RnoINT0072288 @ rn6
Intron Retention
Gene
ENSRNOG00000006595 | Htr3a
Description
5-hydroxytryptamine receptor 3A [Source:RGD Symbol;Acc:61818]
Coordinates
chr8:53213929-53217282:-
Coord C1 exon
chr8:53217113-53217282
Coord A exon
chr8:53214090-53217112
Coord C2 exon
chr8:53213929-53214089
Length
3023 bp
Sequences
Splice sites
5' ss Seq
CCAGTGAGT
5' ss Score
8.28
3' ss Seq
CCTTTCGTCTTCTCTCTCAGTCC
3' ss Score
10.17
Exon sequences
Seq C1 exon
TGTGGACGTGGGGAAGTCTCCAAGCATTCCTTATGTGTATGTGCACCATCAAGGTGAAGTCCAGAACTACAAGCCCCTACAGCTGGTGACCGCCTGTAGCCTTGACATCTATAACTTCCCGTTCGATGTGCAGAACTGCTCTCTGACCTTCACCAGCTGGCTGCATACCA
Seq A exon
GTGAGTATGTGGGCTTGTGGGTGGGGCAGAGCTTGGGGCTCCTAGGGACCGGGGGCCTGGATTCATCTTCTCTTAACCAAGTCACCACTATTTCTTCCCTCCCTCCCTCCCCTCATCCATTTCTTTCATTTGTCTGGTTCCTTTGTGGTTCTGGGGATCTAACCTAAGTAAGACCTTGCACATGCTAGGCAAATACTCCACCACTGAGCAGATATATCTGCCTCTTGTCTTTTTAATGTCAATGAGCCTCTGTTTCCTCTTCCTCCAGATGGACTCAATATTGCTGTCCTCACTGCCTCCTTTAGTTGCTTCAAGGATTAATGAGGCTCTAAGGCACCCAGCAAGGGACAATTCTTACCTAGCTCCTCAAAGACCTGACAGGAAGTGTGTCCCAGATCCACCCACTCCTCTTCAGTCCTGGGTCAAGCCACTACCTCTGCCCAGGTGTCCTCATTCCCTTCCTTCCCTGGTCCTCCCCATGCACCAGCCCCACTGTGGGTTCACGTTCCCACAGCCAGGGAGCTCTTATTAAAATGCAAATCTGATCATGTCATTTAAAGCCCTCAATGGCTTCCCAGCAGTCCTGGGACCCAATCCAAATCCTTGACCTGGTCCTGCCCACAGTGTTCCACAGCAGTTTCATCTGGTGCGTGCCAGCCCAGCTGTCTTCCTCTGGACGCTGCGAGGTCCTGCCTGTTCTTTTTATTATAGGCTGTCTCCTCTCCTAGGCTACACACTTCTCCTCCTGCTTGCCGCACCCCAGCCACAGCCTGGTCAACAACTCCAGTCACCTGGTTATGCCACAGGGCTCATCAGCTCCTGGAAGGCCCTTCCATGGCTCCCTAAACTAGCTGTCTCCCAGGCAGCAGTTAAAAACCGTGCGTTTTCTTACAGACTTCATCTCTTGACAATACTTGTTCAGTCCGTGTCTAATTTTCTCATGGATATAATTTCAGAGGAATGGGAACGTGGTTTCTGGTTCACTCTTAGACTCTCCAGCACAGTGTCTGGTCCTGAGGGTTTTTTTTTTTTTTTCAGAGCTGAGGACCGAACCCAGGGCCTTGCGCTTGCTAGGCAAGCGCTCTACCACTGAGCTAAATCCCCAACCCCGGTCCTGAGGGTTTTTATTGAGTGCATACATGCCAGGCACACTGCTGGACTATAGCAAGACAGTCCTTCCTTCTCTGACCTATTCGTTACATTAAACTTCAATTATGGGGGCCGGAAAGATAGTTCGCTCTTCCAGAGGACCCAGGTCCAGTTCCCACCACACCACAGGATAGCTTTCAACTGCTTGTAACTCTAGTCCCATAGAATATAATGCCTTTTTCTGGCCTCCACAGGATGGATGGATATATATATATATATATATATATATATATATATATACATATATATAAATATATAAAGAATACAACATGACATGATAGAGTCTTCCAGTCCCTTCTCTTTGCATCTCCACCCACATACATGTGCATGCACACACATGTGCTACTATGAAGAGCACATATTGCATACACTATCATATAGGGCTACTTGACCTTTTTTTACTGACAATGAGTCCCTGACCCTTTTCCAACTTAGCGTATATGAGTTCTTCCTCATAAACTTTAACTGCAATAGACTCAAGTAGGTGTATCGTTGGACACCTAGTATTTTATTCACCAATGGACAGTTAGATCTTTTCCTTTATTTTCTTTGAGGTGTGTGTGTGTGTATGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTTCATGTACATGGTGCTTATATATGTGGGGATCAGAGATCAGCCCAGGGTGTCTTCCTCAGCTGTTTTTCATCTTGTCTTTTTAGGGAGGATTTCTCACTTTTCCCCTGTACTTGCCGATGAGGCTAGGCTGGCTGGCCAGTGAGCCCGAGGGACTCCATTGTCTTTACCTCTCCAGAACTGGACAAGTGTGCTCCGCCACACCCAGATTTCTTGTGTGACTTTTGGGGATCAAATTGAGGTCTCATGCTTGAATAGCAGAAACTTTACTCACAGAACCGTTTCCTCAGCTCTTCTTCTACTTAAAAAAATTTATTTAGTTTACTTTTTGTGTATGAATGTTTTGCTTGCATGTATATACCTGCACCCTGTGTGTTCCTGGTTTCCATGGAAATCGGAAAAGGACATCGGATCCTCTGGAACTGGAGTTACACATAGTTGCAAGCTTCTATGTAGGTGTGCGGAACCAAACCCAGATCCTCTGGAAGAGCAACAAGTGCTCTTAACTGTTGAACTATTTCTCTACTGGCCACACCAACACTTTTTGGCTTTGAACTCAATATATGAGTTCAGACTGGCCTCCTAGATTGGTCTCCTGGAAATCCTCCTGGCTCCCACGTACTGAGATTATAGGCATGTGCTGATAAGCCTGGCAGGATATTTAGATCTTTTGGCTCGATGGACATTATTGTGTTTCCAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGTAGATGGTAGATGGGTAGATGGGTAGATGGGTAGATAGGTGGATATGTGGATAGGTGTATAGGGAGATTGATAGATTGATGATTAAGATATATAGGAGAATTTATTTTCTTAGTTATTCAAAGACAGGTAGTTAGTTCTATGAAGGCAGAGGTAAAAATCATTGTGCTCTATTCATTTTCTAGATGCAAAATTCTAACAAAGAAACATAGAAGGCTGTTTGGAAGGTATGTGTAAACAAGTGAGAGACAGAGAGAGACAGCATCTGATGGATGCTTCCTCTGGTTCTTTGCACTGTGCTCTCACTATAGGCTTGCGAGAAGACAAAATGTGTTCTATCACCCCCTGTATGGCTCAGGAAACCAGGACTGAGAGTTAAGGGCTGAGTCTGCGGTCTAGAGATCTGACGACAGGGTTCCTTGGGTACTGTCTACCCTACACACCTACCTTCCACACTCAAAGGTTCTATGATTGAGATTCCAAAGCTTGTTTGGCCTTTCGTCTTCTCTCTCAG
Seq C2 exon
TCCAGGACATCAACATTTCCCTGTGGCGAACACCAGAAGAAGTGAGGTCGGACAAGAGCATCTTCATAAATCAGGGCGAGTGGGAGCTGCTGGGGGTGTTCACCAAATTTCAGGAGTTCAGTATAGAAACCAGTAACAGCTATGCGGAAATGAAGTTCTAC
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000006595:ENSRNOT00000008965:5
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(27.3=100)
A:
NA
C2:
PF0293118=Neur_chan_LBD=FE(25.4=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal4)
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]