RnoINT0071338 @ rn6
Intron Retention
Gene
ENSRNOG00000020638 | Hmx2
Description
H6 family homeobox 2 [Source:RGD Symbol;Acc:1565366]
Coordinates
chr1:203521013-203523358:+
Coord C1 exon
chr1:203521013-203521281
Coord A exon
chr1:203521282-203522129
Coord C2 exon
chr1:203522130-203523358
Length
848 bp
Sequences
Splice sites
5' ss Seq
TGGGTAAGG
5' ss Score
9.08
3' ss Seq
TGTTTGTGTTCATTCTCCAGGTA
3' ss Score
10.43
Exon sequences
Seq C1 exon
GATGGGCAGCAAGGAAGATGTGGGGAAGGGATGTCCGGCGGCCGGTGGCGTCTCCAGCTTCACCATCCAGTCCATCCTGGGCGGGGGCCCCTCCGAGGCACCGCGGGAGCCCGCCGGGTGGCCAGCCAGGAAACGCAGCTTGTCTGTGTCCTCGGAGGAGGAGGAGCCGGAGGAAGGCTGGAAGGCTCCGGCTTGCTACTGCCCAGATCCGCACGGCCCCAAGGAGCCAAGCCCTAAGCACCATCCCCCCATCCCTTTCCCTTGCCTGG
Seq A exon
GTAAGGATCGCACGTCGGGAGTCTGGGCCTGAGTGAGCGTGAGCCGACGCGGTGTGTGTTTGTCGGAGACTCGCAAGCAGGGCATCCTTGGGTCACAGCCGGGCTGCTGGGGGTCCAGGCCAAGGGGAGGGGACTACGCACCAATGGAGCCTTCTCGAAAAGGGCCGGAAGGGCCAGTGCTGGGGAGAAGTAGGAATATTGGGGGCAGTAAGGGGAAAACTGGGTTGGAAGGAGGTTGAACAGGAGTGGGCCAGGAACTCTGCGGGCAGCACACAATGCTGGCCAAAACGTTTTCGCACGCCGGTTACTTTCTGTCCTGACTCCAGTTCTGCAGGTCTGGTCTGGGTGTTCTGTCAGTCCTGCAGGCTCTGCGTTTTTTCCCTCCTCTCATTCTCTTCTCAAGTGATTAGTACTCTAAAATGATTGACAGTGGTGAGTTTCAGGGAGGTAAAAGCTAACGGAGGAGAGCCAAGGAGTTAAGTATAAAATTAACCTGACTCCCAAAGAAAACGGCCTGTAAAATGAAGTTACCTTGTAAAGCTCAGTTCTCACAAGGCAAAAATCACCTTTTAAAAATGATGTTAATGTCCTCATTCCAGACCTGTTACCACCTATACTTATGTAAAAGTGGGAACGGAGACCCTCAAGTTCGGATTATATGGAACCCTCTTCTGTTGCTATGAAAGGCCGAGTACTTTGGACGCTAGTAGGACACAAAAGAAAAGAAAGGGGCTAGGAATAGGGGAATCAAGGATGCAAGTGTCAGCCAACCTCCTTGTCCTAGGCAGAGCTGAGAGTCTTCTAGAAGCATCAACTCCATGGTCATTCTGTTTGTGTTCATTCTCCAG
Seq C2 exon
GTACCCCCAAGGGCAGCGGAGGCGCAGGGCCTGCGGCCTCGGAGCGCACGCCTTTCCTTTCTCCTTCTCACCCGGACTTTAAGGAAGAGAAGGAGAGGCTCTTGCCCGCAGGCTCGCCTTCTCCGGGCCCGGAGCGGCCACGGGACGGCGGTGCAGAGCGCCAAGCCGGAGCGGCCAAGAAGAAGACGCGCACCGTCTTCTCCCGCAGCCAAGTGTACCAGCTCGAGTCCACCTTCGACATGAAACGCTACCTTAGCAGCTCGGAGCGCGCTTGCCTCGCCTCCAGCCTGCAGCTCACCGAGACCCAGGTTAAGACTTGGTTTCAGAATCGCCGCAACAAGTGGAAGCGACAGCTTTCCGCCGAGCTAGAGGCGGCCAACATGGCACACGCGTCGGCGCAGACTCTCGTGGGCATGCCGTTGGTATTTCGGGACAGTTCGCTACTGCGAGTGCCGGTGCCACGCTCTCTCGCCTTTCCGGCTCCGCTCTATTACCCCAGCAGCAATCTCTCGGCCTTACCGCTCTACAACCTGTACAACAAGCTTGACTACTGACACGCCCGCTGGCTCCCGGGGCGCCTCTGGTCGCCTGCAGTTGCCTGCATAGTCCGGCGCGGTCGGTATCCTTACTGGGGCTCCGGAGCAGAGCGGCGCGTGTCCAGAAATATTAAGAAATACACCATGTGTATTCGTTATGTCTTATTTATGGCCTCTTCCCTACTTTTTGGGTTTTTTGTTTTGTTTTGAGTATTTATCCGCATTCCTCACACCAGAGCACCTGCTTTCTACACAAAACCAAACCAACACGCCACGCGTATGAAACTATTTTGGAAGGGGAGATTCTCGGGTAGTGGTGGGAAAGGGGGTTTTGATTGGCCGGTAGCAAGAAAAAAAACATCAGAAAAATACCAACAAAACCAGGTAGTCTTTCTCCCATATATACACCTGTATATGTATATAAATAGTGTACAAGGACACAATCTCAGCCGAGCGGAGCCCACTAGGACGTTGGCCATTGAACCAATCACTTCTCTTTATTCCCTTCATCTTGAGGATGAGTAGGGGTGAAACGAGGAGAGTACAGATCTGTAAATATTTTTAAAGAGAAAAAAAATAAAACGTTTTAAACATGGTTGCTAACTTTGGAGGGATTGTCCCACCAGAAAGCGCGCAGAGGAGTTTCTGGATTTTTAGCGCCAGGGCGAGCAAGATTCTGTTTCCTCTCTCCGC
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000020638:ENSRNOT00000028011:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.989 A=NA C2=0.348
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0004624=Homeobox=WD(100=30.8)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ATGGGCAGCAAGGAAGATGTG
R:
CCGGGTGAGAAGGAGAAAGGA
Band lengths:
343-1191
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]