GgaINT0039176 @ galGal3
Intron Retention
Gene
ENSGALG00000011413 | E1BVV4_CHICK
Description
NA
Coordinates
chr8:27492534-27494430:-
Coord C1 exon
chr8:27494230-27494430
Coord A exon
chr8:27492697-27494229
Coord C2 exon
chr8:27492534-27492696
Length
1533 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAGA
5' ss Score
10.57
3' ss Seq
AGTGATGGGCTCTCTTTCAGCTT
3' ss Score
5.96
Exon sequences
Seq C1 exon
ATGGATTTTCGCTTTTGGCCCATTTCCCAATTGGGAAAGCTGAACGTTTCGATGCTCTTGGTGGTTCTTGTCATGTTTCTTTTGATTATTGACTTTGTGAGAAAGAGACGTCCCAGGAATTTCCCTCCTGGGCCACAGCTATTTCCTCTTGTGGGAACCATTGTGGATTTAAGGCAACCTCTCCATCTGGAGATGCAGAAG
Seq A exon
GTAAGACCTTCATGGACATTTCTCCTACTAATAATATTGTATCTTTTCAGTGATTTTTGTCACCTATCAAAGGCAAAACAAAGGTAACTTCTGGTTTACAAGCTGTATAATAACAATGTAGACGACTGTTGGGTTTATCCCTTGCTGCCACCCCCTCTTCCACAGGAGTTGGACAGTTTGATCAGAAGGAAATTTGTACCAGAGTACAAAGGAGGAAATTTGCACCAGAGTATAAAGAACATGTCTGCATGTTCCTCCTTTTTCTTCTCATTTTATCATTTTGTGCTTCAGCTCAGGAATGGTTTGGAGGGTGGGAAACAAATTGTTTGAGCAAAGAACATCACCTCTGAAAATTGTGTTGTCACTGTCTTTGCCCAGAGACCTGCAATTTGCACCAATACATCTGAAAGAAAGACTAAGGTCCAGAGTTCCAGAGTTAAACACCTCAGTGGCTGCTTCTTTGTCACAGAAAGAGGCAGTGATAGCTTTAGAAAGATTTCCAGAGCCAACAATAGAGTGATAGTTCATACACGTGGAGTACCTTCTTTGAGAAAGTGGGAAATAAGGTTCTGATGTGCTGGTTGCAAGTATCCTTCTGGTGTTTGACTTTTAGTCTCTTGCTTTGATTTAAAAGAGGACCCCATCTCATCTACCCCAGCCATTAGCAGGACTATCCCCCAGGGAACAGAGGCAGTACACTCAGGCCATTTTACCAACATATATAATTATTACTAATAAAATTAATCACATTCATTTACATGCAAGCACTGTCAAAGCTGCCCATTTGATCCCAGGCTCATTTCACTATCCACCATGTCAGTTCAGGGTGACCATGCATGACCTCTCCTGCAGAGTCACACTAAGAAGCGTGTGCACTGAATTCCTTGGCAAATGAGGACCCAAGAGAGGATATAATTGTCCTCTGCCCTTATACATCAGGGAGCTAAATGTTGAAGAGGAGAGGCTAATGCTCGCAATGTCCATGCAAGGAAAATGGCTATAAATTGGCTATAAATGCATTCAGGCTTAAAATTAGAGGAAGTTTTCTGAGCATCAGCAGTTGGAGCCACTTTCTAACTGTGACAGCTGGAGCAAGAAATCTCACTACTTACAAAGTTGGTGAAATAGTGTATGTGTTGTGCCTTGCTTTCAGCAGCAAGAGCCTGGTCTCAGTGACCCAGGTGGATCCTTTTCCTTCTGCACTCTTCCTGTGAAGAAGAGGGAAGGAGCAGGTGCCCATCAGTCATAAAGTCCCTGGATTCAAGTTAAATTGACACAACAGCCTGGTGAAAGCCAATATGCAAACCATGCCTGCCACACCACGGCTTACTAATATTGCTTGTGCCATCTCCAGCCTTTGTGAAATAGTTTAGGTTGAGTGGGACCTGTGGAAGACTTGGGTTTGGATTTTTCTTAAGCCCAACCCAGTGCTCCAAGTGGAAATAAACTCAAAGTTAGATCCCAGGTCTTGTCTATGTTCATTTAGAAACTCTCCATCTTCTTGCTCTCAGAGAGTGATGGGCTCTCTTTCAG
Seq C2 exon
CTTACTGCGAGGTATGGAAACATCTTCAGCGTGCAGTTTGGAGGTCTGACTTTTGTGGTGGTCAGTGGGTACCAGATGGTGAGAGAAGCCCTTGTCCACCAGGCTGAAATATTTGCAGATCGACCACATATTCCACTTCTCCAAGAAATTTTTAGAGGCTTTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000011413:ENSGALT00000018621:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0006717=p450=PU(5.4=37.3)
A:
NA
C2:
PF0006717=p450=FE(11.7=100)
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:
TGGATTTTCGCTTTTGGCCCA
R:
TGGAGAAGTGGAATATGTGGTCG
Band lengths:
343-1876
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]