GgaINT0074477 @ galGal4
Intron Retention
Gene
ENSGALG00000015599 | SOHO-1
Description
sensory organ homeobox protein SOHo [Source:RefSeq peptide;Acc:NP_990717]
Coordinates
chr4:80966340-80969431:-
Coord C1 exon
chr4:80968383-80969431
Coord A exon
chr4:80967929-80968382
Coord C2 exon
chr4:80966340-80967928
Length
454 bp
Sequences
Splice sites
5' ss Seq
CGGGTACAA
5' ss Score
2.62
3' ss Seq
GCTGTGTTTTGCCATTGCAGGCA
3' ss Score
8.58
Exon sequences
Seq C1 exon
CTCACCGGCAGAGAAGGGGTCCCTTCTGCTCGGAGCGCTCTGTGGAGATGCGCTGATTGCTCCCCTTGCTCCTCTGCTTACCCATTTCTGCGTTTCTTAGAATTACGGAGTATCCCGAGTTTAAAGAAAGCCACGAGGACCATTGAGTCCAACTCCTCGTGGGTCATCTCCCACTTCTCAAATGCCCGTTCTCATACCTCGCCTTCCTTTTCTCTACTTTTATCTCTATTCCCTGCACTCAGTGCCTGTTCTCTGCCTCCTCCCTCTTGATGACAGCCCTCTGTCACTCACTCTTTTGTCACACTTTTGTCCTCTGTGTAAAATTTCCCCTTCACCTCTTTATTCTTCCAGATTCCAAACCCTCTTCTTCCACATCCCGCCTTCCGCTCGCACTCTCTCACATCCAACCCCACCCACCTCATTTCTTTCTCCCTCACCTTCACGCCCACATTTTCACCCTCCTCCTCATCGCCTTTCCCTGGACTCCGTGGATCTACCTCTCCCTAAGTGAAGGTACTGAGCAGGGCACTCAGCCCTGCCTTGCCCTACTCCGCCCTGCCTAAGGAACCTTATTCTCAGCCAATAATAATAATCCCAAATCCTTCTCTCCCCGCTTCCTTCCTGCTCCCTCCTTTCAGCGATTCCTCACGGCCTTTCCTTTCTCTCTCCTCCTGCACCTCTCCCCAAGCCCTCAGCCCTTTGGCTCCGTCTAGCTCCATCCCCTCCCTCCTCCTCCCCGACCCCTCCTCCTTCTCCCCCCCCGTCCCCAGCCCTCCCTCCGCCCCGGCTGCCGCCTTCCCTCCGCCGCCACTCCTGCGGTTAGGCTCAGCGCGCCATGGTGCAGCTCGGGGGAGGCCGCGGAGCCCCACCGCCTCTCCTGGCCCCACCGTCGGCCTTCAGCATCGACAGCATCCTGCAGCCCGGTCCCCGCTGCCAGGCCCGGGAGCAGGGGAGGGCCCGCTGCGCGCTGCCGGAGGACGAGGAGGAGGAGGAGGAGGAAGAAGAGGGGCCTGCGGAGGAACACCCCACTAAAGGCTCCACCGACTCGG
Seq A exon
GTACAAAGCAGGCAGATCCGCACGTCCGGTCGCAGCCAGGCACCCACCCAGGACGGGGGTTTAGCCTCGGGCCTCCAAACGGCACCGCGCCCAGGAGGTTCGGGTGGGGCGGGCACACCCACACCCGCAGGCTTCATTCCCCACAGCAGTTCGAGGAAGCGAGGCTCCGTGGGAGGACATGAACCCCTCTCGAAACCACCTGCTTCTAGAGGCCACTCCCGGCCTCTTTGGTCGTTTTTCCCGTGTCCTGGAGCCCCTTCCCACTCCAATTCACGGCGGCAGAGAGATATCCTTTAGATGTATACTGCGAGCTCGTCTCCCTCCTCCCCACGGAGGCTGGAGGTGGGAGGTGGTGGGCAGTCCCCGGCCTCGGCCCCTCTCCACGGCCGTGGATGCGTGCATGCGGGGCGGCGGCGGCAGGGTGGGGGGCTGACGCTGTGTTTTGCCATTGCAG
Seq C2 exon
