GgaINT0142825 @ galGal3
Intron Retention
Gene
ENSGALG00000017353 | F1P4P5_CHICK
Description
NA
Coordinates
chr27:3578954-3580469:+
Coord C1 exon
chr27:3578954-3579415
Coord A exon
chr27:3579416-3580227
Coord C2 exon
chr27:3580228-3580469
Length
812 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGG
5' ss Score
9.16
3' ss Seq
CCTTTGCAATTCCCCAGCAGCCG
3' ss Score
3.79
Exon sequences
Seq C1 exon
TTTTCCTCCTCCTCCGTACAAATATTATTATTTAAATTAAGATGAGCTCCTATTTTGTCAACTCACTCTTCTCCAAATACAAAACCGGGGACTCGTTGCGTCCCAATTACTATGACTGCGGGTTCGCTCAGGATCTTGGGGGCAGACCCACGGTGGTGTACGGACCCAGCACGGGGGGCACCTTCCAGCATCCGACCCAAATCCAGGAGTTCTACCACGGAGCATCCTCACTCTCCAGCTCCCCTTACCAACAGAATCCCTGCGCCGTGGCGTGCCATGGGGACCCGAGCAACTTCTATGGCTACGACCCTTTGCAAAGGCAGAGCCTCTTCAGCGCCCAGGAGTCGGACTTGGTGCAGTACACGGACTGCAAGCTTGCTGCCAGCGGCCTTGGAGAGGAGGCGGAGAGCTCGGAGCAGAGCCCTTCTCCGACCCAGCTTTTCCCCTGGATGCGACCGCAAG
Seq A exon
GTGAGGCGAGATGGGAAGGACAACGACGAGGCATTTCCTGAGCCCATAAAGTATCCCTCCTTCCTTTCTTTCTGCCCCTCTTTCTTTCTGCCCCCCTTTCTTTCTCTCTCTCATTTTCTTTCCTTTCTTTCTTTCTCCCTTTCTCCCTTTCTTTCTTTCGCTCCCCTTTTCTTCCCCAATGACTGTATTTTAGTGCTTTATGGGGGTAAACTTTTGCACTTGTAAATTGCTTTATAGTTTAATTACCCTGAAGGAGCCCTTTTCTTCTGGGGGCTGAACGAGCCGGGCTTTCAGTGGAAGGAAACGTCCTTAAAGTTTATGGCACTTTTATAGCCTTAAGAAAGCCCCTTCATTTTTTTGTTTCGCGTTTGATTCGGGATTTCGGCGGTGCTGTTCGCTCTCCCCGGGCTGCGGTTCTTTTTTGTGCCCTTGCATCCCCCGGAGCCGGAGCTGTTGTTGTTGTTGTTCGGGTAATAAGGAGTGCGCGAGTGGAGGAGGCTTTGCTGGGCTGCTCGGAGTGGGCTCGCGGTGACCCTCCCCCCCCTCCCACCACCATCACCCTGTTCCTTTCGAACCATCTCCCCCTTTATAATATCATAGAGCAGCCTTTCCTCTCGCTCTTTGCTTCCTGCCTCGCTTCTGCGAGTCCTTTCTCCCCCCCCCCCCCCCAACCTCCTCTATGTGTGTGTGTGTGTGTGTGAGTGTGTGTGTGTCTGTGTGTGTGTGTGTGCGCCCATTCCCGAGCCTGGTTTATGTATCTTTCAACCTCCTCTTCTTCCCCTTTCCACCCAACCTTTGCAATTCCCCAGCAG
Seq C2 exon
CCGCTGGACGGAGGAGGGGGAGGCAAACCTACAGCCGCTACCAGACGCTGGAACTGGAGAAGGAATTTCTATTTAATCCCTACCTGACCCGCAAACGGAGGATCGAGGTCTCGCATGCCCTGGGATTGACAGAAAGGCAGGTCAAAATCTGGTTCCAGAACAGGAGGATGAAATGGAAAAAGGAAAACAACAAAGACAAGTTTCCCAGCAGCAAATGCGAGCAGGAAGAACTGGAAAAACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000017353:ENSGALT00000028037:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.271 A=NA C2=0.346
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0004624=Homeobox=WD(100=70.4)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Cow
(bosTau6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TTACCAACAGAATCCCTGCGC
R:
CCTTTCTGTCAATCCCAGGGC
Band lengths:
355-1167
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]