GgaINT0123851 @ galGal3
Intron Retention
Gene
ENSGALG00000004701 | F2Z4L4_CHICK
Description
NA
Coordinates
chr17:5834726-5836331:+
Coord C1 exon
chr17:5834726-5834814
Coord A exon
chr17:5834815-5836273
Coord C2 exon
chr17:5836274-5836331
Length
1459 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGG
5' ss Score
10.07
3' ss Seq
CATTTTCATTTATTTTTCAGAAA
3' ss Score
9.48
Exon sequences
Seq C1 exon
GCTCCGCACCACCACCATGTCGGCGCCGGCGGCCAAAGTCAGTAAGAAGGAGCTCAACTCCAACCACGATGGGGCCGACGAGACCTCAG
Seq A exon
GTGAGGCCGCGCCGGGGGCGGGAAGGGAATGGCGGCCTCCGGCTCGCACCGCGCCGCACCGACAACCATTTTCCCCAAGCACACGGGCCGCGGCCGGGCCCTAAAAGGGAAGAGCGCGGGGCCGGCCGGGCGGATGTGCAGGCCCCNNNNNNNNNNCATTCTGAGAATAGATGGGGGCTTCTACTGAGATTTAAATCTCACATTGTGTAGGTTGTGTAATAGTCAAAACAGCATCTGTTTCAACACGAAAATAGGAATGCGCCGCGTTCGGACAACACTCCCCAAATAACGGTTGAAACGTCATGTGTGCGGGTAGCGGTAAGAATTACGTTTTGGTGCCGCTGTATCATAGAGAGCCCGCACATGTCCGATTTGAAGCAGAAATCCTTTCCGACCCGCAATTCAAGTTTGGCGTAATGCATACGCATATATCGATGAAATTCGGTTTGTTTTTCCGGCCAGGTCCACCTCCCTCTCCGGCATTCGAGGAACATCGGGGAAATCATCGCCAGCCTCAGCGCGGTTGCAAAATCATCCTCATCCTTAAGGCATGGTCCGGTTCCCGGTGAGCCAATCCGCCTCGCGGGGATGGAACGAATCACCACGGATCTACGCGGTGCTCGGCCGAGCGAACCGCCCGCGCCTCCCCACGTGCGATCGCGGCGGCGGCGGCTCCGCGCTTTTGAAAGGTCGCCGCCGCGCCGCGGGTTTCCTCCCGTTTGCCGCCGCCGGGGGAAGGGCGCAGCGCTCTCCTTCCTCCGAGCCCGCCGCACGCTGCGGTCACACACGTGCTCCCCGCGGCGCGACCGGGCCCTTTCGGGGAGAGCCGAGCCGTGCGGGGAGCACTGAGCGCGCCGCGCCGACCCCTTCCCGCTGCCGCTCATTCATCCCTGGGCGCGATGGGTAAACAGGCGGCCTTTAACAGAGAGCTTCGCCGGCCGTGTCCGAGGGGACGTAGCGATGGGAAAATACCCGACGAAGCGTGACCTCGGAGTTCTGTCCTTGTAACTGACCCATCCGGTGTGCTTTTCGGTTTTTAGAAGGCAGCGCGTTCCGTGTTGGGCTATTTCCATCGATATTTCTGTCTTTCCGAATTACTTAACGCACGTTCCTTGAGATCTGTTGGTCTTAGGCTTGCAACTTCTTAGCGAAACTGTTAGTAATCTCTCCTGATTCACTTACTGCCTATGTTGATTTGTAAAACCACATAGAGGAACTGGAGCTGTGATTTTTGGAGGTAAACTTGTAAGGAGTCCCATTTCTGTGAACTTTCTGGCACTTCGGCCGTACTTGACCATAAAGTAGGTGAAACTCGAAGGCCTGGTAGTGCTTAAGGCACCAAATAGAAATGCCTGTGTTTCTGCATTAGGTCACTGGAAGAGGCCTTAGGAGAAAACGGGAAGTGATTCCTCAGGTTCAAGGATTGAGGGATTTTGATGCATTTTCATTTATTTTTCAG
Seq C2 exon
AAAAAGAGCAACAGGAAGCAATTGAACACATTGATGAAGTACAGAATGAAATAGACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000004701:ENSGALT00000007488:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=0.950
Domain overlap (PFAM):
C1:
PF073527=Phage_Mu_Gam=PU(1.5=4.0),PF060057=DUF904=PU(2.4=8.0)
A:
NA
C2:
PF073527=Phage_Mu_Gam=FE(28.4=100),PF060057=DUF904=FE(23.2=100),PF0095613=NAP=PU(7.7=75.0),PF116293=Mst1_SARAH=PU(29.7=55.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Cow
(bosTau6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]