Gene loci information

Transcript annotation

  • This transcript has been annotated as hypothetical.

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_3 g535 g535.t4 TSS g535.t4 3970722 3970722
chr_3 g535 g535.t4 isoform g535.t4 3970971 3974006
chr_3 g535 g535.t4 exon g535.t4.exon1 3970971 3971019
chr_3 g535 g535.t4 cds g535.t4.CDS1 3970971 3971019
chr_3 g535 g535.t4 exon g535.t4.exon2 3972602 3972630
chr_3 g535 g535.t4 cds g535.t4.CDS2 3972602 3972630
chr_3 g535 g535.t4 exon g535.t4.exon3 3972699 3972892
chr_3 g535 g535.t4 cds g535.t4.CDS3 3972699 3972892
chr_3 g535 g535.t4 exon g535.t4.exon4 3972963 3973001
chr_3 g535 g535.t4 cds g535.t4.CDS4 3972963 3973001
chr_3 g535 g535.t4 exon g535.t4.exon5 3973444 3973657
chr_3 g535 g535.t4 cds g535.t4.CDS5 3973444 3973657
chr_3 g535 g535.t4 exon g535.t4.exon6 3973718 3974006
chr_3 g535 g535.t4 cds g535.t4.CDS6 3973718 3974005
chr_3 g535 g535.t4 TTS g535.t4 3974186 3974186

Sequences

>g535.t4 Gene=g535 Length=814
ATGGAGAATTGTGAATATAGCATTATTGGAACGGGTCGTCAAGTAGGAGACTCAGACGTT
AGGATGACATCGAAATGGGCCAAATTTAGACTGTTGATGTGGAAAAATTACCTTCTTCAG
TATCGTCATCCATTTCAAACAATTCTTGAGATTGCTATACCAGTATTATTTTCAGCATTA
CTCGTACTCATTCGTAGCTTAGTATCACCCGACATTTTTTCAGATCCAACGATCTATCCA
CCTTTACCATTAACTGATATCAAACAGACCTTTGGCGCTAGAGGAGAGTTTGCTTTCAAA
GTTCTCTCATTTAACAAGAACATCAATATTTCACAATTTACAAACTTTTCTAATGAAATC
GTCTACTCACCGGATAACATTGAAGTCAATGCATTGATGAAAGAGTTAAATAGTTATGTG
AAACCTTTCCTTAAGGTCACTCCTGTGCCTTCATCAAATGAACTAGCTCCGTACTTAAGA
AAATCAAATGCTTATGTTGGAATTGAATTTCCTGATAACTATAAAAACATAACAGAACTA
CCAGATGATCTCGAATACAGTATACGATATCCAGGAGAATTACGAAGAACAGGAGGAGCT
TTAAATCCATTATTTTTCAACTGGCGAACAGATTTTCTTTTTCCACTTTTTCAACCGGGT
GGCTCGAGAAATTTCAACAACACTCATGACGGATTGCCTAGTGGCTATTATATTGAAGGA
TTTTTATTTGTTCAACAATTTATGTTTAAAGCTTTCTCGACTTTGAAAAATAAAATGGAC
ATTGACCTAAAACAATTACCAAAAATCAATATAA

>g535.t4 Gene=g535 Length=271
MENCEYSIIGTGRQVGDSDVRMTSKWAKFRLLMWKNYLLQYRHPFQTILEIAIPVLFSAL
LVLIRSLVSPDIFSDPTIYPPLPLTDIKQTFGARGEFAFKVLSFNKNINISQFTNFSNEI
VYSPDNIEVNALMKELNSYVKPFLKVTPVPSSNELAPYLRKSNAYVGIEFPDNYKNITEL
PDDLEYSIRYPGELRRTGGALNPLFFNWRTDFLFPLFQPGGSRNFNNTHDGLPSGYYIEG
FLFVQQFMFKAFSTLKNKMDIDLKQLPKINI

Protein features from InterProScan

Transcript Database ID Name Start End E.value
1 g535.t4 PANTHER PTHR19229:SF139 ATP-BINDING CASSETTE, SUB-FAMILY A (ABC1), MEMBER 14 27 258 4.2E-16
2 g535.t4 PANTHER PTHR19229 ATP-BINDING CASSETTE TRANSPORTER SUBFAMILY A ABCA 27 258 4.2E-16
3 g535.t4 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 47 -
5 g535.t4 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 48 68 -
4 g535.t4 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 69 271 -

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

Data is missing for g535/g535.t4; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g535.t4.fa.iupred3.txt does not exist

GO terms from InterProScan

GOID TERM ONTOLOGY
GO:0055085 transmembrane transport BP
GO:0042626 ATPase-coupled transmembrane transporter activity MF
GO:0016021 integral component of membrane CC

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