Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative Zinc transporter 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_1 g9716 g9716.t5 isoform g9716.t5 4782353 4783787
chr_1 g9716 g9716.t5 exon g9716.t5.exon1 4782353 4782813
chr_1 g9716 g9716.t5 cds g9716.t5.CDS1 4782414 4782813
chr_1 g9716 g9716.t5 exon g9716.t5.exon2 4782887 4783071
chr_1 g9716 g9716.t5 cds g9716.t5.CDS2 4782887 4783071
chr_1 g9716 g9716.t5 exon g9716.t5.exon3 4783549 4783787
chr_1 g9716 g9716.t5 cds g9716.t5.CDS3 4783549 4783641
chr_1 g9716 g9716.t5 TTS g9716.t5 4784302 4784302
chr_1 g9716 g9716.t5 TSS g9716.t5 NA NA

Sequences

>g9716.t5 Gene=g9716 Length=885
AAAACCTCCATCACCGAAAAAACCTTCAGGTGGTCATGGACATTCACATAGTGCCGGTCA
AATGAATATGCGTGCAGCATTTCTTCACGTTCTCAGTGACGCACTTGGTTCAGTTATTGT
TATGATTAGCGCATTGATTATCAAGTACACTAATTGGGAATATAAATATTACTGTGATCC
TGCCCTTTCGATGCTTCTTGTTGCACTTATTCTTCATTCTGTTTGGCCCTTACTTCGAGA
ATCTGCACTTATTTTGCTTCAAACTGTACCAACACACATCGAAGTTGACGCAATTCAACG
TCGTTTATTGGAACGTGTAGATGGTGTACTCGCTGTTCATGAATTTCACGTTTGGCAGTT
GGCTGGAGATAGAATTATTGCTTCAGCTCACATTCGTTGTCGTAATTTAAGCGAATACAT
GAAATTAGCAGAGAAAGTGAAAGAATTTTTCCATAATGAGGGTATTCACAGTACGACGAT
TCAGCCAGAATTTATTGAAATAGAAAATATGAATAGCTGTTCAGCATCAGATGGAATTTC
GACAAGCTTGAATATAAGTGGAAAAGAGGAAGGTTGTGTTCTAGATTGTCCAAATATTGA
TGAGAATTGTGTCAAAGCAACTTGCTGCCAAAATACAAACAATAAGACTCATAGTCCAGC
CGCTTCTCCATTTTTATGTCGTCAGCGACCAATAATGCGCGGCACAGAAAATGAAAACGG
AGAAAAAGGTAAAGAATGATGCATAAACAATTTAATTAATTTAATATTTATTCAATATTT
AATCTCTAAGGCTCATTGCTCGATAACGCACAAAGTATTCCAATCGTAATGTCTTCATCA
AATCAAACAGCTGTGGAGAACAACAGTAATAAGATTCTCGTTTGA

>g9716.t5 Gene=g9716 Length=225
MNMRAAFLHVLSDALGSVIVMISALIIKYTNWEYKYYCDPALSMLLVALILHSVWPLLRE
SALILLQTVPTHIEVDAIQRRLLERVDGVLAVHEFHVWQLAGDRIIASAHIRCRNLSEYM
KLAEKVKEFFHNEGIHSTTIQPEFIEIENMNSCSASDGISTSLNISGKEEGCVLDCPNID
ENCVKATCCQNTNNKTHSPAASPFLCRQRPIMRGTENENGEKGKE

Protein features from InterProScan

Transcript Database ID Name Start End E.value
8 g9716.t5 Gene3D G3DSA:1.20.1510.10 - 1 66 1.0E-8
2 g9716.t5 PANTHER PTHR45820:SF2 ZINC TRANSPORTER 63C, ISOFORM F 1 213 1.5E-108
3 g9716.t5 PANTHER PTHR45820 FI23527P1 1 213 1.5E-108
1 g9716.t5 Pfam PF01545 Cation efflux family 1 66 9.1E-15
10 g9716.t5 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 6 -
13 g9716.t5 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 7 29 -
12 g9716.t5 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 30 40 -
14 g9716.t5 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 41 58 -
11 g9716.t5 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 59 225 -
6 g9716.t5 SUPERFAMILY SSF161111 Cation efflux protein transmembrane domain-like 1 67 2.09E-13
7 g9716.t5 SUPERFAMILY SSF160240 Cation efflux protein cytoplasmic domain-like 75 145 2.88E-5
9 g9716.t5 TIGRFAM TIGR01297 CDF: cation diffusion facilitator family transporter 1 143 8.4E-30
5 g9716.t5 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 5 27 -
4 g9716.t5 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 34 56 -

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:0016021 integral component of membrane CC
GO:0006812 cation transport BP
GO:0008324 cation 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