GgaINT0017983 @ galGal4
Intron Retention
Gene
ENSGALG00000002886 | NKX2-5
Description
homeobox protein Nkx-2.5 [Source:RefSeq peptide;Acc:NP_990495]
Coordinates
chr13:8535721-8537935:-
Coord C1 exon
chr13:8537581-8537935
Coord A exon
chr13:8536894-8537580
Coord C2 exon
chr13:8535721-8536893
Length
687 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAAA
5' ss Score
8.38
3' ss Seq
GTCCGTGCGTTTTGCTGCAGAAC
3' ss Score
8.42
Exon sequences
Seq C1 exon
GCAGCGCTCCGGGCCGCCCGCTCCTCGCCTCCCCTTCCATGACCCCGGGCTGCGGCCGCTGCCCCGCTCTCCTCCGCAATGTTTCCTAGCCCTGTGACGACGACTCCCTTCTCGGTCAAGGATATTTTGAACCTGGAGCAGCAGCAGCAGGGCGGTCTGGCCCCCATGGAGCTCTCTTCGCCCTCCTGCATGTTGGCCACCTTCAAGCAGGAGGCGTTCGGCTCCGAGCCGTCCGCCCTGCCCGAGCTCCCCGAGCCGCCCCCGGCCAAGCCGCCCGCCGCCTTCCCCGGCCCCTACTACGTGAAGAGCTACGGGGAGATGGACACGGCCAAGGATTCCAAGGCGGACAAGAAAG
Seq A exon
GTAAAACCTCAGCCCGGGGCTGTGGCACTGCGCTCGGCCCTCTGCAGCCCGGCCCAGGGGCCCGAGGCGAGCGGGAGCTCAGGAGGAGCGCCCTAAGGCTTTTCGAGGTGCCACGATGGGGAGAGATCCCTCGGCTCCTCCCGGGAGCGGGGCTGGGGCTGCGGCACAGGGCAGGGGAGGTGCGGGGGTACGCGAGGCCTCAGCTGTGGCCGGAGAGCGATGAGGCGGCGAATCTTTTACTAACGAGCACAGCGAGCACACCTCTGTGGGGTGGGATTCAATACAAAGGGATGTAAATATGTGATAAATCCAAATACGAGACTAGTCCAAATATGAGACAAACCCAAGCATGAGATAAGCCCAATTTGCGGCAGAACCAAAAGGGATGCGCTGAGCCTTATTTACAACAAACAAAAGCAAACAAACCCTAAAAATAATAATAATAAAAAAACCTAAGCAAACAACAATAATAAAAATAATAATGATAACAATAAGAATAATGACTGCAAATTGCTCACGAGGTGCTCGGAAGCCCCGGGCGGAGCTGCTGCCCCGCAGACCCCACACGGACGGCAGCGAGCGGTGCCGCGGGGTTCCCTCGCGGTGCACACGGGTCAGTAAATCCGCTTTGCTCTTGTTAATGTTTTGCTCTCCCCGTTTTTCCTTTGTCCGTGCGTTTTGCTGCAG
Seq C2 exon
AACTGTGTGCCCTGCACAAGAGTCTGGAGCAGGAGAAGAGAGAGCTGGAGGATCCCGAGCGGCCCAGACAGAGGAAGAGGAGGAAACCCCGCGTCCTCTTTTCTCAAGCCCAAGTCTACGAACTGGAGAGAAGGTTCAAGCAGCAGAAATACCTCTCAGCTCCCGAGAGAGACCATCTAGCGAACGTCCTAAAGCTCACCTCTACCCAGGTGAAAATTTGGTTCCAGAACAGAAGGTACAAATGCAAAAGGCAGAGACAGGACCAGACCCTGGAGATGGTGGGGATCCCACCCCCCCGGCGGATAGCGGTGCCGGTGCTGGTGCGGGACGGGAAGCCCTGCCTGGGGGAGTCTTCTCCCTACAGCTCGCCCTACAATGTCAGCATTAACCCCTATAGCTACAACGCCTACCCCGCGTACCCTAACTACAACAGCCCTGCCTGCAACGCCAACTACAACTGCAGCTACCCGGCCGTGCAGCCCGTGCAGCCCTCGGCGGCAGGCAACAACTTCATGAACTTCAGCGTGGGGGACTTGAATTCGGTGCAGCCGCCCATCCCGCAGGGGAACGCGGGCATCTCCACGTTGCACGGGATCCGAGCGTGGTAGGGCGGCCCGGGCCCGGAGCTGCGCGAGGGGTCGGGACATCGCCGGGCTGCGGGGCGAGGGCGGCTCGGTGCGGGACCGCGGGGAGCTCCCCGGGGCTCTGGGGCACGGTGTTCGACCCGCTCATTCCCCTCTCCCCACCTTCCTACAAAACAGTCGGTCATTTCGCTTGACTTGTTCCTAAACAACGGCAAGCCAAGCCCTACAACTCATTATTATTATTATTTCTTCTTTTTCTTTCTTTCTTTTTTTTTTTTAAACTCTTATCCTAATTATTATTGAGAACCACATTTAATTTTGCACTTCCCGTCCGGTTCCTCCCCCCCCTTTCCCTCCCGGTCGCCGCTCCCCGCGGTCGCTGTCCCCCAGCGCAGGACGGGGACGGCCCCACCGAGCTCCGGGAGCTCCGATCCGCCCCCCCCCCGCTCCCCGTAGGGTTATGCACTAAAACGTGAGTTAGGATTCAGATGCACTGCCCGCTCCTCGCCCCGCCACCCGTTCGGACGTGTTTCCCTTTGCTGTACGAGCTGACGGAGATCAGCGAGTTGTCATTAAAGAGAGTGGCTTC
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000002886:ENSGALT00000004551:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.667 A=NA C2=0.223
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0004624=Homeobox=WD(100=28.1)
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:
GTTTCCTAGCCCTGTGACGAC
R:
CCTCCTCTTCCTCTGTCTGGG
Band lengths:
358-1045
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]