Gene loci information

Transcript annotation

  • This transcript has been annotated as hypothetical.

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 g10769 g10769.t2 isoform g10769.t2 11876369 11877478
chr_1 g10769 g10769.t2 exon g10769.t2.exon1 11876369 11877478
chr_1 g10769 g10769.t2 cds g10769.t2.CDS1 11876369 11877478
chr_1 g10769 g10769.t2 TSS g10769.t2 NA NA
chr_1 g10769 g10769.t2 TTS g10769.t2 NA NA

Sequences

>g10769.t2 Gene=g10769 Length=1110
ATGAATATTTTATCGCAAGAACTCAACTATACAAACAGTATTAAAATTATGGAAGGTGAC
CAACCATGGGGAGTAATATACAGCAACGGAACTGCAACAGGAGCTTTTCTTGAAGTTCTT
GAGAACAAGTCAGACATTGCATTTTGTGAATATTACTTAAAAACCAGTAGAAATCAATTT
TTCGACAGTAGCACAGTATTTTATAGTACACCGCTTATATTCGTCATACCAATGGGTCAA
AAATTGACAAATCTTGAAAAACTTTTGCAACCTTTCAATTGGTTTGTTTGGATAACTTTA
TCATCGACATTATTAATTGCTGTCATTATCATATTAATTATAAATCTTAAATTTAAGTCA
CATAAAGCATTTGTTTATGGCAGTAATGTTAAACATCCAATAATCAATATGATACTAGGA
ATTCTTGGAAATCAACAGACAGTATTGCCAAAAAGGAATTTTGCTCGATTTATTCTTATG
ATGTTTCTTATACTTTGTCTTGTTATGAGAAGTGTTTATCAAGGATCACTTTATCAATTT
CTACAATCTGATGGTAGGAGAAAAGAAGTGCAATCAATTCAAGAGATGATTGATAATGAT
TTTACTTTCTACATGTTTGAGTCTTCACTCGATCTTATTCAAACTCAAACGGAAATTTTA
AGCCGTACAAAAACCTTTAAAGGTGAAAATTTTATTATGAAACGTCCACTTGATGGCTCA
GAAAAGATTGCTAGTCTTGAAGCATTGAGTGATGTTCATGTTGCAAATACAGATCCTGAA
AGAGATTTCAAATTGAAAATATGCAAAGAGCCATTAATGACAATGAATCTTGTGATTTAC
TTTCGAAAAAGCTTTTATTTAATTGATGAAATTAACAAGAAAATTACAGTTCTTATCTCG
TCAGGAATAATTGATTATTGGCTAAGACGATCATTGGACGATTTTCGAGAAGTAAAAAAT
AATCATCCTCGAAAGCTGAATATTGATGATCTTACTGGTCCATTTAATCTTTTAATTATT
GGTCATTTAACATCATTAATAATTTTCTTAATTGAAATCTTCATTTATAAAATGACATTA
AAAATTCAATTGATTAGGCCTATATACTAA

>g10769.t2 Gene=g10769 Length=369
MNILSQELNYTNSIKIMEGDQPWGVIYSNGTATGAFLEVLENKSDIAFCEYYLKTSRNQF
FDSSTVFYSTPLIFVIPMGQKLTNLEKLLQPFNWFVWITLSSTLLIAVIIILIINLKFKS
HKAFVYGSNVKHPIINMILGILGNQQTVLPKRNFARFILMMFLILCLVMRSVYQGSLYQF
LQSDGRRKEVQSIQEMIDNDFTFYMFESSLDLIQTQTEILSRTKTFKGENFIMKRPLDGS
EKIASLEALSDVHVANTDPERDFKLKICKEPLMTMNLVIYFRKSFYLIDEINKKITVLIS
SGIIDYWLRRSLDDFREVKNNHPRKLNIDDLTGPFNLLIIGHLTSLIIFLIEIFIYKMTL
KIQLIRPIY

Protein features from InterProScan

Transcript Database ID Name Start End E.value
11 g10769.t2 Gene3D G3DSA:3.40.190.10 - 2 324 4.9E-36
10 g10769.t2 Gene3D G3DSA:3.40.190.10 - 71 277 4.9E-36
9 g10769.t2 Gene3D G3DSA:1.10.287.70 - 81 352 4.9E-36
2 g10769.t2 PANTHER PTHR42643:SF16 IONOTROPIC RECEPTOR 11A-RELATED 1 359 5.4E-54
3 g10769.t2 PANTHER PTHR42643 IONOTROPIC RECEPTOR 20A-RELATED 1 359 5.4E-54
1 g10769.t2 Pfam PF00060 Ligand-gated ion channel 96 341 1.1E-8
13 g10769.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 59 -
24 g10769.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 60 79 -
18 g10769.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 80 93 -
21 g10769.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 94 116 -
12 g10769.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 117 122 -
20 g10769.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 123 142 -
16 g10769.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 143 153 -
23 g10769.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 154 173 -
14 g10769.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 174 290 -
19 g10769.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 291 308 -
17 g10769.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 309 334 -
22 g10769.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 335 356 -
15 g10769.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 357 369 -
8 g10769.t2 SUPERFAMILY SSF53850 Periplasmic binding protein-like II 2 313 8.91E-14
7 g10769.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 60 79 -
5 g10769.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 94 116 -
6 g10769.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 154 173 -
4 g10769.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 334 356 -

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:0016020 membrane CC
GO:0015276 ligand-gated ion channel 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. There were no conditions that were differentially expressed