DreINT0057765 @ danRer10
Intron Retention
Gene
ENSDARG00000071560 | dlx4b
Description
distal-less homeobox 4b [Source:ZFIN;Acc:ZDB-GENE-990415-50]
Coordinates
chr12:5691829-5693798:-
Coord C1 exon
chr12:5693185-5693798
Coord A exon
chr12:5692023-5693184
Coord C2 exon
chr12:5691829-5692022
Length
1162 bp
Sequences
Splice sites
5' ss Seq
CGAGTGAGT
5' ss Score
8.49
3' ss Seq
TTTCGTCTGCATGCCTGAAGACC
3' ss Score
3.61
Exon sequences
Seq C1 exon
GACGCACCAATCAGCGCGCGCTCTCGCGGAGCGCGAGTCAGTCAGAAACACACAGGACCGCGAGCCCGAGGTGACTTTAGATATTGCGCTGTTTACTCATGATTAAAGAAAGATAACACTCGCGTTCACCTATGAGATTCTTTGCAGTGGTTTTGGGATATACGTTTTTATCCAGAAACTCCTTTTGTCCCGGATTATTTGGGGATGGATCCGGTTCAAGGTCTTTCTCGTGCACTGTGATCGTTCAATGCAGCACTCAGACCATCATCGGGCTTTATGGACTTGACGGTTAATGATGTCTATGAGTTTCATGTCTGATACGCTGAATAGTTCTGATCCTTCCAAATCAGCATTTTTAGAGTTCGGCCACGGGCTTGCAAGCAACCAGCAGCATTTGTCGGGATTCGCGCACAATATTTACCCGGTACACGGATTGCACTCAGGCGGACACCTCCAGCACGATGCTCCCTACCCTTCCAGCGCTCCTCATTACAGCCGGCCGCTGGGATACGCCTACCCCGGGCCGGTGAGCGCTGCTGCTCCGGGTGCTTACATGCCTTACCAGCCAAACAACCACAGCGGTGCTCTGGCGCACACGAGGGCTGAGAACACGA
Seq A exon
GTGAGTATCTCCATAATAATGCATCAACCTTTGAGAACCTGATGCCCCGTTTAGTTCTATGCGCTTGTAATAAACTAAATTAACAATGCAGTTTATTTGGTACATTTTCAACACAAAAATGCAATGTATGGTCGAACTTTATACATGCATCGTTATTTTATATTGAAATAGCTAATATTAAGTAGGTTTGTTTTGCATATTTACTTTGCATTCGTATGGCGCCAGTAGCTAAAATTATTTTTATACACAGTGTATTACCAAATAAATACCAGACTTTAAAAAGCACACGGTCAAATAAGTTTTAAGACCATTTAGAATAAATCGGTTGCAAATGGTAACAAAAGTCTCTGTTGCACACACGATTCTGACCTTTCAGCAGCAAAAAGTAATTTGTAAGCTTTGCTAATCTTCTTTTCCTTGTATAGGCCTCGAACTGGATTGAAACATGTACATTAAACATGCACATCTTTGCATACAATTCAAGAATAATTTTTATGTCACTGTTAAAACGAAAAGACAATGAAATTAATGCATTAATCAAACGTATTTAAACAAAATGTTTATCGACGTGTATTCATGTTCAGCTACATTATGCAGAAATTAGAGCAATAATCACAATTCATGTAGGCTAAACCTAAAATAATATAATTGTTAAAATATTATATTTCCATACAATCTATATTAAGCTGCTAAAGTGTGTAGTTAGAATTGACTTTGGGTATGTGCACCGAAAGTTAAGCGCTGTCTAAATCCCTGTCAAGTTTTGCGAAATTGTAAAGAATCTTTTCTGATTTTGTTTTAATTATTAATATGATTGGTAGGATTTTTTATTCCTCCATAACGATATTATTACGCCTTTTGTTAAATGTCACTGTTTGCTCCGAAGTTCAAGTTTAGGCTCGTAGGCCTGTAAAATTGACATTAAAACGACGTTAATTATGGTTTACCGATCTTTAAAATGATGACCCATTAATGTTTCCTCTAAACCACCTGATAAATCTCTTATTTACCTATTGTAAATCAAGTCGACACTTACAGCTCTTTAGTGCATCATAATTTACGGTTTTCTGATGGTTAAGGAAGGTTTTGCAGGTGTGAACTGTGAAGACAGACATTTACTGTGTCATAATGCTGTCGTTTTATTTCGTCTGCATGCCTGAAG
Seq C2 exon
ACCACGAAAAGCCAGCGGTCATTGAGAATGGTGAGATTCGCCTTAATGGCAAGGGGAAGAAGATCCGCAAACCGCGAACCATTTACTCCAGTGTTCAGCTCCAGGCTCTGCACCAGCGCTTCCAGCAGACCCAGTACCTCGCGCTGCCCGAACGTGCAGATCTGGCCGCCAAACTGGGACTGACGCAAACACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000071560:ENSDART00000105887:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.417 A=NA C2=0.385
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0004624=Homeobox=PU(73.7=64.6)
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:
TCGGGATTCGCGCACAATATT
R:
GAGGTACTGGGTCTGCTGGAA
Band lengths:
357-1519
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]