DreINT0078828 @ danRer10
Intron Retention
Gene
ENSDARG00000011579 | hoxb10a
Description
homeo box B10a [Source:ZFIN;Acc:ZDB-GENE-000328-2]
Coordinates
chr3:23538719-23541315:+
Coord C1 exon
chr3:23538719-23539141
Coord A exon
chr3:23539142-23540321
Coord C2 exon
chr3:23540322-23541315
Length
1180 bp
Sequences
Splice sites
5' ss Seq
AAGGTGGGT
5' ss Score
8.23
3' ss Seq
TCTTTCTTTTATATCTTAAGATG
3' ss Score
7.17
Exon sequences
Seq C1 exon
CGACAGGGCAAGCCAGGCAGCCTCTCGACATCTCCGCTTTCAGCAGAATCATGACAGATATGGGCTCTCTGAACAGTGCAGACGACCATCGTCCAGAAACGTCTTTTTACTCCGGACACAAACTGTTGTCACTCAATACCAACACGGATCCAGAGAGTCCATCGCTTTCTTCCCACTCAGACTCACAACATTTGCACAGTCTGTCTTTGTCCGCACCGTGTTCAGAAACTGACAATAAGCATGATATGCAATATTTAGCAATGGAAAGCACAAAATACCCAAGTCAGTGGAGTGAAAGCAGAACCAACAGGAGCATCATTACTACACTGAGCATCAGTCAGAGAAGTAAAGACGACATAGAGCCAAATAACCTCCAGACAGACTTTACCAGGGGCGATAAAACTCCAAGAGAGAAGACACAAG
Seq A exon
GTGGGTAAAAAGGTTTTTAAAAGAAAACACTGGGTAAAGCAAGTCCATCAAAGACCAAAACCAGATTTTTTTTCTTTCCGAAAGCAATTGAAGGTTGTAGCCACAGAGACACAAAGAGAACCAGGGTTGAAAATGAATTTATTGCACCGAATTACCCTAGACAGACTAAATTGCACGTCGTTTCTCTGAACATCAAAACAGCGGAAGGCTGCCATTGTCAACTGGAAACCATATAGTGTGGGCCAGGTGTGGCATTGCTTTAGGACACTTTTATTGAAGTTATACAGAGGAAACCACTTCTGGATTCAGAATTTGAGGTTTAGAATGAAATTATTTATTATTTAAGTCTACAAGTGTTGCATATCTAGATGTAAACAAAGCAAAATCAGAACAGCCATTTAAGTAGCCTTTATATTATTTTTGTCAAGGCAATTCGTTTAACGTATCCTAGCAAACACAGCAGAGGCCTAAAATGTCTAGACAAAAATGCTCGTGTGCACCTTGTGAAGTAAATTAAAGTCACCTTCATTCGTAAATAACCTTATACAATATAAATTGCCCCAAAACAGCTTAAGAGTAGGCTAACAAACAAACAAACAAAGAATATATATATATATATATATATTTAAATGAAGCAAATTCATTGTGCTTTGAAGCAGCCATAAAATACAAAAGTGTGCGGGCTGCACAATTTTATTTTGCCATTTCCCTTTATTTAGTCCAAAAGCTAAACACAGCAACACTATTAATTTTAATAGTCAAAAGTTGCATTATAAAGGACAAAACTTTGAATAAATGTAAATTATATTTGCTTTTTGATTATCAAAGTCACTAGGCTACTTTATTACATTCATTGTATGAACAAGTAATTAAATGAGTCAAAAGAAAGACTACTACTTATCATAATCAAAAGAATAAATTAAAAATACAATGTTGTTTTAGCTGAGATGCTATCTGCAACAGAATTGCAAACATGTATCTCTTTTTTTCTTCTCGGCAGTTTCCCCCTTTTTCCCCCCCTCTCGTAGGCATAGTGCGCAGTCTGTGCTTACATTATTTCCTGTCATAAAATGTCGGACATAGCCAGGTAATGGCCGCAAGCATCAAGCTCAGTGGCTGTTTGCGCACTGTGAAGGGCGTCTGTATAATACCATTGTCTCTCTTTCTTTTATATCTTAAG
Seq C2 exon
ATGTGACCTTAGAAAATGCTGCAAATGGCTGGCTTTCGGCGAAAGCGGGAAGAAAGAAGCGATGTCCTTACAGCAAACACCAAATCTTAGAGCTGGAAAAGGAATTCCTATTCAACATGTACCTGACTCGCGAGCGCCGCCTGGAGATTAGCCGGAGCATAAATCTCACCGACCGCCAGGTTAAGATATGGTTTCAAAATCGCAGGATGAAACTGAAAAAAATGACTCGAGAGCACCGGACCAGGGACCCTGGTACAAGTTTCACTGTCTAGTTTGTCATGTAATACGGTTGAATAGACCGAACTCAGCGCACAAATCATTTTAGTCATCATCCGTTGCAAGTGGACTGATGCAACTGCTGCTTCTGATGGATTAACGGGAGGAAGCGATCTGTCAAATCTTACTACGGCGGTTCACAATGTGTACTATGATGCAAATGTAAGGGATATAAATTTAATACCTCGCATGGAGAATAAACGAATGTGTAAAAAAAGAAGACACGGCTTTGGCCATTCGGTGAAAGCTGAAAGCTATTCGGAAAGCCCCTGAACACTGTTTATTGATGTCGTTTATGTTGTGACCGACCTTTTTAACGAGGGAATGTTTTGTAATTTTCAATAGGCTATCTGACTTATGATTTCCCACTGTATGAGTTCTTCTTTCTTTGTTTTTTCAGGTTATAAATGCTGTAGCGATTTTTACACAGCCTTAGTATTTATTACTTGAGTAGCCCAACTAAGAACATTTGCGGAAACTACGGAGTGGCCTAAACAAATCTATTAGAAATAGTAAAGTATTTTAAGTGCTAAGATTTGACACCAAGCACAGGTACTGTTGTTGTTTTTTCAAATCTGTGTTGTTTAGTAACCATATTGGCTCGAAAGATTGTTCTGCTGAAGCATGGTTGAATGTACTTAAGCTGTGATACTTCATTTGTTTGTGTTTTAAAAAGCAGATAGTTTTAAATAAAATATTGCCATACGTGACCATAAAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000011579:ENSDART00000111227:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.944 A=NA C2=0.300
Domain overlap (PFAM):
C1:
PF148861=FAM183=PU(67.0=55.2)
A:
NA
C2:
PF148861=FAM183=PD(32.0=36.3),PF0004624=Homeobox=WD(100=62.6)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ACGGATCCAGAGAGTCCATCG
R:
CATCGCTTCTTTCTTCCCGCT
Band lengths:
344-1524
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]