Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative 5-hydroxytryptamine receptor 2A.

Parent gene

Gene structure

  • The exon-intron structure of all isoforms are indicated below. CDS regions are colored in green. TSS and TTs that were predicted with CTR-Seq data are indicated in solid circle and squares, respectively. More specific data are shown in the table below.

Chromosome Gene Transcript Category ID Start End
chr_1 g10381 g10381.t2 isoform g10381.t2 9342587 9344044
chr_1 g10381 g10381.t2 exon g10381.t2.exon1 9342587 9343742
chr_1 g10381 g10381.t2 cds g10381.t2.CDS1 9342587 9343742
chr_1 g10381 g10381.t2 exon g10381.t2.exon2 9344001 9344044
chr_1 g10381 g10381.t2 cds g10381.t2.CDS2 9344001 9344044
chr_1 g10381 g10381.t2 TSS g10381.t2 NA NA
chr_1 g10381 g10381.t2 TTS g10381.t2 NA NA

Sequences

>g10381.t2 Gene=g10381 Length=1200
ATGCTTAATCATGAAATTTTTATTATAGATTTTTTTCTACAAAACACAACAACAAACGTT
ACAGCTAATAATAGAAAAAGACTTCCTCAATTAACCAGAGTTACGACTAAACCACAAAAG
AGAAGAGCATCACTAAGTGTTTTCCACAATAAAAAATCCTCGACACGTCTTCGGCGTTCT
AATAGCATACAAACATTTGAACACGATGAACGTAGTGATAGTACAGATGGCAATTTTTTT
GATGAAATTAATCAACTGAAGCACAGTAACAAAAAGAAGAAACAAAAAAGTGGAAAGAAT
GACAGAGATACAATTTCATTAGAACTGCCACCTCCATGTACTTGTCCTTATTTTGGTGAT
AAACCATGCGCAATGGTAAAACCAACTGAAGTTAAAATCATAACAACATCCTCAAGCAAT
TATTTTGTACCAGAAAACAAACAACATCAATTTCATGACTCAAATCAATTTATCTCGTCA
TTATCGAGTAACAATTCCATATCAAATACGACATCAACTAATAGCTTGCCACTAGCACAG
GGTACAATTAAACGTGGACGACAAAATTATAGTACTAGCAGCAATAATGCTATAACAAAA
TGCACTTCTGTAGTAACATGGGACTCAAGGCGTTATCAAAGACGAGGATCTTCGATAAGT
GGTGCTAAAACAACACTCGTTCTGACACCTAACAAATCATCACTTGCAGCAACGCCACTT
CGTAGATCTGTTACGCTCCGTCATAATACAAACCTCAATTCAACCAATGATACAGAAAGT
ATTGCAGCGCACAAAGTTCCATCATCACCATGTATTCTTCAGAGAACTACAACAATTCGA
TCACATCATTCACGCAATTCAAGTGTTATTTCGCGAAATTCATCACGTCATGGACGCATC
ATCCGACTAGAGCAAAAAGCAACAAAAGTATTGGGTGTTGTTTTTTTCACTTTTGTGATT
TTATGGGCACCTTTTTTTGTACTGAATCTTCTACCTACTGTATGTCCAGACTGTGAATCG
AATATAAGCCACGGAGTTTTTGATTTCGTTACATGGCTCGGTTACGCTTCTTCAATGGTT
AATCCAATTTTTTATACAATCTTCAATAAGGTATTTCGACAGGCATTCAAAAAAGTTTTG
CTGTGTCGCTATAAGAGTAAAGTTATATGGCGTCCCTTACCAATAAACCAACATCGGTAG

>g10381.t2 Gene=g10381 Length=399
MLNHEIFIIDFFLQNTTTNVTANNRKRLPQLTRVTTKPQKRRASLSVFHNKKSSTRLRRS
NSIQTFEHDERSDSTDGNFFDEINQLKHSNKKKKQKSGKNDRDTISLELPPPCTCPYFGD
KPCAMVKPTEVKIITTSSSNYFVPENKQHQFHDSNQFISSLSSNNSISNTTSTNSLPLAQ
GTIKRGRQNYSTSSNNAITKCTSVVTWDSRRYQRRGSSISGAKTTLVLTPNKSSLAATPL
RRSVTLRHNTNLNSTNDTESIAAHKVPSSPCILQRTTTIRSHHSRNSSVISRNSSRHGRI
IRLEQKATKVLGVVFFTFVILWAPFFVLNLLPTVCPDCESNISHGVFDFVTWLGYASSMV
NPIFYTIFNKVFRQAFKKVLLCRYKSKVIWRPLPINQHR

Protein features from InterProScan

Transcript Database ID Name Start End E.value
8 g10381.t2 Gene3D G3DSA:1.20.120.10 - 210 298 1.2E-31
7 g10381.t2 Gene3D G3DSA:1.20.1070.10 - 299 377 1.2E-31
16 g10381.t2 MobiDBLite mobidb-lite consensus disorder prediction 51 71 -
17 g10381.t2 MobiDBLite mobidb-lite consensus disorder prediction 86 105 -
2 g10381.t2 PANTHER PTHR24247:SF228 5-HYDROXYTRYPTAMINE (SEROTONIN) RECEPTOR 2A, ISOFORM B 239 388 1.6E-35
3 g10381.t2 PANTHER PTHR24247 5-HYDROXYTRYPTAMINE RECEPTOR 239 388 1.6E-35
5 g10381.t2 PRINTS PR00237 Rhodopsin-like GPCR superfamily signature 307 331 2.8E-11
4 g10381.t2 PRINTS PR00237 Rhodopsin-like GPCR superfamily signature 347 373 2.8E-11
1 g10381.t2 Pfam PF00001 7 transmembrane receptor (rhodopsin family) 131 365 2.1E-16
9 g10381.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 309 -
13 g10381.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 310 329 -
11 g10381.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 330 348 -
12 g10381.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 349 368 -
10 g10381.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 369 399 -
18 g10381.t2 ProSiteProfiles PS50262 G-protein coupled receptors family 1 profile. 290 365 11.806
6 g10381.t2 SUPERFAMILY SSF81321 Family A G protein-coupled receptor-like 278 387 9.06E-23
15 g10381.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 312 334 -
14 g10381.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 349 368 -

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

GO terms from InterProScan

GOID TERM ONTOLOGY
GO:0007186 G protein-coupled receptor signaling pathway BP
GO:0016021 integral component of membrane CC
GO:0004930 G protein-coupled receptor activity MF

KEGG

Orthology

This gene did not have any KEGG ortholog annotations (KAAS, GHOSTZ).

Expression

Transcript expression in Pv11 cells

TPM values are indicated as average +/- STDEV.

Differential expression

Differentially expressed genes were identified with DESeq2 using the ‘run_DE_analysis.pl’ script from Trinity. Transcripts were determined as differentially expressed when (1) FDR < 0.05 (2) fold change > 2 (TPM calculated by RSEM). DE information and fold change between conditions are indicated in the plot below.

Raw TPM values