GgaINT0145311 @ galGal3
Intron Retention
Gene
ENSGALG00000000406 | F1NRZ0_CHICK
Description
NA
Coordinates
chr28:519738-521201:+
Coord C1 exon
chr28:519738-519907
Coord A exon
chr28:519908-521083
Coord C2 exon
chr28:521084-521201
Length
1176 bp
Sequences
Splice sites
5' ss Seq
AAGGTGGGT
5' ss Score
8.23
3' ss Seq
AACTCTCTTTCCTCTCACAGAAC
3' ss Score
10.51
Exon sequences
Seq C1 exon
AGGATGGGACTGTCGGAGGAGCTCTGGCACCACCAGTACTGGCTGCCACCTGGAGCCACCTGGGAAGACATGAAGGAGTCTGCGGACACACACTACCCAAAGCCTCAGGACCTCTGGCTGTGCCTCCCCGGTGCTCTGCTCCTGATCGTTGTCCGATGCATCTTTGAAAG
Seq A exon
GTGGGTGGCACAAATCCAGCTTCTTCTGTGCTTGTTGTCAGCAGTGTCTGTGCAGGGTTGCTCCGCACTTACCCTTACCCATCTCCTATCCACAGAAAAGCTGGAAAGGGTTTGCTCCCAGAAATACCGAATCTCTCTGTGTTTCGTGGCAATAAGTATTTGTCTGGCAGCAATGTGCCATCTCTCTTTCCTGTACCTGTATCCTCACCTGGACCAGGTGTGAAAACACAAATCCGCCACTCAGCTGCACCTCAGCCGTAGGTGGAGAGTCTCTCTGGAGAGAGGGGGCTTGGGCTCAGCAGAGAGACCAGCTGGGAGCGTGCAACACAAAATAAGGCATTTGCTGGGTACATCAGGGCTGGGAGCCCCTGCTGAGCCGGGGGTCAGCCTGGTCTTAGGGGATACTCCCAAAGATGCCATGCGAGTCCCCACTCTCGGCATAGAGGAAGAAGAAGAGAACAGCCGTGGCTCCTGCAGCCTGCTGTAGGACCGTCCTGTTCACACCACTCCTTCCCCCCTCCCCAGCTCAGCCCTGCTCTGTCCTGGCACCAGAGGTCCCCAGTTCATGCAGGGTTGAGGTGCTGCGGTGCCTCAGCGATGGGCGTTCCACTTTGGCTGACGGAAATGGTATTCCCAAGCAGTGCATGTGAGCTGACAGCCATCTCCTCTGGGTCTTTGGGTGGGAATGATGCAGATCCACGTGGCTGAGCGCAGGGTATGGATTCAGAGTGGGCTTTGGGCGCCTGTTCCAAAACGAGAGACTGACACATGAGGGGATATCAAGGAATTATCAGTGAGAGTGGGGCAGATTGTTGGGCAGACATGCAGTTGTCCGGCCAGGCAGAGCAGGGCTTCAATATCTGTGGAGTGGGAAGGCTGTGCTCAGCAAACCTGCCCTCAGCTGGAACGTGAGCCTTCCCTGATGGTCCTTCAATCCAGCCTATCCAGATCCCTCTGCAGAGCCGCCCTGCCCTCAGGCAGATCAACACTCCCACCTAACTTGATGTCACCCACATACCTCCCGAGGGTGCACTCAATTTCCTCATCAAGATAGCTGAGAAAAAATATCAGAAGAAAGTGGCCTCAATACGAATGATATTTCTTATTGTTGCCGCCGCCTGCGATGGGAGAGGGCACCCACATCCTCTCCGCTCTGAACTCTCTTTCCTCTCACAG
Seq C2 exon
AACCATAGCTCTGCCCCTGGGCAGGAGGCTGGGAGTGAGAGACAAGCGGAGGCCCAAAGCTCAGCCCAGTGCCACACTGGAAGGCTTCTACAAGCTGCTGGGCAGGACTCCAAAGGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000000406:ENSGALT00000000553:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.070 A=NA C2=0.025
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0004624=Homeobox=PU(46.4=65.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGATGGGACTGTCGGAGGAG
R:
CTCCTTTGGAGTCCTGCCCAG
Band lengths:
287-1463
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]