GgaINT0099193 @ galGal3
Intron Retention
Gene
ENSGALG00000010905 | SP4
Description
NA
Coordinates
chr2:30435190-30437325:+
Coord C1 exon
chr2:30435190-30435297
Coord A exon
chr2:30435298-30435767
Coord C2 exon
chr2:30435768-30437325
Length
470 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAAG
5' ss Score
9.65
3' ss Seq
TTTTCTCTCTTTCTGGGTAGGAT
3' ss Score
10.86
Exon sequences
Seq C1 exon
TTTGCAGATCAAAAGAAGGAGGAAACTATGCCCACAGAGGGAGAGAAATCTCCCGAGGCAGAGAATAACAACAATAATAATAAAAAAGGGAAAACTGGAGGCTCACAG
Seq A exon
GTAAAGCACGCACTCCCAAATTGGGAAGTGCACAAACTATTAGCATTTAAAATTAAGTGTTCAGCTAACAGCATTCCCTGCTGAGGGCACCTTTCTTTGGATTGGGTGAAATCTAGTTGTTGGAGTGCAGTATTTTTACTGACTGGACGTGCTTTTTGACTGCGGTATACGGCGATCAGCTGCTTTCCACATAACAGAGGACCTCGTAAAAATTGCCCTTATTTTAGGAAAAAAGGCTGGATTGAGCAAGCGGTGGTGGTCCTGGTTGTCACATAATCATTGATAACCACTGGCTTGTATTTAAAGATTATTTACAGAAACGTATACTTCCCTATTCAGAGCTGTATCATTGGTCTCTATGCAGAAGTATGTTTTTGTCTGCTTCCTGTGTAAGTCTTGATGCTTACTTCTGATGGTTAATGCTTGTGCTCTTCTCCTGAATCTGTTCTGTTTTCTCTCTTTCTGGGTAG
Seq C2 exon
GATTCTCAGCCTTCACCTCTCGCTTTGCTAGCAGCCACTTGCAGCAAAATAGGAACTCCTGGTGAGAACCAAGCAACTGGACAGCAGCAGATTATTATAGATCCAAATCAAGGTTTGGTGCAGCTTCAAAATCAGCCACAACAGTTAGAATTAGTAACAACTCAGCTTGCTGGAAACTCTTGGCAGCTTGTTGCTGCATCTCCTTCTGCTTCAAAGGACAATAATGTTGCTCAACAGGGATCTTCCGTTGCCTCAAGCGCACCAAGTCCCTCTAGCAGTAACAATGGAAGTGCATCTCCTACAAAAACCAAATCGGGCAATTCTTCTGCAACAACCCCTGGACAATTTCAGGTCATTCAAGTACAAAATCCAAGTGGTAGTGTCCAATATCAAGTGATACCACAGATTCAGACAACAGAAGGTCAACAAATTCAAATTAATCCTGCAAATGCTACTGGTCTACAAGATATACAGGGTCAAATTCAGCTTATTCCTGCGGGAAATAATCAAGCTATCCTCACGGCTTCAAATAGGACAGCTTCGGGGAATATTATTGCTCAAAACCTAGCAAATCAGACGGTCCCAGTCCAAATCAGGCCTGGTGTCTCCATACCACTGCAGCTGCAAACCATTCCTGGTACTCAGGCACAGGTTGTGACAACTTTGCCTATAAACATTGGTGGAGTAACCCTAGCATTGCCTGTGATAAACAACATGGCAGCTGGAGGAGGTTCAGGTCAAGTTGGCCAGTCCACAGAGGGTGGAGTTTCCAATGGAAGTCAGTTGGCATCTACACCGGTCACTTCTGCCTCTGTTAGCTCAATGCCGGACTCTCCTTCTTCATCGTCCACTTCTACGACCACTGCTTCAACGTCTCTAACTAGCAGTGACACCTTAGTAAGCTCTGCAGAAACAGGCCAGTACACAAGCACAGCAGGCAGCAGTTCAGAGCAGCCAACGGAAGAATCTCAAACAACTGCAACAGATTCTGAAGCCCAAAGCTCCAGTCAGCTTCAATCAAACGGACTACAGAATGTTCAGGATCAGTCAGGTTCCCTTCAGCAGGTACAGATTGTAGGTCAACCTATTCTACAGCAGATACAGATCCAGCAGCCTCAGCAGCAAATTATACAGGCCATTCCTCCACAGTCATTTCAGCTCCAGTCAGGGCAAACTATACAGACCATTCAGCAGCAGTCTTTGCAGAATGTTCAGCTGCAGGCAGTAAGTCCAACTCAGGTGCTCATCCGGGCTCCAACTTTAACACCATCAGGGCAGATCAGTTGGCAGACTGTACAGGTTCAGAATCTGCAAAGCCTTTCAAATCTTCAAGTTCAGAATGCTGGGTTACCCCAGCAACTCACCATTACCCCTGTGTCTTCAAGTGGTGGCACAACCATTGCCCAGATTGCTCCAGTGGCTGTTGCTGGTACCCCAATCACCCTGAATGCTGCCCAGCTTGCTTCAGTACCTAATCTTCAAACAGTAAGTGTTGCCAACCTGGGTGCTGCAGGTGTTCAAGTTCAAGGAGTTCCAGTTACCATTACCAGTGTTGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000010905:ENSGALT00000017736:1
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=0.500
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGGAAAACTGGAGGCTCACAG
R:
TGTTGCAGAAGAATTGCCCGA
Band lengths:
354-824
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]