GgaINT1014987 @ galGal4
Intron Retention
Gene
ENSGALG00000013455 | HOXB3
Description
homeobox protein Hox-B3 [Source:RefSeq peptide;Acc:NP_990074]
Coordinates
chr27:3644466-3649970:+
Coord C1 exon
chr27:3644466-3645019
Coord A exon
chr27:3645020-3646068
Coord C2 exon
chr27:3646069-3649970
Length
1049 bp
Sequences
Splice sites
5' ss Seq
CAGGTACAC
5' ss Score
7.29
3' ss Seq
TTTCATTTCACGGCCAGCAGAAA
3' ss Score
1.77
Exon sequences
Seq C1 exon
GTCAGCTTCCAATAGACAGCTGGAAACGGCCTGTCACGTGGCCTTGGGGTGCCAATGTTCTGCCATAGGGGTGTCAAGACCCTGGTAGCTGGAAAAATCATTTTGGGGAATCCTGGAGATGCAGAAGACAACGTACTACGAAAGCTCCACGCTCTTTGGGGGCTATTCCTATGGGAGCACCAATGGGTTTGGCTACGAGGGTCCCCAGCAGCCCTTCCAACCGGGTTCCCACGTGGAGAACGACTTCCAGAGGTCCGCCTGCTCCCTCCAGTCTCTCGGCAACACAACTCAGCACGCAAAAAGTAAAGACCTGAATGGGAGCTGTATGAGGCCGAGTTTGCCCCAGGAGCACCATCCGCCTCCGACTGTCTCACCACCCCCAAACCCCACCACCAACAGCACCAGTAGCAACAGCAATAACCAGTCAGGGAGCAGCAAAAGTGCCCCGAGTAAAGCCAACCTCAGTGCAAACGCCAGTCTCACCAAGCAGATTTTCCCCTGGATGAAAGAATCGAGGCAAAACTCGAAACAGAAAAGCAGCTCCCCTAGCACAG
Seq A exon
GTACACCATTCTTCTTTTGTGACCATCCCTTCTCCTGAATTGCTGGGTAACAAAGCCATGGGGTCTTGTTTAGAGAAAGGATGGGGGGAAAGAATACAGCGAGGATGTAGATACTGGGCACGACCCACAGCTGCCAGCCGTGTGCACCCCATGGCCTTGGTCCATCCTGCAGTGCTGGCTGAGAACACTTGGCTTATCCTACAACAACCAGAGCACAGCAGGGAAGTACAGCCAGGCAGCTGAATAGGGCCACTGCCTGACTGTGCAGATACACATACCCCAAAATGTACAGCCACCAATTGCCCAGTGATGCTGAGGCTGAATGCTTGTTCTCTTCCTTCCCCCTGCCTCAGACACAGCAGTGAACACAGTGCTCTGAGTGTACGTGTGCATGCAGGGAGCATATGCATAAATAGGTGGATATTTTTGCATGCACGCACACATCTCTAATGCAATCAAGAAAAAAAGAAAAAGATCAGTGTGGAAACAGCACTGTTGTGACAAATGTATTTGTATAAACTCTGCAGCACACACTTCACTGTATTAATATCATACATCCGTTGTGCACATGCTTATAGTACAAAAATATCAGTACAAATGGGATTTGGTATTTAACAGCGTGCGTGCAGATAGTTCTGTTACGCAAATACGAGGCACAAACAAGACGTGCATGTGTGTGTATCCACACTTCTGCAAACAAAGTGCCTCCCAACACTGCCCCACGTTAATATTAATTGGCTTCGCAGTGACTGCCCCCCTGCCAAATATTATTTTCTCAAAATTATCTGTTGAAAATAATCGACTCCTAAATAAATGGCCCTGGAATCCTTTTCTACATGACATGATCAAATTTTCATAAACCAGGGGCAGCTTTGGAGAACAGAACTCTTAATAAATGACATGATTATGGAGTGCAGGCTAATGCAAAGGGGTGAGGAACGGGGGGAGGGGGGTCGAGCTCTCGTGCCTGTTCCAGGATTTATTAAGAAACGATGCATTCAATTTCTGCATGTAAGTAATTATCTTTTATTTCATTTCACGGCCAGCAG
Seq C2 exon
