Gene loci information

Transcript annotation

  • This transcript has been annotated as CTL-like protein 1.

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_2 g8427 g8427.t6 TSS g8427.t6 30409777 30409777
chr_2 g8427 g8427.t6 isoform g8427.t6 30410755 30411718
chr_2 g8427 g8427.t6 exon g8427.t6.exon1 30410755 30411245
chr_2 g8427 g8427.t6 cds g8427.t6.CDS1 30410776 30411245
chr_2 g8427 g8427.t6 exon g8427.t6.exon2 30411304 30411718
chr_2 g8427 g8427.t6 cds g8427.t6.CDS2 30411304 30411718
chr_2 g8427 g8427.t6 TTS g8427.t6 NA NA

Sequences

>g8427.t6 Gene=g8427 Length=906
TATTGTCGATATGATTTTGATATGAACAAATTGACTAGAGCAAGTGATAATGATGAGTTA
ATTTTCCATCTAACTGGACCTTGCCCAACATTGCCAGTTTATGAAAGTGATCCTGTTTTT
CATCGATGTATTCCAACTGGAAAAAATGCACCAATCAAAGAGGCTCAAGAATTATTCAAT
GTAGTTTCAGGTTGGGACTTTGTAGAAAAAACTGCACACGATTTATACAAATCTTGGCAT
GTGATTGCTCTCGTTTGTGGTTTGAGTTTAATTTTTTCAATCATTCTCATCGGATTACTT
CACTACCTTACACAAATTATTTCTTGGCTGATTTGCATTTTTGTTGGAGTTGCTAGCATT
GCCATTACTATTTTATTATGGTACACATATTTTGAAATTAAGAAGAAGAAAGATTCATCC
GAACTATCTCAACTTGCTCAATATCTTCAAAATGAAACTGCTGTATATGTCTTTGCCATC
ATTGCTACAATCGTCATGATAATTTTGATTGTCGTCATCTACTTCATGTCATCAAAGTTT
TCAGGGTTGGCAGCATTATTTGAAGAAGCTGGCAAATGCATTTACTCGATGCCACAAATA
TTTGGACCACCACTTCTTGCATTCATCGCACTCATGATTTTCTTTGCATTTTGGGTCACA
GTTGTTGTTTGTCTTGCAACTGCAGCAATTCCTGGATTCAAACCAATTTTAGATGTGACA
AATCCTCAAGAAAATATTCCAAAAGATCCAAAGAATGGCGCTGATTTACAAAAAACTTTC
AAACTCGTTGAATATCAAGAAGTTGACTATACAAGATACATGCTTTACATCTACCTCGTT
GCACTCGTCTGGGTTTCTGAGTTTATTTTTGCTGCTTCTCAATTATGTCTTGCCGGTGCT
GTTGCA

>g8427.t6 Gene=g8427 Length=295
MNKLTRASDNDELIFHLTGPCPTLPVYESDPVFHRCIPTGKNAPIKEAQELFNVVSGWDF
VEKTAHDLYKSWHVIALVCGLSLIFSIILIGLLHYLTQIISWLICIFVGVASIAITILLW
YTYFEIKKKKDSSELSQLAQYLQNETAVYVFAIIATIVMIILIVVIYFMSSKFSGLAALF
EEAGKCIYSMPQIFGPPLLAFIALMIFFAFWVTVVVCLATAAIPGFKPILDVTNPQENIP
KDPKNGADLQKTFKLVEYQEVDYTRYMLYIYLVALVWVSEFIFAASQLCLAGAVA

Protein features from InterProScan

Transcript Database ID Name Start End E.value
2 g8427.t6 PANTHER PTHR12385:SF12 SOLUTE CARRIER FAMILY 44 MEMBER 1A-RELATED 12 295 2.1E-76
3 g8427.t6 PANTHER PTHR12385 CHOLINE TRANSPORTER-LIKE (SLC FAMILY 44) 12 295 2.1E-76
1 g8427.t6 Pfam PF04515 Plasma-membrane choline transporter 153 295 2.1E-20
9 g8427.t6 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 71 -
18 g8427.t6 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 72 93 -
12 g8427.t6 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 94 98 -
19 g8427.t6 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 99 126 -
11 g8427.t6 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 127 146 -
17 g8427.t6 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 147 169 -
14 g8427.t6 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 170 197 -
16 g8427.t6 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 198 223 -
10 g8427.t6 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 224 267 -
15 g8427.t6 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 268 294 -
13 g8427.t6 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 295 295 -
5 g8427.t6 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 72 94 -
7 g8427.t6 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 99 121 -
6 g8427.t6 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 147 169 -
4 g8427.t6 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 197 219 -
8 g8427.t6 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 268 290 -

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.

Raw TPM values