DreINT0078508 @ danRer10
Intron Retention
Gene
ENSDARG00000070955 | hmx3a
Description
H6 family homeobox 3a [Source:ZFIN;Acc:ZDB-GENE-001020-1]
Coordinates
chr17:21770770-21773277:-
Coord C1 exon
chr17:21772662-21773277
Coord A exon
chr17:21772275-21772661
Coord C2 exon
chr17:21770770-21772274
Length
387 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAGA
5' ss Score
10.57
3' ss Seq
TTTGGCCTCTATTACTGTAGCAG
3' ss Score
5.75
Exon sequences
Seq C1 exon
GCTATTGTACGTGCCCAATCGCCGTATACTTTCTGCATTTAACTCGGGTGACATTTTTATTTCATCATTAGCATCTGGCGCCAGACGGTCGCGGTGAGCATCATTTTCACCAAGGAACTCTCGGAAGATGATCAGCAAGATTAATATTGTTTATCTCGATCCGCGTTATTGTCTTTCGTTTTAACGTCAATGCTGACCGTAAACAACCGCGTTTAAGTTCCCATTGCTGGAAGAGTTTACCAAGGACTTTTAAACTGTTTAAAGATTTTCTTTTTTAACGCGTTTTTAACGATTTATAAATTGTAGTATAAACCCGAATATCAAGCCAACATGCCCGAAACAACACAGGATACGTGTGCTTCAGCGAAAGACTCTCCATTTTTCATTAAAAATCTTCTCAATTCTGACAGTAAGCCGTCAAAGCCTAAGCCTATTTTGGCACCCACTAAAGCAGGACTTGATGGCAGCTTCTCCCTTTCTCAGGTTGGGGAAATAAACTTTCCTCGCTTTGAGTTACCCACCCAGCGCTTTGCGTTACCGGCTTACCTTGAGCGTGCCTCGGCGTGGTGGTACCCGTACACACTCAGTGCATCCGCGCATCTTCACAGAACAGAAG
Seq A exon
GTAAGATTTATTATCTCATAACTGCTTTGTTGAGTAATCTGCGCTGATTTATTATTTATGATAATTAATAGCGTGATTCTGATATAAAATATTGGTGCATAAGCATGCACTGTAGCAAGCCAGCCTATAGCTTGTTTCCCGACAGATTATAAATAATATAGGCTAAGTATCAAACATAACAGCAGCTGTTATCATTCTTTAAATATGAAAGCTCGCATGTTTTTAGTTTAAAATGCAGGGTTGAAGTTTTAAAAACACTGAGATTTTGGACAGTGCGAATCACAATTGTTTGCACCTGTCATGTGGCAAAGTGACACGACCAGTGAAACTTGATATGAATATGTTTCTGAAAGAAAACGAATGCTAATTTGGCCTCTATTACTGTAG
Seq C2 exon
CAGCACAGAAAGCGAGGGACTCTTCGCCGACCACAGGCACCGACCGAGATTCCCCCGAGCTTGTGCTCAAATCAGATCCGGACGCCAAGGACGATGAAGACGACAACAAAAGTGGCGACGAGATTGTCCTCGAGGAGAGCGACACCGAAGACGGTAAAAAAGAAGGCGGCATAGACGACTGGAAGAAGAGTGACGACGGCGCTGACAAGAAACCTTGCCGGAAAAAGAAAACTCGCACGGTGTTCTCGCGGAGTCAGGTGTTCCAGCTGGAGTCCACCTTCGACATGAAACGCTACCTCAGCAGCTCGGAGCGCGCGGGCCTTGCTGCCTCCCTTCACCTCACAGAGACTCAAGTGAAAATCTGGTTTCAGAACCGCAGAAACAAATGGAAACGTCAGCTGGCCGCAGAGCTGGAGGCCGCCAACTTGAGCCACGCAGCAGCACAAAGGATTGTGAGAGTACCCATCCTGTATCACGAGAACTCGGCCTCTGAGAGCACCAACACAGCGGGCAACGTTCCTGTAAGCCAGCCGCTGCTCACTTTCCCTCATCCGGTTTACTACTCGCACCCCATCGTCACCTCCGTGCCCCTCCTCAGACCGGTTTGAGAGGACGACAGATGTCTTTTTCTATGTAACTATGTAACTAAATTTTACAGAGACTCGAAAGAGGGAAAGAGAGAAAATGGGAAAATGAAACCAAGAGACAAAGATATTTTTGTTTAGAAAATACAAAAAAAAAATTAAAGAAAAGAAAAAAATGTACAAAGACGCACTATCATGCATTTGAGCCCGACATTTTTTGTTTTGTTTTACAATTCCTAAAAATACCCATAAAACTACACATAAATAAGGCTGTTTAGAGGCCTGTATTTCAAATGTTGATGTTGGTTGGTGGTAAATTTCTGACTTTGTTTATTCACTTTGTCATTATACAACTACTACTAATAATAATATTAATATTATTATTATTATTAATAATAATAATAATAATTATTATTATTATTATTATTGTACCTGCTACGGTTTATCTGTTTATATAACAAATCAACTTGTTCAACTTGTTGACACGAAAAGTCTTTAATACACACGTTTAAGTTTCTTTACAGCACCGAAAACGCGTACCCACAGACAGCCCTGAACACGGATGTGCAATACTACTGTGTATGATCTGTATATTTAGACAACATTACTATTCTTATTTTAGACACGTTTTCTTACCAAACATTTCTTAGGTTAAGAAGTTAACCGTTAAAACGATTTAACTGCTTGGTCCCGCGTTCAATAGACAATCATATATCTGACAGACATTACAGTTAAACTGAAGACAAAAACACGAAGAATAAATACTTTTACTTTTATCTATATTATTTACAGATGTATATGTACATGTACAGATATAACGAACCAAAAGGAAAGGTGTCATTTGTACAGTAACAGATACGTTCTTTTTTACATTGTATTGCTAAATTCTGTTGTGAAATAAACGAAGACTACTGAAGTCAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000070955:ENSDART00000104612:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.312 A=NA C2=0.416
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0004624=Homeobox=WD(100=28.1)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGATACGTGTGCTTCAGCGAA
R:
TTGGCGTCCGGATCTGATTTG
Band lengths:
357-744
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]