Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative CTL-like protein 2.

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 g9822 g9822.t4 isoform g9822.t4 5388476 5390512
chr_1 g9822 g9822.t4 exon g9822.t4.exon1 5388476 5388649
chr_1 g9822 g9822.t4 cds g9822.t4.CDS1 5388476 5388649
chr_1 g9822 g9822.t4 exon g9822.t4.exon2 5388936 5389045
chr_1 g9822 g9822.t4 cds g9822.t4.CDS2 5388936 5389045
chr_1 g9822 g9822.t4 exon g9822.t4.exon3 5389840 5390512
chr_1 g9822 g9822.t4 cds g9822.t4.CDS3 5389840 5390512
chr_1 g9822 g9822.t4 TSS g9822.t4 5390987 5390987
chr_1 g9822 g9822.t4 TTS g9822.t4 NA NA

Sequences

>g9822.t4 Gene=g9822 Length=957
ATGGACGACAGTGGAAAAGAATTGTTAAGAAATGATTCTAGAAGATTATCAACAATATCC
AATTCTAGAAGATTTTCTAATGTCTCTAACTCGAAAAGATTATCGATAGTGTCAGATTCA
AGAAGATTTTCAAGAAGTAATCACTTAAAAAGCACTTTATTAAAAATTCTAATTGCTTTT
TTATTTACAGGAGAGTCATTCCGCTATGATGGAGAGTTTCGTGGTCCTTTAGCGAACAGA
AGTTGCACTGATGTCATCTTTCTACTCATGTTTTTCATATTTTTAATCATCTTTGGTTTT
GCTGGTTATTATGCTCATCGTGAAGGTGATTTAAATAAATTATTGGTACCACGTGATACA
AAAGGCTGGCAATGCGGAAAAGACAGTGAAGTAGTGGACAAACCGAATTTATTTTTCTTT
GATTTATCAAAATGTGCTGATCCTTTGGTTCCAATTGAGGGTTGTCCAACACCGCAAGTA
TGCGTAAAAGAATGTCCAAAGACAAGCTTTTATCATGAAAGAGCTCAATGTGATCGTGAA
AAAATTCAAGTTTATCGACAAAAACTCATCTGTACATCTGAGATAGATTTGAATAATATC
ACAGATTGTAATGAGGTTGATAAATATGTTAAAGACAACAAATGTGCATTATGGTATTTA
CCATCAGAATCATTGAGCAATATATGTATCCCAGCGTCATTTCAAGATGTATGGCAAACA
ATAAATCGTTCAGAAGTTATTCAAGGTCTGCTTAATATTCAAATGATGGGCTCAATTAAT
GGAATCGGACAATTAATAGTTGAAGACACTATAAATTTATGGCCTGTTCTAGCCGGAGGA
TTCATCATTGCTGCAGTTTGTTCGCTGATTATTATTGCTATTATGAGATGGGTTGCTGGG
CCAATAGTATGGATATCAATAATTGGAGTTTTAGCATTATTAGGAATTGGTGAGTAG

>g9822.t4 Gene=g9822 Length=318
MDDSGKELLRNDSRRLSTISNSRRFSNVSNSKRLSIVSDSRRFSRSNHLKSTLLKILIAF
LFTGESFRYDGEFRGPLANRSCTDVIFLLMFFIFLIIFGFAGYYAHREGDLNKLLVPRDT
KGWQCGKDSEVVDKPNLFFFDLSKCADPLVPIEGCPTPQVCVKECPKTSFYHERAQCDRE
KIQVYRQKLICTSEIDLNNITDCNEVDKYVKDNKCALWYLPSESLSNICIPASFQDVWQT
INRSEVIQGLLNIQMMGSINGIGQLIVEDTINLWPVLAGGFIIAAVCSLIIIAIMRWVAG
PIVWISIIGVLALLGIGE

Protein features from InterProScan

Transcript Database ID Name Start End E.value
1 g9822.t4 PANTHER PTHR12385 CHOLINE TRANSPORTER-LIKE (SLC FAMILY 44) 65 317 3.5E-45
2 g9822.t4 PANTHER PTHR12385:SF90 CTL-LIKE PROTEIN 2 65 317 3.5E-45
9 g9822.t4 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 51 -
14 g9822.t4 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 52 69 -
11 g9822.t4 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 70 84 -
15 g9822.t4 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 85 105 -
8 g9822.t4 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 106 272 -
12 g9822.t4 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 273 295 -
10 g9822.t4 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 296 300 -
13 g9822.t4 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 301 317 -
7 g9822.t4 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 318 318 -
6 g9822.t4 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 51 68 -
5 g9822.t4 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 83 105 -
3 g9822.t4 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 273 295 -
4 g9822.t4 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 300 317 -

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:0055085 transmembrane transport BP
GO:0022857 transmembrane transporter 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