GgaINT0047297 @ galGal3
Intron Retention
Gene
ENSGALG00000012538 | E1C6K9_CHICK
Description
NA
Coordinates
chr7:37666464-37668026:-
Coord C1 exon
chr7:37667163-37668026
Coord A exon
chr7:37666594-37667162
Coord C2 exon
chr7:37666464-37666593
Length
569 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGC
5' ss Score
9.6
3' ss Seq
CGTCCCGTCCCGCCCCGCAGCGC
3' ss Score
10.63
Exon sequences
Seq C1 exon
ATGCCCTGTGTTCAGGCTCAGTATGGGTCCTCGCCTCAAGGAGCCAGCCCGGCCTCCCAGAGCTACAGTTACCACTCTTCAGGAGAATACAGCTCCGATTTCTTAACTCCGGAGTTTGTCAAGTTTAGCATGGACCTCACCAACACTGAAATCACTGCCACCACTTCTCTCCCCAGTTTCAGTACCTTTATGGACAACTACAACAGCAGCTACGACGTGAAGCCTCCTTGCTTGTACCAAATGCCCCTGTCCGGACAGCAGTCCTCCATTAAGGTGGAAGACATTCAGATGCACGGCTACCAGCAACACGGCCACCTGCCCCCCCAGCCCGACGACGTGATGGCCCATTCGGGCTCCGTCTACTACAAGCCCTCGTCGCCCCCGACCCCTTCCACGCCCGGCTTCCAGGTGCAGCACGGCCCCGTGTGGGACGACGCCGGCTCCCTGCACAACTTCCACCCCAACTACGTGGCCACCACGCACATGATCGAGCAGCGCAAAGCGCCCGTCTCCCGCCTCTCGCTCTTTTCCTTCAAGCAGTCCCCCCCCGGCACTCCCGTCTCCAGCTGCCAGATGCGCTTCGACGGGCCCCTCCACGTGCCCATGAACGCGGAGCCGGCAGGCCCCCACCACGGCGTGGACGGGCAGCCCTTCGCCGTGCCGAGCCCCATCCGCAAGCAGCCGGCCATGGCCTTCCCCGGGCTGCCGCTGGGCCACGCGCCGCAGCTGCTGGACAGCCAGGTGCCGTCGCCGCCCTCGCGGGGGTCCCCGTCCAACGAGGGGCTCTGCGCCGTCTGCGGGGACAACGCTGCCTGCCAGCACTACGGCGTGCGCACCTGCGAGGGCTGCAAGGGCTTCTTCAAG
Seq A exon
GTGAGCGGGGCTGAGCCGGGGGGGGGGGGGGGGAGGAGGGGGCGGTCGGGGCAGAGCGGAGCGGAATTCCCCGCGGCGGAGCGAAAGGATCTCTTTATTTCGGCGTCCTGATTGAATAATCGGATCGTTTGGAATGGAGAAGGTCTCCAAGGGATGTGAATAGTATGAGTGCCCACGGATGTGTATTTGCTGAGCGCCTCCGTCCCTTCTCTCGGCATATAAAGCGCTGTGGGGTTAGCTCAGATGTTAACGCTGTCAATATTCTGCTGTTAAATGCCCTGGGAAAAAAAGAAAGGGAGAAGGGGAGGGGAGGGGGGGAGGAAAAAAACGGGGGAGGAAAAAAAAAGAGAAAAAAATAGAAAAGGGAAAAAGAAAAAAAAAAAAGGAGGAAAAAGAAAAAAAATGGGGAAAAAAGAAAAAAAAAAAAAGGAGAAAGAAAAGGGAAAGAAATGGGAGAAGGAAAGGGAAGGGGAGAAACGCGGCGGCGGGGAGCGGGGATGGCGGCTCCTGCGGACCCCCCGCTGACACCGCGATCTCCCCGTCCCGTCCCGTCCCGTCCCGCCCCGCAG
Seq C2 exon
CGCACGGTGCAGAAGAACGCCAAATACGTGTGCCTGGCCAACAAGAACTGCCCGGTGGACAAACGCCGCCGGAACCGCTGCCAGTACTGCCGCTTCCAGAAGTGCCTGGCCGTCGGCATGGTGAAGGAGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000012538:ENSGALT00000020478:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.476 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0010513=zf-C4=PU(38.6=9.4)
A:
NA
C2:
PF0010513=zf-C4=PD(58.6=93.2)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTCTCCAGCTGCCAGATGC
R:
TTGGCCAGGCACACGTATTTG
Band lengths:
347-916
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]