Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative High affinity copper uptake 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 g7767 g7767.t5 TSS g7767.t5 25870003 25870003
chr_2 g7767 g7767.t5 isoform g7767.t5 25870027 25872670
chr_2 g7767 g7767.t5 exon g7767.t5.exon1 25870027 25870031
chr_2 g7767 g7767.t5 exon g7767.t5.exon2 25871684 25871867
chr_2 g7767 g7767.t5 cds g7767.t5.CDS1 25871697 25871867
chr_2 g7767 g7767.t5 exon g7767.t5.exon3 25871928 25872157
chr_2 g7767 g7767.t5 cds g7767.t5.CDS2 25871928 25872157
chr_2 g7767 g7767.t5 exon g7767.t5.exon4 25872469 25872670
chr_2 g7767 g7767.t5 cds g7767.t5.CDS3 25872469 25872670
chr_2 g7767 g7767.t5 TTS g7767.t5 25873093 25873093

Sequences

>g7767.t5 Gene=g7767 Length=621
GTGTGAATATTATAAAATATGGGAGATCACGCACATCATCATCATCATCATATGCCAGAC
CTTGATGCAACAAGTGCTATGCCAGTGCTTTCAACTGGAATGGATCATCATCACATGCAT
TCCGATATGGGACATTCAATGAATGACTCAGCTGCATCTCATGCTTTTCATCACATGATG
TCCATGGCTTTTCATGGCGGTTGCAACGAAACAATTTTATTCACTCAATGGACGATTGAC
AGTTGCTTTGGTCTTGTGTGGTCAATGATTGTTATTTTCATTTTTGGTATTCTATATGAA
GGTTTAAAATATTATCGTGAACATTTATTCTGGAAGACTTATAATGCATTGCAATACAGA
GCAGTAGGTGCTCCAGAGAAAAATGGAACATCTGAAAATGCCGATTCACGTGTTGTACAA
CCAACAATATTTTCACTGATGCATCTTTATCAATCGTTTCTACATTTAATTCAAGTAACA
TTATCACTAATGCTGATGCTCATATTTATGACATACAACACATGGTTATGTCTTGCCGTT
GTTTTTGGAGCTATGGTAGGATACTTTTTGTTCGGATGGAAGAAATCAATAGTAGTCGAT
GTTACAGAGCATTGTCATTGA

>g7767.t5 Gene=g7767 Length=200
MGDHAHHHHHHMPDLDATSAMPVLSTGMDHHHMHSDMGHSMNDSAASHAFHHMMSMAFHG
GCNETILFTQWTIDSCFGLVWSMIVIFIFGILYEGLKYYREHLFWKTYNALQYRAVGAPE
KNGTSENADSRVVQPTIFSLMHLYQSFLHLIQVTLSLMLMLIFMTYNTWLCLAVVFGAMV
GYFLFGWKKSIVVDVTEHCH

Protein features from InterProScan

Transcript Database ID Name Start End E.value
2 g7767.t5 PANTHER PTHR12483:SF27 COPPER TRANSPORTER 1A, ISOFORM C-RELATED 28 199 4.2E-40
3 g7767.t5 PANTHER PTHR12483 SOLUTE CARRIER FAMILY 31 COPPER TRANSPORTERS 28 199 4.2E-40
1 g7767.t5 Pfam PF04145 Ctr copper transporter family 56 185 1.5E-28
8 g7767.t5 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 75 -
12 g7767.t5 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 76 96 -
10 g7767.t5 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 97 142 -
13 g7767.t5 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 143 162 -
7 g7767.t5 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 163 168 -
11 g7767.t5 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 169 187 -
9 g7767.t5 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 188 200 -
6 g7767.t5 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 77 96 -
4 g7767.t5 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 141 163 -
5 g7767.t5 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 170 187 -

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:0035434 copper ion transmembrane transport BP
GO:0016021 integral component of membrane CC
GO:0005375 copper ion transmembrane transporter activity MF

KEGG

Orthology

Pathway

  • This transcript belongs to the following pathways

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