DreINT0078837 @ danRer10
Intron Retention
Gene
ENSDARG00000070351 | hoxc11a
Description
homeobox C11a [Source:ZFIN;Acc:ZDB-GENE-990415-111]
Coordinates
chr23:35975995-35979329:+
Coord C1 exon
chr23:35975995-35976797
Coord A exon
chr23:35976798-35978177
Coord C2 exon
chr23:35978178-35979329
Length
1380 bp
Sequences
Splice sites
5' ss Seq
TAGGTACCG
5' ss Score
5.99
3' ss Seq
TAAGGTACCCCGCGCACAAGAAA
3' ss Score
-6.24
Exon sequences
Seq C1 exon
GTGTTGCGGGGCGACTTAGACGGATTGCGCGTCATCTCGCCTTCCCAAATTTTCTCCTTCTGCAGCTCGAATCCAAAACATCATATCTGTAGTACGGACTACAGGAGAAAGATGTTTAACTCTGTTAATCTGGGCAACTTCTGCTCCCAGACGCGTAAAGACCGGACGTCCGAGTTTGGGGACAGGACGGGCTGTGCCTCCAACATCTACCTCCCCAGCTGCACTTACTACGTTCCTGAATTTTCCGCCGTCTCTTCGTTCCTTCCACAGGGGCCCTCGCGACAAATCACATACCCATATTCCACAAATCTATCTCAAGTGCAACCGGTACGAGATGTTTCCTATGGTTTGGACCCGTCCAGCAAGTGGCACCACAGATCCAACTATGCATCTTGCTACTCAGGAGAAGACCTGGTGCATAGAGACTGTCTTCCGCCATCCACCATGACAGAAATGCTCATGAAAAACGAGAGTGTGTACAGCCACCACCACCAGCATCATCCGAACTCTAGCCACCCTTCCACCGGGTTCTACACCGGCGTGGGGAAAAACAACGTGCTCCCTCAAGGTTTTGACCGTTTCTTTGAAACCGCTTATTGTAGTACGGACAATCAGTCAGAACATTGTTTACAAAAGAGCGAGATGAACAAATTAGAGACTTCGTCCCAGCAACCCACAGCTGTTTCCGCAGCACGAGAGCCGGAAAAGGACCCAGAGGATGAGGAGGAACACACAAATTCGGGCTCGTGCACTTCAGCAGCTACTAAGGACGGGAACGCAAGCAAGAGCAGCCATTCGAGTAG
Seq A exon
GTACCGAAGCTGTAAATGGGGAAAGGTTAAGGGACTAGCCCGGTGTTTTGTCGGTCAGATTTTATGTGGAGTTTTATAAGCATTCAAAGGATTTTATTATAACCTACAAAGCTCTTTCCTCCAACGAAAAGAATTTTTACGATGGGAAAGCGCTTTGAAAAAGGAGGATGTTATACACAGACGCTACTATCCCAGAGTCTGTGAAATTTTAAGAGCGCGCTATTGTGACAAATGCTAACTTTGATCATGAACTTGCGTTGAGCATTGCGAGGGATTTTCTCGTTTAGCTGTCGGGGGTAAAAACCAATTGGGCAGAACATTACTTTTGGCATACTGTGAATTTTGTTTTAGCAGCTCGAATGTAAACTAGCTAGGTCCTTATTAGCTTTTTAAACGTGCTGTGACTGCAGTTACCGTGGGGTGTGTAGTCAATGGCTGCAACCTTAGTGCTTGTTCAGTGCTAATGACAGATAGATGGATAGAATAGAACTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATAAACAAAATAAATACAAACTAAAGAGGCCTTTTTTTCTTTTGAGATTTGTTGTTGTGTAAAATTCGCATCAAACTATTTAACGTTTAAATAATCCAGTTATTATTATGCATTTTAGAGTTATCCTTAATTTTAGATGTCTCTCTATTGCGGCGCTTTTAACATTTATGTACAGAACAACAAAAGAGAAGCAAGCGTTCACGGTCATGCACATTAGACAATATTGCAGGCCTATTGTAAGATCCATTTTGTAACAATATAAATAACACATTTTCACGTGCACACGGCCATGGGTCATATAATTTGCCAAATGCACGCATTAATATGATGCAAAACAGGGATAATTGCACAGACCGAAAAAACACTCTCTACGATCAAAAGATTAAAGAAGAACATTTATTTACCGAGTTTATCAGTTATATGTTGTTGTTGTTTTTTTTTTTTTTTTGCTGCTGCTGTTGTTATTAGTATTATTGTTATTGTGATAATTATTTTGTATTTAAGATTTTTATTTTCCCCAGGGTTACAAAAATTGTAGAGTGACAAATTGTGTTTGCTTCCTCACATTGGTAACCATAGATGCAGTCCACGAGGCATTTAGTGAAATTTGATATTACAAATGTATCTTCAATAAATAAATGAACAAAAATAAAATAAAAAAATGTACATTTATAAACATCTCATTTTGTTTTTGCTGAAAATAAATGTTGCTTTAAAATGTTTATTTTAAAATGTTAATCATTGTAATTGTCTCTTTTTTTATATTTTTATCCTAAGGTACCCCGCGCACAAG
Seq C2 exon
AAAGAAGAGATGTCCATACTCCAAATTTCAGATTCGTGAACTGGAGCGAGAATTTTTCTTTAACGTTTACATCAACAAGGAGAAAAGGCTACAGCTATCCAGAATGTTAAACCTTACTGACAGACAAGTCAAAATATGGTTTCAAAATCGTAGAATGAAAGAAAAGAAATTAAGCAGAGATCGCCTGCAGTATTTCTCTGGAAATCCGTTGCTGTAATTGTTGAAATGGCGTTGCCTGTTATTTAATATTTTTGCAAACAAACTCTATTAAATATGTCAAATATGCCCTTCAGTCTAATTAAATAATTAGATATGTTTTTGTCTAGGCCAGCAACAGTACTGAAGAAGCCTAAGACAGTTGGAGGCTAACAGGATTGTAATGGCTGAGGGTGGGGACAGACAATACAAATTTGCTTAATGTCAAACTGATATTTCAAGTTTAAAGTTCACAAACCAAAACGTAATCTTCACAAACTTAAGGTTTCTATTTGTTTGTGACCCGTCTTTTAAGTGAAAATAATTAAAATATTCACTTTGAATAAGGCGACAAAATAGCCTACTATAATATATTATAAAATTGTACCCTTATCATTTTATGCTTGTATATATGTACATTAAAACACACTCTCGACTCTGGTTTAAATCTGGAGATGTCATACTTTTTTATGTTTTCACCATTTAGAACTGTGACTTGTACAATCTGTAATAATGTATTCCTTGTACAGAGATTATGCATTGTGCATTCGTGAATGTAAATATAATGTTATTTTGAGTATCCTCAACTTATCCCTGCTGCTATATTTCTTTACATTGCCTTTGCAGCCTTGTGAGCTTTGTTGTTCAATTCTTTAAATTATTTGCTGTACGCCCAAAGTTCTCTATCTTTTTTTTTTTCTTAAGGGGAAGTTCGGCGGTCCGATTTGGCCTGTGTACTGCGTATTAATCAAAAATAAACACGAATAAAGGTAAACTGTTACATGTCACTGTGACTTGATTTTTAAAACTAATAATAATTATGGAAAATAAGATGATTAATCAATAGGAAAGTCTATGGTGAGGAATGTAGTGATGTGTACAACACTGCCGAGACCCAAGAGAAGGTAGAAACTGACCACTATATCAAGAAAAAAAATTAAATAATCTATTTCTCTC
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000070351:ENSDART00000133760:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.424 A=NA C2=0.042
Domain overlap (PFAM):
C1:
PF120453=DUF3528=WD(100=63.2),PF0004624=Homeobox=PU(0.1=0.0)
A:
NA
C2:
PF0004624=Homeobox=WD(100=78.1)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Rat
(rn6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TCCGAACTCTAGCCACCCTTC
R:
CGCTCCAGTTCACGAATCTGA
Band lengths:
351-1731
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]