GgaINT0068407 @ galGal3
Intron Retention
Gene
ENSGALG00000013571 | F1NUN5_CHICK
Description
NA
Coordinates
chr4:63215033-63217172:+
Coord C1 exon
chr4:63215033-63215114
Coord A exon
chr4:63215115-63217009
Coord C2 exon
chr4:63217010-63217172
Length
1895 bp
Sequences
Splice sites
5' ss Seq
GCGGTAAGT
5' ss Score
11.37
3' ss Seq
GTTTTGTTATTTCATATCAGAAT
3' ss Score
6.12
Exon sequences
Seq C1 exon
GTTTGTTTTGTTTTGTTTTTTAGGATGATTTGGATTTATCAGACTTTTTATTTCATTTTCTTATTTGCTTCAGTTTACAGCG
Seq A exon
GTAAGTCAATATATAATTCCTAAGATTGGTATAGAGTAACACAAGTCTTCTAGGAAGGAGCGGTTAAAAAGAGTAATATTCAAAATGATCTGAATATGTATTTGTACATGGAGTGAAATGAGGTAGAGCTACAGAGCAGCATGATTTTGGAAGGGGAGCACATATTGGTATAAGCAACCTGGTCCCAAAAGAGTGGGGTTGCACTGTATTAAGTCTGGGTAACTCAAAGGGGAGTGGAAGTTTCTAATCTTTTGATTCTGACTATTAGGGATGGAAGTTTTTAGTAGGCTTTGCTGACAGTGATTAGTGTCAGTGCTGAAGTCTGCAGTGACTGTGTTTTTCAACGTCAGTATGCGTTAATGATTTACTTTGGCTAGCAGAAGTAAACTACAAAAACTCACATTGCATTTCCCTGAAATTCCCTGTGCCAGAAGATTATAACCAATGCCCAACAGAGTTTGTTTAGTAATATGTTAAGCATTTTCTCAGTGGACAATGAGATAATTAACTTTTTTTTTTTTTTTTTTTTTAGCAAAGTCTGTTTGACTACTGTAGTGTTATTTCAGAAATATTTTACCTGGATTGAAATTTAAGAAGACTAAGATCTTAGAAAATTTTTGAGGATCCAGATATTTTTAAAGTTCAAATTTCATATTAATAAAAGACTAACTTAAAAAAATATTAGCAGATTTAGCAAACATTGCCAGTAATTTGTTACTTTGTCAATTTTTTGTTGATAAATTTTACATTGTTGCAGTAGACACTGAATTTCTTAGTACAGATTATAAACGTATTTACCAAAAAAATCTTCTTGCAGTATTTTAAAATTGTAAAATCCAATATGTTCTTTGCATTTGTTTTAATCTTACATAGCTTTTGATACAATATGCTATCTTTATAGTGACAGATTAAGAAGTTAGATGAAATCTTTTCAGTTGGGTTTCTTTTCAGTCTGTAAAAATAGAAAATTTCCTCTTCATCTTTTAGCTCAGAAAGAGAACTTCTGTAGATCCAATAATAAAAATTAATGTATTTTCTACCAACTGACAGGGACAAATACAAGGAGTGTGTGCGCTCCTCTCTGAAGCCAGTCCTCTTGTGCTTTAACATCGAGATCTGAGTAATTCCATGATTTAGAAAGACAAGATGTGGTTGCCAGTTAGATATCTTCGTGTCATTGACAAAGCCATGCAGTGTGAACAGATTTACTTACAGAGAATTCAGTATGGGATTGACAAGATATTCCTGCAGATCCAAGGTGGTAATCCAGCATATTTTGGTTCTGGTTGATTCCTGAGAGTGCTCTTGTAGCACTATATTCTTATTTATTTATTTGTTTGTCCTGTAGCAAGTTGGACAGGGTTCAAGGCAAGTTGAAAGGAAGGAAGTTTATAAAAAGCTGAGAACCACTGAAATAGTTTCACACATGGCACTAGCTAGGAATCTGACCTCAAAAAACCCCCCAACAATTGGACTACCTTCTTGTATTTTCTAACTCCTTTTGCCATCTGTACATCCTTCTCCTGATTTTCCTCTTAATGGCTCCCTGTACCTGTCTCCCTTGGAAAATGCTTTTGCTGCTCCTTAGATCTGCTGTGAAGGATCATCACCTCAAGGCCTATCCTAATCCTAGGGCATCTGCCACCACTCAAGCTGCTTTCCTACAGCCTTGAGAATGGGGCGAGAGACACCAGAGGGTTTCTGTTTTACCAGGGTGGAGAGCAGGAATGATACTCTGGGAGGAGCTGTGCCACTCCCCCCGCTTGCTTTCTTTTCCTGCCATAGGGGTCTACTCCTGCAAAAAAATGGTAAATAAGGTGCAGTGTCTTCACCCTCTCATGAGCTGTCCATACCCACATCTCTGAAAATTTACTCGTTTTGTTATTTCATATCAG
Seq C2 exon
AATGTGTGACGCAGATCTATGAAAATACTTACTTTCAAGGAGGAGACCTCACTACGGTTTTCACACCAAGTGCCAATTACTGTCAAATAGTTTGTACTTACCATCCTACCTGCCTGTTCTTCACATATTTGCCAGTGACATGGACTAAAGATCCTGCACAGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000013571:ENSGALT00000037595:1
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:
NO
A:
NA
C2:
PF0002421=PAN_1=PU(63.1=96.4)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TTTTCTTATTTGCTTCAGTTTACAGC
R:
CTCTGTGCAGGATCTTTAGTCCA
Band lengths:
190-2085
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]