BtaINT0073935 @ bosTau6
Intron Retention
Gene
ENSBTAG00000010791 | HTR3A
Description
Bos taurus 5-hydroxytryptamine (serotonin) receptor 3A (HTR3A), mRNA. [Source:RefSeq mRNA;Acc:NM_001193169]
Coordinates
chr15:24843919-24845612:+
Coord C1 exon
chr15:24843919-24844028
Coord A exon
chr15:24844029-24845442
Coord C2 exon
chr15:24845443-24845612
Length
1414 bp
Sequences
Splice sites
5' ss Seq
GTTGTGAGT
5' ss Score
6.59
3' ss Seq
CACCCCTCTTCCCTGGCCAGTGT
3' ss Score
7.84
Exon sequences
Seq C1 exon
TACTGGACAGATGAGTTTCTCCAGTGGGACCCTGAGGACTTTGACAACATCACCAAATTGTCCATCCCCACAGACAGCATCTGGGTCCCAGACATCCTTATCAATGAGTT
Seq A exon
GTGAGTACTGTCATCAGACGCGTGGCAGCCAGGGGCGGCGGGGGCGGGGGGGGGGGCGGTGCTGGGGACGGCAGGGGGTCAGGAGACAAGATCACTGCTGTTGTATTTGAGATGCTCCACCAGACCTGCAGAAATGGAGGTAAAGTTGCATTGGGCCCTCGTTCCCCTTTATCTTTTTCTCCCTTTTCTTTTAAAAACTCCCCTTTTTCTATGTCTGATGCTGAAACTTTGCTCTTCTCCTTGACCCAAGGATCCCTTTCCAGGGAGAAAGGAGGCCAGTGAATGAATCCACATTGTCATAATAGTCTAGTGGGGAACAGTGTTTTTAAAGGGGACAGGAATATTTCTGAAAGGAATAAAGTGCCAGCGATGGTTGGCAGAGGAGACTTGGGGCCAGGAGACACTCAAACTTTCAAGCCACACATGTGCCTGAGTGGGCACAGATTGCACCCTGGGATGAAGTAGGTCCCACCAGCCTTTATTCCCAGCAGCCAACATTCCTTCTCCCCATCCCTCAGGCTCCACTGCCTGGGCTTCTGAATCCAAGGTCTGGGAAGATGGCTGGGGAGACAGATGGAAGGAGAAGGTGGTGGGGGCCAGCTGTCCTCCACCCAGTACCCACTGCATTGCCCATGTCCAGGGGGTTCTGCTCACAATTCAGGGAGGCAGCTGACTGAGAGCCTCACTCCCTGCAGAGCTGAGTCTGGAGGGACTGGGGATCTCTAGTTTCAGGCTGGATCTCCATTTTCAACACTGAAGTAGCCTTGGCCTTGACTTCTTGTCTCTCAGCCTGATGCCACAGAAGGCCACAGGCTCAGGACCCCAGGCTTAGCTCCAGGGCTCCCTTGGGGGAGCTCGGCCTGGGGTCTGCCCAAAGAGAGTGGGATGAGCTCATACAGGACTTTGTTACTTGCCCTAATTCTTCTCAATGATTTTTCCAGTTCTGTTCCCACCCCCACCCCTGGAAATGATTGTTTTAATTTCAAGGATTCCTAGGGATGGAACCCAAGGGTCTGCTCTCCCACCAAGCCTGCCTGTTGCCACCAGGCGGTCGATCCTGGGAACTGAGCTCTGCCCATCCCGGGTGGGCGGCATGTGGGGGACAGCTGGGTGTTCTTCTTATGGCCTGGGGCTTTGGGGTCCATGGACTCCTGGCTTGCATTTTGTGGCTAGGTTGCCAGGGGAATAAAGGAGAAATGCTCTTTAACTGCTTGAAAAGTGGCCTTGGCGATGGCAGGTAAGGAAGCCTAAGATAAGAAGCTTAGACACGCCGAGGCCAGACAAAACTGCCAGGTTGTCCTGTTGTCTGGACCCTCTCTGCATCTCTTCCCCTGCCGAGCTGCTCAGAGACCTTCTGACATCCAGGGCTTGGCCTGCTTCTTGAGCCCCAAACCCACCCCTCTTCCCTGGCCAG
Seq C2 exon
TGTGGACGTGGGGAAGTCTCCAAACATCCCGTATGTCTATGTCCGGCATCACGGCGAGGTCCAGAACTACAAGCCCCTCCAGGTGATGACCGCCTGTACCCTGGACATCTACAACTTCCCCTTCGACATACAGAACTGCTCGCTGACCTTCACCAGCTGGCTGCACACCA
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000010791:ENSBTAT00000014292:4
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
Rat
(rn6)
No conservation detected
Chicken
(galGal4)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TACTGGACAGATGAGTTTCTCCAGT
R:
GTGTGCAGCCAGCTGGTG
Band lengths:
278-1692
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development