GgaINT1014985 @ galGal4
Intron Retention
Gene
ENSGALG00000025774 | HOXB2
Description
homeobox B2 [Source:HGNC Symbol;Acc:HGNC:5113]
Coordinates
chr27:3652538-3655356:+
Coord C1 exon
chr27:3652538-3653035
Coord A exon
chr27:3653036-3654215
Coord C2 exon
chr27:3654216-3655356
Length
1180 bp
Sequences
Splice sites
5' ss Seq
CAGGTTCGT
5' ss Score
7.97
3' ss Seq
TGAGGTTTTGTGTGTTTAAGACA
3' ss Score
4.44
Exon sequences
Seq C1 exon
GAACCATCATCATCACTGCCATAAAAACTGAGGCCCTCAGATTTCTTCCTCTCTTCCCCTCCTCCTTCCTCCCCCCTCCCGCTTTTTAAACCCTGGGCCCTGGAAAAGCCATGAATTTTGAATTTGAGAGGGAGATCGGGTTTATAAATAGCCAGCCTTCGCTCGCAGAGTGCCTGACGTCTCTTCCCGCTGTCCTGGAGACATTTCAAACTTCATCAATCAAGGACTCGACATTAATTCCTCCTCCTTTTGAGCAAACCGTCCTCAGCCTGAATCCTTGTTCCAGCAGCCAGGCAAGACCGAGGAGCCAAAAAAGAGCATCCCATGGCCTGCTCCAGCCTCAGCCTCCGGCACAGCCCGGCCCCTTGGCAGCGGAATTCCCCTGGATGAAGGAGAAGAAATCGTCCAAGAAAGCTACCCAGGCTCCATCCTCGTCTTCCTCTTCTTTCCCCCCATCATCTTCCTCGGTGCCGATCCCCGCCGCAGGATCTCCTGCAG
Seq A exon
GTTCGTATAATGAGGGGGTGAGGGGGTGTTGGCTGAAATCGGAGAGGATCCGAATCATAAACAATCCCCTTCCCACCAGCAGCCCTACCCGCACCCCCCCCCCATCAGACTTTTTGTCCCGCGCCTCTCCGAAACTGTGTCACGCAATAAAATACACTGCAGCAATGCACACAGCCGGGGTGGGGGGGCANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTGGCAGCTGAGCCACGGCTCCATTTTCTTGACTTCCCCTGCCAGCCTCGAATTCTTTTACAGCCTACAGGGGGAATAAAAAAAAAAACCGAAAGCAGAGTGGAGAGGGAAAAGAAGGACGGGTGGGTAACGCGGGGTTTGCTGCAGGCGAGATGGGGAGGCAGAAGGAGAGCGAGCAGAACTCCCCGAGCATCCAAGGCAATGGGAAGAGCCAGATCCCTATAGCAAAAATAAACGAATGGATAGATAGGAACTCCCAACCCCCCCCAACCCCCGGTTAAATGAACGTCTTCTCTCCGAGGCGTCCTTTGGATAGGGAGCTCGGCAGCCCCGGCCAGGGATCCTCCTTCTCCGGGGACAAAACGTTCGAGGCACAATTCACTGTTGGAGTATTTTTGTAGCACCGTTCGGGTCTAAGAATGTTCAGGCAGAAGAGCGGATATCAGAGCTCAGTGATCAGATAACGCAGGAATAATGAAATCAAAGCTCCGCAGCGTCAGTCTTTAACCTACTGGCTTTAAAATAATAGTAATAATAATAATAGTAATAATAATAAAAAGGGAAGGAACAGGTCGAAATTCCCCCTCCCTGAGAAGAAGGCGGGGAAGGAAGGTGTCTAAAAGGAGAAGCCAGGGAGCAAAATCCTTTCTCCTCCTTGGGACAAGGCAACAAGAAAGCGATTTCCAGCCTTCATTCCCATTGGAAGAGCGCCATTAAACATTTATTTTCTTCCGTAGCGGCTCCCCAACCCCACCTCCCCCCCGATGGGTACCGTGGGGGCACGCTGCGCTCTGCCCGTAGGGGGGGGGGGGGGGAGACGACGACTCCATCCCCTCCATCCTCGCCCCGGCCCCGCTCCCTCCCCGCAATGTGAGGTTTTGTGTGTTTAAG
Seq C2 exon
ACACGCAGGGGTTGGCAGACAGCAGCGGCTCTAGGAGGCTCCGGACAGCGTACACCAACACACAGCTCCTGGAGCTGGAGAAGGAATTCCACTTCAACAAATACCTCTGCAGGCCCCGTCGGGTGGAAATCGCGGCTTTGCTCGACCTGACCGAGCGACAAGTCAAAGTGTGGTTCCAGAACCGCAGGATGAAGCACAAGAGGCAAACACAGTACAAAGAACCCCCCGACGGGGACATCGCTTACCCCGGCCTGGACGAGGGCAGCGAAGCCACGGATGAGGCCGAGGAGAGCCCCGCGTTGGGGCCGTGCCCGGGGCCGTACCGGGGTGCGCAGCCCGAGCAGCCCCGCAGCCCTCGGGGTACCGATCGGCCCGGAGCCCCCCCCTCGGAGCTCGGCTTTCCCGAGAGCCAGGGCTCGCCTTGGTTGCCGGAACTCAGCATCCTCTCGGCAGAGTCCTGCCTGCAGCTCTCTCCGGCTCTGCAGGACTCCTTGGAGAGTCCCCTCCACTTCTCGGAGGAAGATCTGGACTTTTTTACCAGCGCACTTTGTACCATAGATCTGCAACACTTCAATTTCCAATAGCGGTCCCCGCCTGTCTCTCTCTCTTTTTTTTTTTGTTTATCCCTTTCTGTCCCACCCCGAGCCGCTCCAGCTCTCCAAACGAGAGGGGGTCACCCCAAAAACAAACCCAAATCATCCCGCATTCAATCACCCCATCCCGTTCGACGGACATTTTAAAGCTCTTCAAGTTGAGGGACCCGAATCTCAGCCGCAGTATTTATTTGAGAAGGCTCATATAAAAAGAGCTTTTTATTTACAAGATAAATTAGTTGCTAAATGGTAGGCTTGTTCCTTATTTATTTTAAAGGAGGCACCCAATAGTTTCCATGCGCATCAGAGATGACCGCCCTCGAGAGAAAACCATTGTGAATCCTCCAAGCGACTTTCTCAGGAATCAGAATGAGCCTTTTAGATTTCTTAAGGAAATAATAATGAGAAAAAAGCAGAGGAATTTTCGTTCCTCCTTTTTAAGTTTTAGATGTAGATTATTTATTCAGATCCTTTAATAGCAAATGGCAAATTATTTATTGTACATTATTTTCATAGAGTAAATAAATGCCTTTATAAAACCGAGGGAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000025774:ENSGALT00000046008:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.694 A=NA C2=0.577
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0004624=Homeobox=WD(100=29.2)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AAAAGAGCATCCCATGGCCTG
R:
ACTTTGACTTGTCGCTCGGTC
Band lengths:
356-1536
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]