GgaINT1014988 @ galGal4
Intron Retention
Gene
ENSGALG00000000284 | HOXB4
Description
Gallus gallus homeobox B4 (HOXB4), mRNA. [Source:RefSeq mRNA;Acc:NM_205293]
Coordinates
chr27:3621645-3626317:+
Coord C1 exon
chr27:3621645-3622065
Coord A exon
chr27:3622066-3626306
Coord C2 exon
chr27:3626307-3626317
Length
4241 bp
Sequences
Splice sites
5' ss Seq
CGGGTAAGT
5' ss Score
10.75
3' ss Seq
AAGCTTTATATTTGGGGGAGAAA
3' ss Score
-8.2
Exon sequences
Seq C1 exon
ATGGCCATGAGCTCGTTTTTGATCAACTCCAACTATGTGGACCCCAAGTTCCCACCCTGTGAAGAGTATTCCCACAGCGATTACCTTCCCAATCACTCGCCGGAATATTACAGCAGCCAGAGGCGAGAGAGCACTTTCCAACATGAAGCGATGTACCAGCCGCGGTCAGCATGCAGCGAGCAGCTCTACCCGTCCTGTCAGAGCTCCGGGCACCAAGCAGCGGTGTTATCCCCCCGGGGTCATGTCCATCCTCCGGCCGGACTGCAGAGCCATCTCTCTGAGCCAAACCATCCCTGCGAGCCGGGCACCCCCAGCCCTCCACCCTCCTGCAGCCAAAACTCTCTGAACCAAAGCCCTTCCAATTCCTCTTGCAAAGAGCCGGTAGTTTACCCCTGGATGAAAAAAGTCCATGTAAGCACGG
Seq A exon
GTAAGTGAACTAAAGTGGCTTTGCTTTATACTAAGTAGCACCTCAAAGTCTTGTAGAAATCTTATTGCACCAGTTGTAAAATAACCATTCGTGGAGATTTACGATCGCCTGTTTGCAGAGCGGTATAATTACATCCTCCATAAATTTTTATTGCTCTGCTTGGCCATGTGCCTTTGAAGTCTCTGTTACCATCCTCCTCCAATTTCTTGCAGGCTACTTTTTTTTTTTTTATGGCAGTCGAATCTTCATAAGTTAAGTTTTATGCTTTCGTAATTTGTATTTAAGTGGCGGGTTGAGTAAACTTTTACTATTTTCCCTTCCTTTCCTTTCACCTTTTTATTCTTTTTTTTTCTGGTGCATGTGTGATATTTAATAGAAAAGGAGCGTGTCTGCTCGTTTGTGTGCATGCGTGCAGGGGAAGACTTGAAAGATTTGGGGATAATAGAGCGATGCCCGAGTAGTGGTGTGTATATATGTGTACATACACACGTAGAGGGCATGGAAAATGTGTCTGGGGGACCTTATAAAAACGTTTGGACAGGAATACACGTCAAGCAACGAGGCTGGAGGTGGAGATTTGGAGATAGGCTCCGGGTGTATTTTTAGATTTGCGCTCTATTTTTTTAGTATTTCCCCCCGCCGAAAGAATGTGCGATGCTTTTGGGAAAGGGGGGGGGGNGGGGGGGAGGGGGGGACGGACGTAACNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNGTGAGCGGGTGGGGAAAGGGGGGCTCTGCTGAGGCCCCCCCCCCCCCGTCCTGGCCGCCTCCATTACCTCCTATTGTCCTTTGCGATGTCCACGATTAAGTGTAAATAGCCGAAGAAAAGCCAAAAAGAAGTTAAAAAAAAAAAAAAAAACAGAAAAAAAGCGCAATTGGAAATAAATTTGTGTTTTCTTTTTCTTTGTGAAGCCGATCCCGTGTGGTCTGTTCGGTTGTTTGGGGGTTGTTCTTTTTAGAGGGGGAGGGGGGGGGATGCAGAGAGGGATCTTTTTATTCAGGCGGAGAAGGCAAAAAAAATCTATTAAAGAAATTAATTAAAAAGCACATCGCTTTTATTTATTTGTTGGTTTGGCTGTTGTTGTTGTTGTGTTATTTTGCATGGATTTCTGTTGTCAGTGGCACTCCGTAATGAAAACAAAGGATGTTTGACTATGGGGTATATCAGCCTTAAGTACTGCTAAGCCTTACATATGATGATTTATTTATTCTAAGCATATATTAATACGCTCTTCCCAAACTGGTCCCAGACAAAACAGAGGCAGTCATTAGCGCTTTGCTTTGCTGGAAGGAATGGATGCGGCGCTGTATTTCTCCAGAGACGCTCCTGGAGATAGGGAAAAAAAAAAAAGAAATTAAAAAGAACCCAACCCTTTCTCTGAGGTAGTTAATGCATTAATGAGTCTAATTTCTGCACAGATGTTTCTCGGTGTTTGCAGGTTTTCTGTGTATTTTTATATTACAAAGGAGCTGGCTCCTGCGATAGCTCACAGCCTGACAAGCAAATAGATAATCAAGAAGACAAATGGCTCCTTTTGTGCGCCGCAGCTCTTGTATTAATTTTCATTTTCTTTCTCATAGAAAGTATCGAAAATACTGTTCAGGGTGGAATAACATTCCGGTTCAAAGTTAAAAAGAAAGAAAAGAAAGAAAGGAGGAGAGGAAGAGGAAGAGAAAGGGAAATGGAAAGAAGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGGGGAAGAGAAAGGGAAAGAGAAAGGGGAAGAGAAAGAGAAAGAGAAAGAGAAAGGGGAAGAGAAAGAAAGAGAAAGGGGAAGAGAGGAAGAGAGGAAGAGAAGGAAGGGAGGAATGGAGGGAGGAAGGGAGGAAGGGAGGAAGGGAGAGGGAAAGAGGGAGAGAGAGAGAGAGAGAGAGAGAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAGGAAAGAAGGAAAGGAGAGAGAGAAAGAGAGAAAGAAGGAAAGAAGGAAAGAGAGAAAGAAAGAAAGAAAGAAGAGAAAGGAAAGGAAAACCTATTGTGTGGAGGGGGGTTGAGGGAGGAGGGCTCGCAGCAGTTGAAGGAAATAATGATTTTTCTTTCAAAATAAAACGGCTTTCGTTTATTTGTTTCTGGAATTCTCCGGGACCCCCCCAGCAATAACGAAGTACCCCCCCCGCATCGCTCCCGAACAAAGGATGGAGCTGCAATATTTAAAGGCAGGCGATGTCTGTGCGCTGTTCCCTTATTTGCAGTCATTCTCCGCGCGATCACCGCGCAAATAAATGCCCACCACAGTGCCCCCCCCCTCCAAAAAAAAAAAAAAAAAAAGAAAAGAAAAAACCACCCAAAAACAGAGAGCCGTTATATTTCTTTTTCTATCGACATTTTCAGACGTTAAAATAATATTAACGCAGTGACAGGGGTCGCGTCTGTGACACGTTCAGATGGAGAAGAAAAGGATTTATGGGCGCTTTTGGGGTCGGCTATCGCAATTGTAGAGATAGCAGCAGCGAACGCGTAGAGTTTCTTTATTTTTATATTTATTTTCTTCTATTATTATTATATATTCTTTTTTTTTTTTCCCAGGGAGGATTTCAGGGCCCGTTGTCGTATGGCAGTGCCGGAGGTGGGGGTGAATTTTTGCTGCTGGTGCGTTTTATTTGAGCGTTTCTCGCTTTGATGTGTTGTGGGGGCAAAACCAAACCCTAAAGGGTGTTATGTGCGAGAGAGTGAAGAGATGGAAGGGATCGTTCTTAAAAAAAAAAAAAAAAAAAAGCATATGCTTCCAGGAATGCGGGGTCTATAGAAGCAAATCAAAGCTGGAAAGTATGAATAGAATAGAAGGGGGAGAAAAGAAGATTTCTATAGGACCTAAAAGTTCACAGCCATTATAAGCAGACAGAAGCCAAGAAAAATGCGAGAATTATACAGAAAATCATTAATCACTTCTTTTCTTTAAATACTTATCCTTTTCCCATTGTTATTCAACAGCAAATCTCCGCAGACCGTCTGTTGGGGAAAAAGCACCCGGAGTTCGACCAGAATCTTCAGGGGAAATAATAATACTAATAATAAAATCTGGATCGTAAAGGTGAAAGCTTTATATTTGGGGGAG
Seq C2 exon
AAAACCCAAAC
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000000284:ENSGALT00000000373:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.589 A=NA C2=1.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
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:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]