Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative 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.t8 isoform g8427.t8 30412119 30413248
chr_2 g8427 g8427.t8 exon g8427.t8.exon1 30412119 30412426
chr_2 g8427 g8427.t8 cds g8427.t8.CDS1 30412313 30412426
chr_2 g8427 g8427.t8 exon g8427.t8.exon2 30412484 30413248
chr_2 g8427 g8427.t8 cds g8427.t8.CDS2 30412484 30412651
chr_2 g8427 g8427.t8 TTS g8427.t8 30413247 30413247
chr_2 g8427 g8427.t8 TSS g8427.t8 NA NA

Sequences

>g8427.t8 Gene=g8427 Length=1073
TTGCCATTGAAAGTATTAACTTTTGCCCGGCTGCCGGAGTTGCTTGGAAGGCGATTTGGA
CGCATGTTGTCAGCGTTGGTACAATAAATAGTATTGGAGATTTAGTACTTTTCTTGGGAA
AACTTGCTGTTTCTGGAATTTGTGGCTTCATTGCTTTACTCTTTTTGAAAAATGATTCTG
AAATTCAATTCTACATGGTTCCAGTATTTATCATTGCTCTATTTGCTTTCTTTGTGGCTC
ATGTCATTTTGTCACTTTATGAAATTGTCGTTGATACTCTCTTCTTGTGCGTTTATGAAG
ATCGCCATATTAATGGACCAAATGGTCGTTGGAAAGAATCAAATTTGGCCAATTTGTTGG
GTGAAGAAAAAGCTGTTGCAGTTGAAGGTCAAATGCATGAAGTCGAACTGCAACCAATCA
CCAGACAACCTTTCGGCCATTACCGTGAAGCTCAACCAACTACCTTACCAGTTTAAATAA
ATAGCCATCAAAACTCTTGAAATTGTGACCAAATACTTTTAACTCATTTCATTTTACATA
CCTAATGTATTATTCTACCTCTTAAGACAATGTGCTTTTCTATCTAAACTTTTTAACACA
ATTTCAAGAATAACATTTATACCGTAAAATTTAATTTTAATCATCACTTCTTAAAGCTAT
TTATTAAGCCATACATTAAACCATTTGCACTCATATGCTTTCAGTACAAGCAAATTTGCA
CAAATTTAATGTTTCATCAAATTTAAAAATTTTAATTCATGTTATTAAATATAAAATGCC
CAGCTTTATATGTAAACTTTACAGTAGAAATGTATACCATATACTATATATAAGTTTACG
CTTTTTGAACTATGATATTAAAAATTATTCAAAAACTTGAATGTCAACTTGAATACAGAA
TATAACATCGCCTTAATTATAATGAAAATCAAACTAACAACAGAAATCTTGAATGTATTT
TGATATTTTTTTATTGATTTAAAACAGACAAATTTAATTCATGATGATCTTTAAATTTAT
TACTCGCATGAATATATAATAAAATATAATCCATATATGTATAACATTATGCT

>g8427.t8 Gene=g8427 Length=93
MVPVFIIALFAFFVAHVILSLYEIVVDTLFLCVYEDRHINGPNGRWKESNLANLLGEEKA
VAVEGQMHEVELQPITRQPFGHYREAQPTTLPV

Protein features from InterProScan

Transcript Database ID Name Start End E.value
2 g8427.t8 PANTHER PTHR12385:SF12 SOLUTE CARRIER FAMILY 44 MEMBER 1A-RELATED 1 65 8.3E-14
3 g8427.t8 PANTHER PTHR12385 CHOLINE TRANSPORTER-LIKE (SLC FAMILY 44) 1 65 8.3E-14
1 g8427.t8 Pfam PF04515 Plasma-membrane choline transporter 1 37 8.9E-8
6 g8427.t8 Phobius SIGNAL_PEPTIDE Signal peptide region 1 20 -
7 g8427.t8 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide. 1 3 -
8 g8427.t8 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide. 4 15 -
9 g8427.t8 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide. 16 20 -
5 g8427.t8 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 21 93 -
4 g8427.t8 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 4 26 -

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