GgaINT1014986 @ galGal4
Intron Retention
Gene
ENSGALG00000013455 | HOXB3
Description
homeobox protein Hox-B3 [Source:RefSeq peptide;Acc:NP_990074]
Coordinates
chr27:3643412-3645019:+
Coord C1 exon
chr27:3643412-3643635
Coord A exon
chr27:3643636-3644465
Coord C2 exon
chr27:3644466-3645019
Length
830 bp
Sequences
Splice sites
5' ss Seq
GGGGTATGT
5' ss Score
7.48
3' ss Seq
GTTTTCTCCTAACCTTTCAGGTC
3' ss Score
11.79
Exon sequences
Seq C1 exon
GAGGCTTCGCAGTGGGTTTTTAGACTTTTGGAGCTTGGACTGAGGGAGGCAGGAATGCTAAAATACCAAAGGGTTACAAAGTTAGGAGCAAATGGTCCGGAGACGTGTTTGTTTTCTGAGGGGGAAAAAAAAAACAACAGCAATCAAAGTGGTTTCGGAATTACATCTCGGCAGTGGTAGTTCCAGATTCAATACCGACGGGCGTGAAGCAGTGCAGTGAAGGG
Seq A exon
GTATGTTTTCTAAATACAACCTGTGCTGCCAGAGAAGGGGGGGGAGGGGGGAGGCTGACAAACAGGCCAAAGGAAGCACATTCTTGAATTCGTGCCCTTACTTCAATCTGCTTGAAATATTTGCTCTGAATTCCATAGACATTGTGAGTCTCTGAGTAAACAGCAAATCGAGCCAACTGTGTCAGGACAGGGCTACCTGGATAGGGCATATCAAGGCTTTGCTGTTTTCTGATTAAAAACAGAGCAGAGAATGGCCTTACCCTAAACTTAGTGCACTTCTCTGACTCAGTAACATCCTGCTGGTTTTTATGTCTGATTTGGATAGGAGATGGGAAGGCCAGAGTCTCATTCCTCTCGTGCTTGTAGTTAGCAATTATCAATTCTGTAGGCTTATATTTACATTAGTGTGTGTGTTAGCTGGACATGGATCTGCATATATACCCATACACCCATAACTGTGGGTGTATGTGTGAATGCATGTGTGTATATACTTATACACAGAGAAAAATATGGATGTAAATAGATGTATTTAGATGTAGCCACGTGTACTTGTAGAGAATGCATGTAGTTCTACAACCTTGCTGCTCTGCTTTAAGGGAAAGAAAGGGGCAAACAAACAACAGCCAGGAAAACTTCCCCCCAGAATCAGCTCAGCACTTTTGCACTGCAACATTTGATGAGCCTTCTGAGGCTGCACACAGGACAAAATCTGCTCAAAGCATCTGTTCACCCTGTTCTGCGGGACCCTATTCATGTCATGTGCCTTTCAGGCCCCAAGATGGATTCATAGGCCGGGTACTATTATTGTGTGTTTTCTCCTAACCTTTCAG
Seq C2 exon
GTCAGCTTCCAATAGACAGCTGGAAACGGCCTGTCACGTGGCCTTGGGGTGCCAATGTTCTGCCATAGGGGTGTCAAGACCCTGGTAGCTGGAAAAATCATTTTGGGGAATCCTGGAGATGCAGAAGACAACGTACTACGAAAGCTCCACGCTCTTTGGGGGCTATTCCTATGGGAGCACCAATGGGTTTGGCTACGAGGGTCCCCAGCAGCCCTTCCAACCGGGTTCCCACGTGGAGAACGACTTCCAGAGGTCCGCCTGCTCCCTCCAGTCTCTCGGCAACACAACTCAGCACGCAAAAAGTAAAGACCTGAATGGGAGCTGTATGAGGCCGAGTTTGCCCCAGGAGCACCATCCGCCTCCGACTGTCTCACCACCCCCAAACCCCACCACCAACAGCACCAGTAGCAACAGCAATAACCAGTCAGGGAGCAGCAAAAGTGCCCCGAGTAAAGCCAACCTCAGTGCAAACGCCAGTCTCACCAAGCAGATTTTCCCCTGGATGAAAGAATCGAGGCAAAACTCGAAACAGAAAAGCAGCTCCCCTAGCACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000013455:ENSGALT00000043870:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
5' UTR
No structure available
Features
Disorder rate (Iupred):
C1=NA A=NA C2=0.903
Domain overlap (PFAM):
C1:
NA
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Main Skipping Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Mouse
(mm10)
No conservation detected
Rat
(rn6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TTTGGAGCTTGGACTGAGGGA
R:
GCGTGGAGCTTTCGTAGTACG
Band lengths:
350-1180
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]