GCAGCGAGAGGCTGCTGGCGGAAGGGCCGCGCCGCGCGGATGCCGAGGCCGAAGGCGCGGTTTCACCGCTCTCCACGGAGAGGTTCCGCGGATGCCGACAGCCGTCGCTGCGGGATACCGGGGGCTGCGGTAGAGAGAGCGGCAGGTGTTCAGCGGCGGGAGGCAAGAAGAAGACGCGGACCATCTTCTCCAAGAGCCAGGTCTTCCAGCTGGAGTCCACCTTCGACGTGAAGCGCTACCTGAGCAGCGCCGAGCGGGCCGGTCTGGCCGCTGCGCTGCACCTCACCGAGACGCAGGTGAAGATCTGGTTCCAGAACCGCCGCAACAAGCTCAAGAGACAGCTGTCGGCTGAACCCGAGGGTCCGAGCCAAGCGGAACCCCCAGGGGAGCCCCCTCCGCCTCCCGCCGCCTCTTTCTCCTTCCCGGCCCTATACAAGGACAGCGCCCTGCTCAGCCGCTGCCTGCTGCCACTCCCCTTCCCTCTGTTCTACCCGGGCAGCGCCATCCCCTACCTCTGCCTTCCCGGTCCGGTCAAGCACTTCAGCCTGCTGGACGGGGACGTATAGCGTCTCACCTCGGCCCCCGCCCTGTCTCTTGCAGGGGGCCGATGGTCCCTGTGGCACAGCCGTACCACCATCAGCTTTCGCCCCGACACGCGGCAGCCGCTCCCAGGCCCGGGGTCCCCCACACGCTGCCGTGTGCCGTCGTGTCAGAGGAGCTTCAACGAGCGCTGCACTCTGCTCGAGACGGAGAAGAACGGAGCTGCCAAAGAAACCGGGATGCGCTGTGTCTCCTTTCCCTCCACAGCCTTTCCGTGGCCGCAGTTTAGGAAAGATGATATTCTGCCTCAGTCCACGGGAATGGTGCCATCGCGGCTGCCCCCGCACCGTACCGCCACCCGAGAGCGTTGGGTACAGCCCCATCCACTCCGTACGCTCCTCTATCTCACATTCTCCGCCTTTAGTACACCTTCAATTAACGCTTCCCCATCTCTGACACTATCAAAATGCAGACACCTCTCTAAATCTCTGTAGCTTCTCTGAATTTTGAATTTTCGAACCAAACAAGTCCTCTGTCACACTTTGTGCTAACCGGTTCCCAAATCAGGGCCCGTCTGATGTTTGGCGCACAAGTTACTCATGCTCCTTACGCTAACCCCGCCCCCGGTTGCTCAGGGGATTATTTTATCTGCTGCCCTACTGTAACGAAGTGCTTTCTTTTGTTTTTTGTTTTAATCCCCCTTAAATCTCCAACCACATTTGTCTTCTTTTGGTTTCCGAGTTCACACGCTTTATATTACAAATTGGGAAATAAAACTTTTCTATCAGAAACCCGAGCTGCATGCCTGTTCCGTACAGCCGCTCCAGGGCAGTGTCCAAAGAAAGACGTTTCCTAGAGTGCATCGACGGGTGTTTGTTTTAAAAATAAAGGTTGAACGTGCAATCGTGGTGTGGCGAAATTCAGAAGTGCGTGCTAAAATGGGAGACTTGTTGAGTTTTCCGGAGGGAAAAAAAAAATAATAAAATGAAAAAAAAAATAAAGAAAAGAAAAAGAGAACGAAAGAGGTATTTGGACTTGATAAGCATTGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000015599:ENSGALT00000025152:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=0.491
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0004624=Homeobox=WD(100=30.2)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Rat
(rn6)
No conservation detected
Cow
(bosTau6)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AGGAACACCCCACTAAAGGCT
R:
GGAACCAGATCTTCACCTGCG
Band lengths:
345-799
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]