GgaINT1014989 @ galGal4
Intron Retention
Gene
ENSGALG00000027903 | HOXB5
Description
Homeobox protein Hox-B5 [Source:UniProtKB/Swiss-Prot;Acc:P14838]
Coordinates
chr27:3604171-3606516:+
Coord C1 exon
chr27:3604171-3604777
Coord A exon
chr27:3604778-3605752
Coord C2 exon
chr27:3605753-3606516
Length
975 bp
Sequences
Splice sites
5' ss Seq
ATGGTACAG
5' ss Score
3.5
3' ss Seq
TTGTTGTCCGTGTTATTCAGACA
3' ss Score
6.42
Exon sequences
Seq C1 exon
CGTCAAGCACAGGGTTATAACGACCACGAGCCACAAATCAAGCCCTCCAAAATAACCCAAATGAGCTCTTACTTTGTAAACTCGTTCTCAGGGCGCTACCCAAATGGCCCCGACTATCAGTTACTAAATTATGGGACCAGCAGTTCCATGAACGGTTCTTACAGAGATTCAAGCACCATGCATTCCAGCTCTTATGGCTACAACTACAATGGGATGGACCTTAGCATCAACCGCTCAGCCTCCTCTAGTCACTTTGGGGCTGTGGGGGAGAGCTCCCGCGGTTTCCCTTCTCCAGCTCAGGAGAGCAGGTTTAGACAGGCGTCTAGCTGCTCCTTATCTTCTCCCGACTCCCTTCCCTGCTCCAACAGCGAGAGCCATGGAGGCAAGCCCGCCCCGTCCCCCTCCGACCAAGCTACTTCTGCCAGCACCAACACAAATTTCACAGAACTAGACGAGACCAGCGCGTCCTCGGGAGCCGACGAGGGCACTCCAATAAGCAGCAGCATCCCCCGAGCGCAGGCAGAGCCCATCGCAACCTCCACGGCAGCAACAGAAGGGCAGGCACCTCAGATATTCCCTTGGATGAGGAAACTTCACATTAGCCATG
Seq A exon
GTACAGCTACTTCTTTTTCGGTCGTTGTCGTTGTTGTTGTTTATTTTCGCACACCCCTCTTTTTTTTTTTTTATCCCCCCCTTTCCCTTCCCACACCCGCCCCCCCCCCCCCCTTTTTTTTTTCTCTCCTTCCCTTTATTCGGTGCTCTTTGATCAGAATCGCAGCTATTTATGGCTTTTTGCATTTCTTGCTCTGATCACTGCTTTAAAGCTGCCTCTGGCGCCTGGAGGGGGGAGAATTTATTTTAGTTTCGCTATTCCGTCCGCGAAATGTGCGCTTATTTCAGGCTAGTAGCGATATGTCCATGGTGGGAGAAGGTAATTTAAAAATTGAGGGAAGGGGGTGTTCCTTTGGGGTGGGGGGTGGGGGGGCAGAAGAAAGGAAAGAATTGACCATTAAAATGGCATTATATGCACAGATGGATCCCTCCGTCCTTTCCTTCTCTTCTTCTGCTGGGGGTACGTTTGACATTCTGCTCTTGATAAAACCCAAATTGTAAAGAGATACAGAAAACAGTGAGTCGTCCTCCCCCCCCCGCACCCCCCACCCCCAAACTCGCTTTTTTTTTTCCTCCTGGAGGAAAGAAAGCAGCATTAAAGCAGATGACCCAGCAAGCAGGCGCACACACACACACAAAAACAACAGGCGGGGGTGAAAAAGGGCGATTTCAGGATCTCGGTTCTTCGGTTAAATTATGAATATTGAGTCCTCGGGTGTCGGTTCTGGAGGGGCCAAAGGTGGGGGGATTTCCACGTGTCGGGGGGTGTGCGGGAAAGAGAGGGAGACCGGGGGGAGAGGCGGGGAGGCTGCTATTTTGGGAATAAGCAGCGTTCCTAATTGCCCGAGGAAGGTGAATCTTTTACCTCGGTGTTAAATATACGTAGGTGTATATATATATAGCCGTAATGATAAAAAACCCTGGCAGAAAGAGTTGAAGAGAAATTCAAAATCCCGTTGTTGTCCGTGTTATTCAG
Seq C2 exon
ACATGACTGGACCAGACGGGAAGAGGGCGAGGACAGCGTACACTCGCTACCAGACCCTGGAGTTGGAAAAGGAATTCCACTTCAATAGATATCTCACCCGCAGGAGGAGAATAGAGATCGCTCACGCTCTGTGCCTCTCCGAGAGGCAGATCAAAATCTGGTTCCAGAACAGGAGGATGAAATGGAAGAAGGATAATAAACTGAAAAGCATGAGCTTAGCTTCTGCGGGCAGCGCCTTTCAGCCATAAATTATAGAGGAAGGAATATCGAGGAAAGAAGAGGAAACATTAAATAAATCCGTAAATAAATAAAGCGCAGCAGATCTTAGTTTTGGAGTACTGTACAGTGAGGCACCTTCTTTTCGGCATGTTGTTGCTATTCGAAACCGACGCGTATGGTACCTTTATCCCAGGACTGAGTTCATGTCGTGGTTTCTTCTTTTTTGGGTTGATTTATTAATTTTTTTTCCTATTATTTTTTTTTAATTATTATTAAATTTTATTTCCAGATGCTCCCCATGCTCTCGTTGTTCTTATAAATGTACGTGTCCGTGCTATCTTGATGCTTTCTGGAAAGCCAGCATGTTTTATGTGAGCCCTATAAATGTTATAACTTATTTATGAGATGGTAACAGATAACGATTGTTTGTTTATTTGTTGCTTTTTCCCCTTCCTGAGTTTACTGCTTTGGGGGTGAGTTCTTCTCTGCCTGAGCTAAAATCGGGGGTTCCTGCACTACAGTCGCAGTAAAAAATAATAATAAGC
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000027903:ENSGALT00000045325:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.727 A=NA C2=0.183
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0004624=Homeobox=WD(100=68.7)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GACGAGGGCACTCCAATAAGC
R:
CGCAGAAGCTAAGCTCATGCT
Band lengths:
357-1332
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]