGTTTCGCTTTGCAG
Seq C2 exon
ATCAGCAGAAAACGACGGTGATCGAAAACGGCGAGATCAGATTCAACGGGAAAGGGAAAAAGATCCGGAAGCCCCGAACCATTTACTCCAGCCTTCAGCTGCAGGCGTTAAACCACCGCTTCCAGCAGACTCAGTACCTGGCGCTCCCGGAGCGAGCCGAGCTGGCGGCCTCCCTCGGCCTGACCCAGACGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000023195:ENSGALT00000038006:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.892 A=NA C2=0.367
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0004624=Homeobox=PU(73.7=64.6)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AATCCGCCTTCATGGAGTTCG
R:
CCCGTTGAATCTGATCTCGCC
Band lengths:
356-852
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]