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.t5 TSS g8427.t5 30409777 30409777
chr_2 g8427 g8427.t5 isoform g8427.t5 30410473 30413248
chr_2 g8427 g8427.t5 exon g8427.t5.exon1 30410473 30411245
chr_2 g8427 g8427.t5 cds g8427.t5.CDS1 30410776 30411245
chr_2 g8427 g8427.t5 exon g8427.t5.exon2 30411304 30411723
chr_2 g8427 g8427.t5 cds g8427.t5.CDS2 30411304 30411723
chr_2 g8427 g8427.t5 exon g8427.t5.exon3 30411789 30411922
chr_2 g8427 g8427.t5 cds g8427.t5.CDS3 30411789 30411922
chr_2 g8427 g8427.t5 exon g8427.t5.exon4 30412115 30412426
chr_2 g8427 g8427.t5 cds g8427.t5.CDS4 30412115 30412128
chr_2 g8427 g8427.t5 exon g8427.t5.exon5 30412484 30413248
chr_2 g8427 g8427.t5 TTS g8427.t5 30413247 30413247

Sequences

>g8427.t5 Gene=g8427 Length=2404
ATCGTTATTGCTGCTTTTGCTTTTGTATATGGAAATCCACAACGCATAATCAACGGCTAT
GATTCATTCGGTAATACGTGTGGTGTTTCTGATAATAAAAATTATGCAGACATCTCTTAT
GGAAAGGCAGCCGGTATTGATACAAGTGATAAGAAGTTTGTTTATTTCTTCAACATAAAG
GAAATTAAAAAGTCATTAAAAATTTGTGTAAAACAATGCCCATCAAAACAGCTAAATACT
TCCGTTCAATTATATGATTATTATAGAGAAAAGGATACAAGCTATTGTCGATATGATTTT
GATATGAACAAATTGACTAGAGCAAGTGATAATGATGAGTTAATTTTCCATCTAACTGGA
CCTTGCCCAACATTGCCAGTTTATGAAAGTGATCCTGTTTTTCATCGATGTATTCCAACT
GGAAAAAATGCACCAATCAAAGAGGCTCAAGAATTATTCAATGTAGTTTCAGGTTGGGAC
TTTGTAGAAAAAACTGCACACGATTTATACAAATCTTGGCATGTGATTGCTCTCGTTTGT
GGTTTGAGTTTAATTTTTTCAATCATTCTCATCGGATTACTTCACTACCTTACACAAATT
ATTTCTTGGCTGATTTGCATTTTTGTTGGAGTTGCTAGCATTGCCATTACTATTTTATTA
TGGTACACATATTTTGAAATTAAGAAGAAGAAAGATTCATCCGAACTATCTCAACTTGCT
CAATATCTTCAAAATGAAACTGCTGTATATGTCTTTGCCATCATTGCTACAATCGTCATG
ATAATTTTGATTGTCGTCATCTACTTCATGTCATCAAAGTTTTCAGGGTTGGCAGCATTA
TTTGAAGAAGCTGGCAAATGCATTTACTCGATGCCACAAATATTTGGACCACCACTTCTT
GCATTCATCGCACTCATGATTTTCTTTGCATTTTGGGTCACAGTTGTTGTTTGTCTTGCA
ACTGCAGCAATTCCTGGATTCAAACCAATTTTAGATGTGACAAATCCTCAAGAAAATATT
CCAAAAGATCCAAAGAATGGCGCTGATTTACAAAAAACTTTCAAACTCGTTGAATATCAA
GAAGTTGACTATACAAGATACATGCTTTACATCTACCTCGTTGCACTCGTCTGGGTTTCT
GAGTTTATTTTTGCTGCTTCTCAATTATGTCTTGCCGGTGCTGTTGCATTATGGTATTTC
AAAAAACCAACAGATTCACCAGTTTGTGATTCTATGAGCAAGCTTATTAAATATCATCTT
GGATCAGTTGCAAAAGGCTCTTTTTTGATCACTCTCTTCAAAATTCCTCGATTGATTTTG
AGCTATCGTCATTGCCATTGAAAGTATTAACTTTTGCCCGGCTGCCGGAGTTGCTTGGAA
GGCGATTTGGACGCATGTTGTCAGCGTTGGTACAATAAATAGTATTGGAGATTTAGTACT
TTTCTTGGGAAAACTTGCTGTTTCTGGAATTTGTGGCTTCATTGCTTTACTCTTTTTGAA
AAATGATTCTGAAATTCAATTCTACATGGTTCCAGTATTTATCATTGCTCTATTTGCTTT
CTTTGTGGCTCATGTCATTTTGTCACTTTATGAAATTGTCGTTGATACTCTCTTCTTGTG
CGTTTATGAAGATCGCCATATTAATGGACCAAATGGTCGTTGGAAAGAATCAAATTTGGC
CAATTTGTTGGGTGAAGAAAAAGCTGTTGCAGTTGAAGGTCAAATGCATGAAGTCGAACT
GCAACCAATCACCAGACAACCTTTCGGCCATTACCGTGAAGCTCAACCAACTACCTTACC
AGTTTAAATAAATAGCCATCAAAACTCTTGAAATTGTGACCAAATACTTTTAACTCATTT
CATTTTACATACCTAATGTATTATTCTACCTCTTAAGACAATGTGCTTTTCTATCTAAAC
TTTTTAACACAATTTCAAGAATAACATTTATACCGTAAAATTTAATTTTAATCATCACTT
CTTAAAGCTATTTATTAAGCCATACATTAAACCATTTGCACTCATATGCTTTCAGTACAA
GCAAATTTGCACAAATTTAATGTTTCATCAAATTTAAAAATTTTAATTCATGTTATTAAA
TATAAAATGCCCAGCTTTATATGTAAACTTTACAGTAGAAATGTATACCATATACTATAT
ATAAGTTTACGCTTTTTGAACTATGATATTAAAAATTATTCAAAAACTTGAATGTCAACT
TGAATACAGAATATAACATCGCCTTAATTATAATGAAAATCAAACTAACAACAGAAATCT
TGAATGTATTTTGATATTTTTTTATTGATTTAAAACAGACAAATTTAATTCATGATGATC
TTTAAATTTATTACTCGCATGAATATATAATAAAATATAATCCATATATGTATAACATTA
TGCT

