GgaINT1014996 @ galGal4
Intron Retention
Gene
ENSGALG00000026249 | HOXC6
Description
homeobox C6 [Source:HGNC Symbol;Acc:HGNC:5128]
Coordinates
AADN03022165.1:21-2230:-
Coord C1 exon
AADN03022165.1:1562-2230
Coord A exon
AADN03022165.1:347-1561
Coord C2 exon
AADN03022165.1:21-346
Length
1215 bp
Sequences
Splice sites
5' ss Seq
GTGGTAAGT
5' ss Score
10.36
3' ss Seq
TTTTGTCTCGGCTCCCCCAGGCG
3' ss Score
8.93
Exon sequences
Seq C1 exon
AAAAAGGCCCCGGGGCCGCCGGGGGGGGTCTTTTGGGGGTTCAGGACTTACTTTCAATGCACACTTAGTTTCAACTAGGGAATCAACAGAAGCAAAAGCAATTTTCCCTTTTTGACACCCGCCTCCCCATTGGCTCCCCCCGGGTCAGCTGACTTTGTCATTTTGTCTGTCCTGGAGCAGAGCCTTCCCTATAACAATCTAGTTCAGACTACAAACTGGAGACAGAAATAAATATTAAAGAAATCACACAGCCAGGTATAGAGGACGATATGAATTCCTATTTCACAAACCCATCTTTATCCTGCCATCTAACCAGTGGCCAAGAGGTGCTTCCCAACGTAGCCCTCAATTCAACTGCCTATGACCCTGTCAGGCATTTTTCTACTTATGGAGCAGCCGTTGCTCAAAACCGGATTTATTCTTCTCCTTTTTATTCACCGCAAGATAATGTTGTGTTTAGCTCCAGCCGAGGACCTTATGACTATGGATCTAATGCTTTTTACCAAGAAAAAGACATGCTTTCTAGCTGCAGGCAAAATTCTATGGGACATAATACACAGACATCAATCGCACAGGATTTTACCAGTGACCAAAACAGGAACACTTCGCAAGAACAAAAAACTAGCATTCAAATATACCCATGGATGCAGCGTATGAACTCCCACAGTG
Seq A exon
GTAAGTTTTACAGCTCGGAGATATAAATTAAATAAACTGAACCATCTTTACGACCTTCTCCCTAGCAGAACAGGCTGAGCGACTTTTTATGGCCCCATAAAAACAATAATATAGCTCCTTCACAGTTGCAGCTACAGGCCTTTTATTTGTTAAGTTGTTGCAAGCAAATATGGCTTGTTATGCTGTTTCTAATTAAAAGACTTCGAGAGTGTAAAATATCTATAATAAAGTGCAGCGAGCTCTGCTCGGGAGTTAAGCACAAAATATTACTGGGGGGAAATAAGTTTTAATGACGGGGGCTGAAAGTGTGGCTGTGCTGCAAGCAGGACGAGGGGCACATCGCCCTCCCCTCTCCCCTCAAATTGGGTGGGAAAGGGAGGAAAACGGTGGGGGGGTGGGGGAGAAGAGAGGGATAGGGAGAGAAAAAGAGGGGAAGGGGAGAAAGGGGGGATGAGAGGGAAAAGGGAGGGGGGGAAAGAGAGGGGGAATGGAGAAATAAAGAGGTGAAGGAGAAAGGGATATAAGAGGGGATGGAAAAGGAGAAAAATAAGGGGAGAAAGAGGGGAAAAATGGAAAAATTGAGGCAGAAGAGAAAAGAGAGAGAAATAGAGAGAAAAAAAGAAAAATAGAGAGAAAAAAGAGGAAAATAGAGAGGAGAATGGAGAGATAACAGGGAAAGATAAGGAGCAAACAGAAAAATAAAGAGATAAAAGAGAAAATAAAGAGAAAGAAGGAGAAAGGAGGGAAAGAAAGAGGGAGGGAGAGAAAGAGAGAGATAAAAGAGGAAAATGGGAAATAATGGAGAAAACGAAGAGGAAAAATAGGGAAAATAAAGCGGAAATGGGGGAAATAAATGGGGAAATAGGGACAAATAGGGAAATTAAAGGGGGAAATAGAGAAATTAAAGGGGAAAATACAGAAATTAAAGGGGAAAATAGAGAAATTGAGGGGGAAAAATAGAGAAATTGAAGGGGAAAAATGGAGAAAATAAAGAAAGAAAAATAGAGAAAATAAAGAGGAAAAAAATAGAGGGGGAAATGGGAAAATAATAGGAAAAAGCGTGGAGAAATAAATAAAAATCAAGGCTGAAAATGAGCCTGCGGGGGGAGGGTGGCTGAGGGGGGGATCCGTCCACGGGAGCCGGGGGGTGCGGGGGGGTCGGGCGCTGCCCCCCGCGCTCACGATTTTTAGTGTGTTTTGTCTCGGCTCCCCCAG
Seq C2 exon
GCGTGGGCTACGGGGCCGACCGCCGGCGGGGCCGCCAGATTTATTCCCGTTACCAAACGTTGGAGCTGGAGAAGGAATTTCACTTCAACCGCTACCTGACGAGGCGGAGGCGGATCGAAATCGCCAACGCTCTCTGCCTGACGGAACGGCAGATCAAGATTTGGTTCCAGAACCGAAGGATGAAATGGAAAAAAGAAAGCAACTTAAGCTCGACCCTCTCCGGGGCGGGTGGTGGAACCGCGGCCGCCGCCGCCGATAGTTTGGCCAAGGAGGAGAAGCGAGAAGAGACAGAGGAGGAGAAGCAGAAGGAGTGAAAAGTGGCAGCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000026249:ENSGALT00000043584:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.239 A=NA C2=0.423
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0004624=Homeobox=WD(100=54.3),PF0042814=Ribosomal_60s=WD(100=54.3)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Human
(hg38)
No conservation detected
Human
(hg19)
No conservation detected
Mouse
(mm10)
No conservation detected
Mouse
(mm9)
No conservation detected
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:
CTCCAGCCGAGGACCTTATGA
R:
AGAGCGTTGGCGATTTCGATC
Band lengths:
342-1557
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]