RnoINT0072287 @ rn6
Intron Retention
Gene
ENSRNOG00000006595 | Htr3a
Description
5-hydroxytryptamine receptor 3A [Source:RGD Symbol;Acc:61818]
Coordinates
chr8:53217113-53219093:-
Coord C1 exon
chr8:53218984-53219093
Coord A exon
chr8:53217283-53218983
Coord C2 exon
chr8:53217113-53217282
Length
1701 bp
Sequences
Splice sites
5' ss Seq
GTTGTGAGT
5' ss Score
6.59
3' ss Seq
GATCCCTCTTCCCTGACCAGTGT
3' ss Score
7.68
Exon sequences
Seq C1 exon
TTCTGGACCGACGAGTTTCTACAGTGGACTCCTGAGGACTTCGACAATGTCACCAAATTGTCCATCCCCACCGACAGCATCTGGGTCCCTGACATCCTCATCAATGAGTT
Seq A exon
GTGAGTCCTTTTGTCAGAGCATAGCGGGCTGGGAGGCTATGGTTAGGGAAGCCAGGGACAGTGACAATTTCCTCTCTTGATCAAGTTCAAGCTCTCCTTGACGCAGTTCTCTCTTGTTCTTGATCACCCTCTCCCTTTCTTTCTGAACTGGATGCTACAACCTTATGCTTCTTAGTCCCAGGGACTCTAGCATAGGAACAGAAGCCAGTGAGTGATGTCACACCGAGTTCTAACAACTTAATGGAGACAGCTGCATTTGTCAGAGGGGACAGTTACATTTTTTTTTTTTTCTTTTTTGGAAAGGAGCAAAACTCTGATGACAGCCAATGCTTCTGGTCACAGAAAAGATTGGGAGCCAAGGAACATGTTCAAACCTCCCAAGCCACACGTGTGCCTAGCAGGCCACAGTTGGCACCTCTAGTATGAAGTGGGTCCCATTACCTTTTGTTCTCAGCAGCCCAACATTCTCCCATTGCCTTCAGCCAGCTGACTTTCTCTCCATTCTGCAAGTTCATCCAGGGTCCACCAACTGGACATCTGAGTGCAAAGGCAAGGAAAATGCATGGGGGAAAGACAGGACAGGGAGAGTAGGCTGGGGCTGTGATTCAGTTGGTAGAGTATTTGCATAGCACGCTCAGTGTCTGGCTTCCATGTCTAAACCCAATGTGGTGACACACCTATCATTTTAGCACTTGGGAGATGGAGGCAAGATTATTAGAAGTTCAAGGCCATTCTTGACTACATAGAAAGTCCAAGACCAGCCTGGACTACATGAAACCTTTTCTCAAACAACAACAACAACAACAACAACAACAACAACAACAACAACTACTACTACTATTACTACTAATGGAGGTGACAGAGGGATTCATTCAGTACTAACTGCACTGTCCAACTTTGACCCACCCTTGAATGCCCCACATGGCACAGGTGGCAAACATTCTAGAAATTTCTTTCTGCTCTTATCTTTCAGTCTACCCCCAAGAAGGCCAAAGGCCGGGGCTGGGGATTTTGCTCAGTGGTAGAGCGCTTGCCTAGGAAGCGCAAGGCCCTGGGTTCGGTCCCCAGCTCCAAAAAAAAAGAACCAAAAAAAAAAAAAAAAAAAAAGGCCAAAGGCCAGGCCCTGGGCTCAGTCTACCACATGCCTTAGAGTCCAGGCTCAGTAAAGACAATTCCTGTTGGATTTTCCTAGGCTCCTCTACTCCTCTTGAACTCTATGCTCTTCCCTCTGGAGATGATCGCTCTCATTCTGGGGGCTTCTAGAGATGGGAAGCAAAGCAAAAATCAGAGTCAGAACAGAACATATGATTCTTCTCTCCTATCAAACCACTGGCTCTTCTGGGAGCCAGCTCTACTCTAGTGCAGGCTGGTGTGCCAGCCTGGAGAGAGCTGGGCGAGCTCCCTTCAGCCAGTGGCATTACAATCCATGGGTTCCTTCTCTGCCTTTGAGAGCTAGGTTGCTAAGGGAGTTGAAGAAAAGAAACATCCCTCATTGTTTGGAGCACAACCTCAATAATGGTGGGTCAGAAAGCTAAGATTGATAACATTGGAAAACCATGGCCAGATAAAATGTCTGGATTATCTTGCTCTCTAGATCCTCCCTGAATTTCTTTCCCTATCGGGCTACTGAAGAGTTCTTTAGCCATCCATGGTGAGGGTCTGCCTCTTCAGCCTACAAATCGATCCCTCTTCCCTGACCAG
Seq C2 exon
TGTGGACGTGGGGAAGTCTCCAAGCATTCCTTATGTGTATGTGCACCATCAAGGTGAAGTCCAGAACTACAAGCCCCTACAGCTGGTGACCGCCTGTAGCCTTGACATCTATAACTTCCCGTTCGATGTGCAGAACTGCTCTCTGACCTTCACCAGCTGGCTGCATACCA
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000006595:ENSRNOT00000008965:4
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0293118=Neur_chan_LBD=FE(17.2=100)
A:
NA
C2:
PF0293118=Neur_chan_LBD=FE(27.3=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TTCTGGACCGACGAGTTTCTAC
R:
GTATGCAGCCAGCTGGTGAAG
Band lengths:
278-1979
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]