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.t16 TSS g7767.t16 25871683 25871683
chr_2 g7767 g7767.t16 isoform g7767.t16 25871928 25872989
chr_2 g7767 g7767.t16 exon g7767.t16.exon1 25871928 25872157
chr_2 g7767 g7767.t16 cds g7767.t16.CDS1 25872003 25872157
chr_2 g7767 g7767.t16 exon g7767.t16.exon2 25872237 25872266
chr_2 g7767 g7767.t16 cds g7767.t16.CDS2 25872237 25872266
chr_2 g7767 g7767.t16 exon g7767.t16.exon3 25872469 25872989
chr_2 g7767 g7767.t16 cds g7767.t16.CDS3 25872469 25872670
chr_2 g7767 g7767.t16 TTS g7767.t16 25873093 25873093

Sequences

>g7767.t16 Gene=g7767 Length=781
TTTCATGGCGGTTGCAACGAAACAATTTTATTCACTCAATGGACGATTGACAGTTGCTTT
GGTCTTGTGTGGTCAATGATTGTTATTTTCATTTTTGGTATTCTATATGAAGGTTTAAAA
TATTATCGTGAACATTTATTCTGGAAGACTTATAATGCATTGCAATACAGAGCAGTAGGT
GCTCCAGAGAAAAATGGAACATCTGAAAATGCCGATTCACGTGTTGTACATATGGTTGGT
GAAGTTGTTCATCGAAATCCACCAACAATATTTTCACTGATGCATCTTTATCAATCGTTT
CTACATTTAATTCAAGTAACATTATCACTAATGCTGATGCTCATATTTATGACATACAAC
ACATGGTTATGTCTTGCCGTTGTTTTTGGAGCTATGGTAGGATACTTTTTGTTCGGATGG
AAGAAATCAATAGTAGTCGATGTTACAGAGCATTGTCATTGAATCGCTCTGAATCTATTC
GACTCGTTATGTAAAATCTTCAAACGAGTCCAGAGTCTCAATTTAAGAATATCATATGTG
AACATAAACATAATAAAAATCGTAAGATATCATGTCTGGAATTGCCTCCGATCGGTCATA
AGAAGAACTTTAAACAGATTAAGAAGATACACATAAAACACAATGATCAGCCAGTAAAAA
AACATTGTGAAATGTTGATCATATCTGCATTTTGTTTAAAGTGGTGATATAAAGACTCTG
ATAATACATAATACCTAAATAGTTTAATGAAAAAGAATTTAGATGTATAGTTTATATTAT
T

>g7767.t16 Gene=g7767 Length=128
MIVIFIFGILYEGLKYYREHLFWKTYNALQYRAVGAPEKNGTSENADSRVVHMVGEVVHR
NPPTIFSLMHLYQSFLHLIQVTLSLMLMLIFMTYNTWLCLAVVFGAMVGYFLFGWKKSIV
VDVTEHCH

Protein features from InterProScan

Transcript Database ID Name Start End E.value
2 g7767.t16 PANTHER PTHR12483:SF22 HIGH AFFINITY COPPER UPTAKE PROTEIN 1 2 128 2.1E-30
3 g7767.t16 PANTHER PTHR12483 SOLUTE CARRIER FAMILY 31 COPPER TRANSPORTERS 2 128 2.1E-30
1 g7767.t16 Pfam PF04145 Ctr copper transporter family 1 113 4.8E-22
7 g7767.t16 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 1 70 -
8 g7767.t16 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 71 90 -
5 g7767.t16 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 91 96 -
9 g7767.t16 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 97 115 -
6 g7767.t16 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 116 128 -
4 g7767.t16 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 93 115 -

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

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