GgaINT1014984 @ galGal4
Intron Retention
Gene
ENSGALG00000013454 | HOXB1
Description
homeobox protein Hox-B1 [Source:RefSeq peptide;Acc:NP_001074328]
Coordinates
chr27:3662963-3664600:+
Coord C1 exon
chr27:3662963-3663569
Coord A exon
chr27:3663570-3664274
Coord C2 exon
chr27:3664275-3664600
Length
705 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGT
5' ss Score
10.67
3' ss Seq
TTGTTTTTTGCTCCTTACAGCCA
3' ss Score
9.6
Exon sequences
Seq C1 exon
ATGGACAATACTAGGATGAACTCCTTCTTAGAGTATGCAATTTGTAACCGTGGGACGGGCGCCTACCACCATTTAGAGCAAAGCTCCCCTTCCTTCCCCTCTTGCTCAGGTAGCCCCTCCAGTGACACTTTTCATGGAGAAGGGCGCTACGGTGCGGGGGGCAGCGCGGTCGCGGCCGCCCATCTCCCCCCGCAGAGCCCCGGCTTCTTCCCCGCCGCCTCCGGGCGCTCCGTGCCCTTCGCGGCCGCTGCCCCGAGCGCCGGGTACCCAACCCAAAATTGCAGCCCCGGCTACGGGCACCACCAGCTCTACCTCGGCCAGCAGGACGCGGACGGCGTGTACTTCCAGGCGGCCGGGTACTCCTCCAGCACCGGACCCCACCTCGGCTCCCTGGCAGAGGGCTATTGTGGGGCCGTAGGGCAGTACCAGCAGCAGCAGCACCTTTACGGGCAGGAGCAGCCCGGTTACTTGCCCGGGGTTTACGGCAACCTCTCGCCTTCCCTAAATGAGGACAAAGACCCCGCGTGCCCCTCCGAGCCGTGCCCCAATGCCAGCGCGGCGCGGACCTTCGATTGGATGAAAGTGAAGAGGAACCCCCCCAAGACAG
Seq A exon
GTGAGTTTGGGGCGCTCAGGGCTCGGCGGGGGGGGGGGGGTTCCCATCCGGGCTGAGGAGAAGGGCGGGCGGGGGGTGGTCGTTCTGCAGCCCTGCTATGAAATGTTGCCTTCCCAGTTGTTTCTGCTCGAGGTCATTGGGCTCCTTTGCCTGAGGAAGACGCATTTTTATTCTTATTTTTAAGCTCTATAGAAAAACCAGCTAGCGATTTTTCGGGCACACCTGGCAGAGGTCCCTGAGCTCGCTTGCCTTCAGGCCCAATGCAGTTTTAAGCCCAGCTCGGAATAGGAAACACTCCCAGTTTCCTGCTTCCTCCACAAAGGTGGCTTCCACCTCTCTCATTGTTCAACATCCTTCTCTAAAACCTTCCTGAAATCCGGAACTTCCCTCCTCCCCCACCATCTCCCCCCCCCCCCCCCTCCCTTCCACTCCTTCCCACGCACGTTCAAGTTTCATGGCACTTCGCAGGGAGCTGGGAGGACCGTTTGCAAGAGAAAGGAGCAGCTCTGCAGATCCCGGGGCAGCATTTCCCTCCGGGTTACGTCCCTGGAAAGTCAGGGGTGGCTCAGGAGAAGCTGCGAGAGGTGGGGGCCCAACACGCAGCAGAGGGTAGGCACGGGGGATGCCCATTCAATCAGACAGCCCCGGGACCCCCAGGCCCAGCTAAAGCACTGCTTCTGCCCTGTTGTTTTTTGCTCCTTACAG
Seq C2 exon
CCAAAGTGTCGGAATACGGGCTGCTGGGACAGCCCAACACCATTCGCACCAACTTCACCACCAAGCAGCTGACGGAGCTGGAGAAGGAGTTTCACTTTAACAAGTACCTCACCCGGGCCCGGAGGGTGGAGATCGCCGCTACACTGGAGCTCAACGAAACCCAAGTCAAGATCTGGTTCCAGAACAGGCGGATGAAACAGAAGAAGAGGGAAAAGGAAGGTCTCGCCCCTCCTGCTGCCTCCAGGTCCGCGAAGGAAGCGAGTGAAGCCTCGGATCAGTCCAACTGCACCTCACCTGAGGCCTCCCCCAGCTCCGTGTCCTCCTGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000013454:ENSGALT00000021933:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.291 A=NA C2=0.574
Domain overlap (PFAM):
C1:
PF134581=Peripla_BP_6=WD(100=44.8)
A:
NA
C2:
PF0004624=Homeobox=WD(100=52.3)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Rat
(rn6)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGTTACTTGCCCGGGGTTTAC
R:
TGTTTCATCCGCCTGTTCTGG
Band lengths:
344-1049
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]