RnoINT0071339 @ rn6
Intron Retention
Gene
ENSRNOG00000020637 | Hmx3
Description
H6 family homeobox 3 [Source:RGD Symbol;Acc:1559927]
Coordinates
chr1:203509731-203511695:+
Coord C1 exon
chr1:203509731-203510130
Coord A exon
chr1:203510131-203510733
Coord C2 exon
chr1:203510734-203511695
Length
603 bp
Sequences
Splice sites
5' ss Seq
AAGGTACCG
5' ss Score
9.67
3' ss Seq
CCGTTTGTCTGTCTCCCCAGCCT
3' ss Score
9.03
Exon sequences
Seq C1 exon
ATGCCGGAGCCCGGGCCGGACGCCTCGGGCACTGCCAGCGCGCCGCCCCCGCAGCCTCCTCCCCAGCCTCCCGCGCCCAAGGAATCCCCGTTCTCCATCAGGAACCTGCTCAACGGAGACCATCACCGGCCGCCCCCGAAGCCACAGCCGCCCCCACGAACGCTCTTTGCGCCGGCCTCGGCCGCCGCCGCTGCGGCCGCCGCTGCCGCCGCCGCAGCCAAAGGTGCCCTGGAGGGTGCCGCGGGCTTCGCGCTCTCGCAGGTGGGAGACCTGGCCTTCCCCCGCTTTGAGATCCCAGCGCAGAGGTTTGCATTGCCCGCGCACTACCTGGAGCGCTCCCCGGCCTGGTGGTACCCCTACACCCTGACCCCCGCCGGCGGCCACCTCCCGCGACCAGAAG
Seq A exon
GTACCGACCTCCCTTTGAACTTTCGTTCTCCCCTCTTTCCCTGTGGGCCGGTCCCATCCCCGCCCAGGGCTGGTGTCACTGCAGTTACGGGATGCCTGACACCTGCAAACCCGAGTTTTGGTTAACTTCCTTCCGCCTCTAGCCCGCATCTTTCCTGCGTGCTGGGCTACGAGGCCCCGGAATCCAATCCCACTTGCTGAGAAAAGAGGTGGAGTTGGAGGCCCCGGCGCTGCGCTTTCCGGGAAAAGTGGCCTCCAGCAGGCATGGGTGGCTTGGGATGGCCTGGGTGGGGAACTAGGCCTGGAAGGCACAGTTTAACCCTAACCGTGGAGAATTGTTCTGCTGGCCCCTGGCAAGGGAGACACGAGATAAAATGAGCGGCCCTGCTTTTACCATTGCCTCGCCAGTCCAAGGGAGGCGAGATCCTAGATCTTACTGCCCCACTGCAGTCCAGTGGGACACGGGAGGATCTCTGGGAGGACCGAGCCCAAGGGCCAGGAGCCCGAGGCCAAGGTGCGGGTTAAGCCTGCTACTCCCAGATCCCTGCCTCGCTCAAGGTTGTGTCGCTGTGCTTTGTGTGCGTCCGTTTGTCTGTCTCCCCAG
Seq C2 exon
CCTCTGAGAAGGCCCTCCTGCGCGATTCCTCCCCTGCGTCCGGCACAGACCGCGACTCCCCGGACCCTCTGCTCAAGGCTGACCCCGACCACAAGGAGCTGGACTCCAAGAGCCCGGACGAGATCATTCTGGAAGAGAGCGACTCGGAGGAAGGCAAAAAAGAAGGCGAGGCGGTGCCTGGCGCGGCCGGGACGACAGTAGGGGCGACTGCGGCGACACCGGGCTCAGAGGACTGGAAGGCGGGCGCCGACAGTCCCGAGAAGAAGCCGGCGTGCCGCAAAAAGAAGACGCGCACCGTCTTCTCCCGCAGCCAGGTCTTCCAGCTCGAGTCCACCTTCGACATGAAGCGCTACCTGAGCAGCTCGGAGCGCGCCGGCCTGGCCGCGTCGCTTCACCTCACCGAGACGCAGGTCAAGATCTGGTTCCAGAATCGCCGCAACAAGTGGAAGCGACAGCTGGCGGCCGAGCTGGAGGCGGCCAACCTGAGCCACGCCGCTGCGCAGCGCATCGTGCGCGTGCCCATCCTCTACCACGAGAACTCTGCGGCCGAGGGGGCGGCGGCGGCCGCAGGGGCCCCGGTGCCGGTCAGCCAGCCGCTGCTCACCTTCCCGCACCCTGTCTACTACTCGCACCCGGTGGTCTCGTCTGTGCCGCTGCTACGGCCGGTGTGAGACGGGAGAGGGGAGAGGGAATGAGCACCCGGCCACCTTTCGGGGATCCCGGAGGAGACTGGGCCGGGCCGAGGGTGCCGGGCTGTGGCCAGCGACCTTGGGCTCACTGCCTTGCCTCCCACCCCCCAATAGCATTTTGTAAGTATTTGCAATGCATTTTCGTGCAATTCATTCCTATGAATTTGAGGCGCTTCTCCTCTTATTTTTGGTTTTGCTTTCCATTAAGAGAAAACGAGGTGGGGTTGGGAGGGAACGACAAAATAACCAGGTCAAAACTTCCAATTGAAAGTT
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000020637:ENSRNOT00000028007:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.649 A=NA C2=0.439
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0004624=Homeobox=WD(100=25.4)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Human
(hg19)
No conservation detected
Chicken
(galGal4)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTGGTACCCCTACACCCTGAC
R:
CGGTGCGCGTCTTCTTTTTG
Band lengths:
350-953
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]