AAACCTGCAGCGGCGAGAAAAGCCCTCCAGGCTCCTCGGCCTCCAAGAGAGCCCGCACAGCTTACACCAGCGCGCAGCTGGTGGAGCTGGAGAAGGAATTCCACTTCAACCGCTACCTGTGCCGGCCCCGGCGCGTGGAGATGGCCAACCTGCTGAACCTCAGCGAGAGGCAGATCAAGATCTGGTTCCAGAACAGGAGGATGAAGTATAAGAAAGATCAGAAGTCAAAAGGGATGGGCTCTTCCTCTGGAGGGCCTTCCCCCACCGGCAGCCCCCCCCAACCCATGCAATCCTCCGCCGGGTTTATGAACGCCTTGCACACCATGAGCAGTAACTATGATGCCCCCTCCCCACCTTCCTTCAATAAGCCCCACCAAAATGCCTACGCCATGTCAACTAACTACCAAAACCCCATCAAAGGCTGCCCCTCCCAACAGAAGTACACCAACACGGCCCCCGAGTACGACCCCCATGTATTACAAGGGAACGGGGTGGCCTACGGGACTCCCAGCATGCAGGGAAGTCCCGTCTACGTTGGAGGTAACTATGTGGACTCCCTGCCCACCTCTGGCCCATCCCTTTACGGCCTCAATCACCTCCCACATCACCAGGCGGCCAACATGGACTACAGTGGGCCCCCGCAGATGCCTCCAAGCCAACACCACGGACCATGCGAGCCCCACCCCACCTACACAGACCTTTCCTCGCACCACGCATCTTCTCAGGGCAGAATCCAGGAGGCCCCCAAGCTGACCCACCTGTGATCGGGAGCAGGGATGGGCTCAAGTGAACTGGATGGCAACCAACACATGACTTGGATGGGGCACGGGGCAGGACGGCCTTCAGAAACATTTGTGTTGAGCTGTTTTCTTCCTTTCTTCTCTTAGGCAAGTTCTACCAAGCTGTTGAGCTTGCCAGTGTTATTTCTGGGTTCTGTTTGGCACAGTTTCCAAGGACTTCAGTATTTAATGTCAAAAGCATCTCTCTCTCTGAAAAGATGTACCTCCTGTGGGTCAACACAAATGTTTCTGAAGTGGCTTTGGGGGTGTTTAATGGGAACCTAGTAGACGTTTAGCAGCAACACCCTCAATTTCCAAACCCAGGGCAGATTATCACTGATAATTCTTGGCCAATGGAAAGCAGATGGCCAGCCTAACCTTTACAGTTGCTGCCTCTGCATCTACACCTGGCTACACAGGTTAGCACAAGGGATGCACAAGAAAACCGCCCTCCACTTCAGTCCTAATCAAGAGCTTCGTGCTTTCCTCCCCAACCTCCAGAGGCAGGGCATCCTTCTTCGCTGAGTTACTTCCCACCAATCCCGACACAAAAGGCAAATATACACACCTGCCAACGCGTGGGATCCACGCTCTTCCCCTCCCACCCACACAACCCCTCTCAAAAATAATAGTAAGAAAAAAGAAAAGAAAATGAGAGAGGTCTAAGAATTGCAAAAAGGTTTAGGAAACGAGTTTCTAAATTGCCTTGAACCCCACCAACAGGAACGGCAGTCCAAAGAGAGGAAGAAAATGTTGACAGGTCTGAATATTTTTCCACCTTTGCCACTGATGATGTGAAATTTCCATTTGATGATGCCAGGGTTTTTGTTTTTTGGGGGGGGATTTTTCTTAGGGTTCATTAATAGAAAAGCAATCTTAAGACTTAGAAGTCCTATGCTTCTTTCCTCCTCTTCTCTTGACCTTACGTGAAAACAGGGTATATTTGAACAAATGGAATGTCCTCCAATGGAAGCAGAAGTGAATGGATCTCTAGGATTTGCTAATGCTTTATTGTCTGGACATCTTTGTTGCACTTAGAGTTTACATATAATGGGTATAAAAACAACTTTGAAGGGCGTTCATTGAACTCAGTCGAGACGTCCTTCAATAGGTGTGTGTTCTGGTGAACATTCATATATATTTATTGGTTATAGCCAGTTTAAAATATTTTCCTTTTTGTATTATTTATCCCCAATATTATGTATTTATATGAGGGAAAAAAAAAGAATCAAATTGTACTTTTTTAGTATTTACTTGTTATAAAGGACATTGTGTTTCCTTGTCATTGTACAACAAGCTTATTTTAGTTACTGTAATTTAGAAAGACGAGTAGTTTTATGTTACCTTCGTACTTATGAATAATGTAATTAGTTCTACTGGAGGCATGAGAGCAGAACCAGACTGTAATTGTATAGTCCTGAATTAGAAGAACTATAGCTAATCCCTCCCTCCCATCTTGCCCCTCCTCTTTGGAGATCTTTCTTTGTTCTTATAGTAGTTATTTTATTTCCTTGCTTAAGGGTTGTCTGTTGAACAATTCTTGAATAAACTTTCTGTTATCAATTTCATCTCGTCCTATCAGTTGGATTTAAAAGCAGGAAGAGGAAAGGGATAAAGGAAAAGGAAAAACAAAAAGGGGGGGAGGGAAAGGAAACAGGGAAAAGGGGAAAAGAGGAAAGAAAAGATAGAAGGAAAGAGGAAAAAGGGAAAAAATGAAAAAGAAAAGGTAAAAAAAGAAGAAAAGGGGGAGCAAAAAAGAAGGAAGAGGAAGAAAAAGAAGAAGAGAGAGAAGGAGAGAAACGAAGATTAAGAAGAAGAAAAAGAAGAAAAAGAAGAAGAAAAGAAGGAGAAAGAAAAAGAAAAAGAGAAAGAGAAAGAGAAAGAGAGAGAGAAAGAGAAAGAAAACAAGAAAAAAGATAAAGAAAAGGAAAAAGGAAAATAAAAAGGAAAAAGGAAAAGGAGAAAAAAGGAAAAAGAAAAAAAAGAAAAGGAAAAAAAATAAAAGGAAAAGGAAAAAGAAACAAAAATAAATGAAGGAAGGAAAGAGAGGAACGAAGAGCGCTGTAGTCAAGGCCGGGGAGCGGAGCGGCCCACGCGGTTCGCAGAGAGAGGCCGAGATTTGGGGCCGCGCCCTCCCCGGGGCCGCCCCCCACTCCGCGCCCCCTCCCCCCCCCCCCCCACGCACCCACGGTCACAAAGGGGGGTCACGTGGCGCCGGGGCCGGGCCGCCATTGGGCCGTAAATGAAAACAAAGGAAAATGATTAATCACGGACAAAATACTAATAATAATAAAAGAAAAGGGCCCGGGTTTCCACGCAGGGATTTTAAAAGCGGAGAGAATGGGAATTGCCGTGTGAGCACACGCATGCACACGGACGGGGATGGTCACGCGTGCACACGCAGCAACACACGTATCTTCGTGCAAGCACGCTGGAAATTGTCATTAAGAGAGAGAGAAAGCTGCTGCGAAAGGCTGCCCTGTAAGAGACAGCAATGGGGGGAGCAGCCCTTGGCAGCAGCAAGGATCACACAGTGCAAAATTCGGGTTTTTATGCTGCAAAGCCTTAAGAAAACTGATAGGAAAGCAGCGAGGGGCGATATGAGTTTTATGGCTCTGGAAAGGGGGGTGGAAAAGCTTATGGAAAGCTGATGTCAGACTGGAGATGCTCCGATGTTGGGGGGTATGGAGGGAGGGAAAGGTTGGGCAGCACCGACCCGGTGTGGGTGTGTAAGTGTGAGTGTGTGCGCTCTGCCCGTGGTTTTGCACACAGGTGTGCACACTCAGGAACAGCCGTGGGTGTCTGAATAAACACCACCCCCCCCCTCAAGTGAAACTGTGGAGAGGAGAGAGATTTCCGTGAGAAATGATCTCGTGTTCCTTCCTCTCTCCGATCTCGCTTACTAAATGAAGTTCCAGGTTAATAATTATAACCTTCGCGCAATAATAAATAGCGGTATAAAAGAAAGACGGGGCTTGTTTTTCTCCCAAGACCGGTGCTCGGTTCTGCCCATCCATGCAGAGAGCAATTTACCATTCGAGGATACTATAATTTGAAAGCATAAAAGCGTGCAAACACTGATCAGGATCGGGGCAAATAAAAGGCTCAGGCGGTGGCTTCCCC
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000013455:ENSGALT00000043870:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.903 A=NA C2=0.827
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0004624=Homeobox=WD(100=22.4),PF132931=DUF4074=WD(100=25.5)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCCGAGTAAAGCCAACCTCAG
R:
AGAGGAAGAGCCCATCCCTTT
Band lengths:
358-1407
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]