RnoINT0071336 @ rn6
Intron Retention
Gene
ENSRNOG00000009154 | Hmx1
Description
H6 family homeobox 1 [Source:RGD Symbol;Acc:1304928]
Coordinates
chr14:80541075-80544342:-
Coord C1 exon
chr14:80543967-80544342
Coord A exon
chr14:80541701-80543966
Coord C2 exon
chr14:80541075-80541700
Length
2266 bp
Sequences
Splice sites
5' ss Seq
ACAGTGAGT
5' ss Score
8.34
3' ss Seq
TGCCTATTTCTCCCCTGCAGCAA
3' ss Score
10.83
Exon sequences
Seq C1 exon
ATGCCGGATGAGCTGACCGAGCCCGGGCGTGCCACGCCGGCTCGCGCCTCCTCCTTCCTCATAGAGAACCTGCTGGCAGCCGAGGCCAAGGGCTCGGGGCGCGCAGCCCAGGGCGATGGCGTCCGCGAGGAAGAGGAGGAAGACGACGACGACCCTGAGGACGAGGATCCGGAGCAGGCCCGACGACGACGACTACAGCGGCGGCGACAGCAGCGCGCAGGCAGCGGGCCGGGCGGAGAGGCGAGGGCCCGAGCGCTGGGCCTAGGGCCCCGGCCGCCTCCCGGGCCCGGGCCGCCCTTCGCTCTCGGCTGCGGAGGCGCGACGCGGTGGTACCCACGGGCGCAGGGCGGCTACGGAGGTGGTCTGAGTCCTGACA
Seq A exon
GTGAGTGAGGGTGCGGGAAAGGGGTGGGCAATGGGCAGGACTCTGCTCCCTCTCTGCGCATTCTGTTGGTGACACCGGCCTTGTGAGTCCCTAGTCTTCCTGTGTACCGGGATCTGGGTGGTATGAGACCCCTATGGAACGCCAGCGCGGGAGACCAGGAATGGCGCTGCATGCGGGAAGCAACTAAGGCGCGGATTAGGGCTTGAGAACACGAAAATTCGGACAGGAGAGAGGAGAGCGAAATAGGCCTCCGGAAGATGAGAGAGGGAGGAAGGTGAGGGAGTGCGTTGAGAGAAACAAGGAAGGTGAAAGAGAAGTGTGGGAAGAGGAAGAGTGGCAAAGGAGGGGAGTGGGGTCAAGCACTAAAATAAAAGGGGGCTGAACTGAGGGGCCACAGTTGTGGAGGCTGGATGGGAGACCTTCTATAGCGATTGCGATTGCGACCCCCAAAATATCCTTTGCTTTCTCTGCTGCAGTATGAGCCTGGGCTGGCCCTGGGCCTTCCTTTGGGTCTTCTCAGGCCCAGAGACTGAGGTTGGTAGGAGCCCACTCCGAAGGGTCCATCCCACCCCTCTCTTCATTTCTTGCCCCTCCCCCCTCCTTGGCCTTTGTTTCCTATAGCGGGTTTAGAGAATAGGGGTGTGGGCTTCCTCAGTCCCAAAACGCACTTACCCCTCTAGACTGGACATCCTGACTCTGACTGTCTGTTTTCAGAGGGTCCAGACCTCACCTCTCTTAGGAGCTGCTCTTTAGAGAGCAACCCTGGAGACTAGAAGCATATTTTAACCTTCCTCACCTCAGCCCCTTTTGCCAGCCTGCCCCTAAACACACAGACTTCTACAAAACTAAAGATTGCCCACCGAGGCGCCGGGAGCCATCTGTATGTAAGCTTTGGTGTAGAATGTGGCCTGGGACCATTCTTTTCTGTTATCTACCCACCCCCTTCCTGGTATAGAGTAGGACAAGTCTCCCAGCCTATGTTTGGAATGTCTGTCTTCTTTACATAAACTTAAACAGAGTCCAGTAGTATCCTGAAATCCAATGAAAGGCTCGTGCGGGGCCATTTTATTCTCCCTTCTACTTGGGCCATCCTCACCTGTAGTCCACTGGTCACCTCCCACAGAGGTGGCTCCTCTTTATTTCGTGCCATGCGGGTTAGAGTTCTCTGTTCCAGGTGAGTCAGGCGAGCAGGTGAGTCAGATTAGCACTTTGTGGCAACACATGGACCTCCATGACTGTAGGGGCTTGTGGGACCTCCCCGCTGATCTGGCTACATAAATACCACCCCGCTAGGTGACTTTGCATGGGCATTGAGCACAGAACATGGAGGCTGAGCACAATTCGGGATGCTTTCAAGGAAACCTGGCAGAGTTTAGCTGTACATACAAGTCCACCGTGCTGAGGCATAACCTGGGCCAAAATCCACCTTGACCACTGTCTGATCCATTAGTCAGGCAGAGGGACAGGCTGGCCTGAATCGGTTTCATGGGCCTGGATGTCTAGAGGAGAACCAGGAGCCCATAGGAGCCTCTTTAACCTGGTGAGATCCCTTGTCAGCCCTGAGCTTGGGACTTGGAGCATGAGCCCAGAGGTCCTCTGTGGGCAATGTGTAGGAGATGCTTGGGGCAGGGTAGGGATGCTGTGGTGTATAGAACAGCCTTCCTTCCGTAGCTTTGCTGCTGCACTTTGCTGCTGCAGAGGGCCTCCCTCTGAGGGTGCCTGGGTCAGGGTTGTGCCAGTGTGACCCGGCAGTGTTTCTTCAGGGAATGTGCATTCATGTCTCCTAAGAGTTCTTTTCTTAGTGTCTGCTCCCCGGTGCGTGATGGGGAGGGCTTGACTCCTAGCTGATAGGTTGAATGTCAGTCTCTGTGTGTACATAACTTCGAAGGACATCGTTTCTTTTGTCCCGGGCCTCTGCCAGCCTTTTGTGAGATCGTGGGGGTGGGGGTAGGGGGGCTGAGGTACAGCTGAGCCAGGGGCAATCTCAGATGTCAGTTTGTCTTTTAGGTTAGCATTTTTTCTCTGTGTCCTTCTCTGGGTGTGTGCTGCCACGTGTTTGCCACAGCCCGGGTTTCACCTTCGGCCTCTGCTACTTTCCTCCACACCCCCCCCCGCCCCCGCAGTGGTGGATTTTCCCCAACTCCTACGCGGGGAATATTTGCCAGCTTGTAACATTGTGGGTGAGGAGGATTTGGAGGTGGGAGGAGGCCAGTCTCAGTGACTCTGACCCTTAGAGCCCACCACTATGCCTATTTCTCCCCTGCAG
Seq C2 exon
CAAGCGACCGGGACTCTCCGGAGACCGGCGAGGATATGGGCCGCGCAGAGAGCGCCTGGCCGCGGTGCCCGGGGCCGGGAGCCGTTCCGCGGGAGGTGACGACGCAGGGCCCGGCTGCCGGCGGGGAGGAAGCGGCGGAGTTGGCCGAGGCTCCGGCGGTGGCAGCCGCTGCGGCAGGGGAGGCACGCGGCGGTCGCAGGAAGAAGACGCGCACGGTCTTCTCGCGCAGCCAGGTCTTCCAGCTCGAGTCCACTTTCGATCTGAAACGCTACCTGAGCAGCGCGGAGCGCGCAGGCCTCGCCGCCTCGCTGCAACTCACGGAGACGCAGGTCAAGATCTGGTTTCAGAACCGCCGCAACAAGTGGAAGCGGCAGCTGGCGGCCGAGCTGGAGGCGGCTAGCCTGTCCCCGCCCGGCGCGCAGCGCCTGGTCCGCGTGCCGGTGCTCTACCACGAGAGTCCCCCGGCCGCCACGGGGCCCACGCTGCCCTTCCCGCTGGCTCCGCCTGCACCCGCGCCGCCGCCGCCGCTGCTCGGTTTCTCGGGCGCGCTTGCCTACCCGCTGGCCGCCTTCCCCGCCGCCGCCTCGGTGCCCTTCCTTCGCGCGCAGATGCCGGGGCTAGTGTGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000009154:ENSRNOT00000012304:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.992 A=NA C2=0.409
Domain overlap (PFAM):
C1:
PF086195=Nha1_C=PU(62.8=77.8)
A:
NA
C2:
PF086195=Nha1_C=PD(36.5=27.3),PF0004624=Homeobox=WD(100=27.3)
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:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]