>g8427.t5 Gene=g8427 Length=345
MNKLTRASDNDELIFHLTGPCPTLPVYESDPVFHRCIPTGKNAPIKEAQELFNVVSGWDF
VEKTAHDLYKSWHVIALVCGLSLIFSIILIGLLHYLTQIISWLICIFVGVASIAITILLW
YTYFEIKKKKDSSELSQLAQYLQNETAVYVFAIIATIVMIILIVVIYFMSSKFSGLAALF
EEAGKCIYSMPQIFGPPLLAFIALMIFFAFWVTVVVCLATAAIPGFKPILDVTNPQENIP
KDPKNGADLQKTFKLVEYQEVDYTRYMLYIYLVALVWVSEFIFAASQLCLAGAVALWYFK
KPTDSPVCDSMSKLIKYHLGSVAKGSFLITLFKIPRLILSYRHCH

Protein features from InterProScan

Transcript Database ID Name Start End E.value
2 g8427.t5 PANTHER PTHR12385:SF12 SOLUTE CARRIER FAMILY 44 MEMBER 1A-RELATED 12 343 4.3E-103
3 g8427.t5 PANTHER PTHR12385 CHOLINE TRANSPORTER-LIKE (SLC FAMILY 44) 12 343 4.3E-103
1 g8427.t5 Pfam PF04515 Plasma-membrane choline transporter 153 341 6.0E-41
10 g8427.t5 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 71 -
21 g8427.t5 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 72 93 -
15 g8427.t5 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 94 98 -
22 g8427.t5 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 99 126 -
13 g8427.t5 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 127 146 -
20 g8427.t5 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 147 169 -
16 g8427.t5 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 170 197 -
18 g8427.t5 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 198 223 -
11 g8427.t5 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 224 267 -
17 g8427.t5 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 268 299 -
14 g8427.t5 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 300 318 -
19 g8427.t5 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 319 339 -
12 g8427.t5 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 340 345 -
6 g8427.t5 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 72 94 -
8 g8427.t5 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 99 121 -
7 g8427.t5 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 147 169 -
4 g8427.t5 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 197 219 -
5 g8427.t5 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 275 297 -
9 g8427.t5 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 317 339 -

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