Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative Multidrug resistance-associated protein 4.

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 g2628 g2628.t4 TTS g2628.t4 19180386 19180386
chr_3 g2628 g2628.t4 isoform g2628.t4 19181395 19182668
chr_3 g2628 g2628.t4 exon g2628.t4.exon1 19181395 19181933
chr_3 g2628 g2628.t4 cds g2628.t4.CDS1 19181397 19181900
chr_3 g2628 g2628.t4 exon g2628.t4.exon2 19182599 19182668
chr_3 g2628 g2628.t4 TSS g2628.t4 19182679 19182679

Sequences

>g2628.t4 Gene=g2628 Length=609
AGATAGTGAGTGAACGTTGACAAGCAAAGAAGAAAAAATATATTTTACAACAGCATTGAT
TGGTTTTTTTTTGTTTATTTCAGTTATTGTGAAAGAATTCATTATGAATTCACAAAATTC
AAAACAAAAGCCAGAAAATCCTCTACAGAATGCATCTCGATTGAGCAGAATGACATTTTG
GTGGCTTAAAGATCTGTATAAAATTGGTATGACACGACCAATTACGGACGATGATGTTTA
TCAGACAATTGACCATCATGAATGTGATCGAATAGCAAACAAATTTAAAACGTTATGGCA
GAAGGAACTTGATGGATCAAAAAGACCAAGTGCACTTAGATTAATTTACAATGCTTATGG
ACCGCCTGTACTGATAATTGGATTACTTTTCTCGGTCTGTGAAACGTTGATGCGTTGTGC
ACAGCCGTTGTTGCTAGGTGAACTTCTTACTTATTTTGCTGATGAAAGTGCATCGAAAGA
ATGGGCATATATTTACGCAGCAGGAATTGTTATATGCTCGATTGTTCCTGTAATAACATT
CCATCCATTTATCTATTACATTTTTGAAATTGGAATGAAAATAAGAATTGGCTGCTCAAG
ATTAGTTTA

>g2628.t4 Gene=g2628 Length=168
MNSQNSKQKPENPLQNASRLSRMTFWWLKDLYKIGMTRPITDDDVYQTIDHHECDRIANK
FKTLWQKELDGSKRPSALRLIYNAYGPPVLIIGLLFSVCETLMRCAQPLLLGELLTYFAD
ESASKEWAYIYAAGIVICSIVPVITFHPFIYYIFEIGMKIRIGCSRLV

Protein features from InterProScan

Transcript Database ID Name Start End E.value
1 g2628.t4 PANTHER PTHR24223 ATP-BINDING CASSETTE SUB-FAMILY C 3 167 1.9E-34
2 g2628.t4 PANTHER PTHR24223:SF324 LD17001P 3 167 1.9E-34
7 g2628.t4 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 88 -
10 g2628.t4 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 89 110 -
8 g2628.t4 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 111 129 -
9 g2628.t4 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 130 154 -
6 g2628.t4 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 155 168 -
5 g2628.t4 SUPERFAMILY SSF90123 ABC transporter transmembrane region 86 163 1.83E-7
3 g2628.t4 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 80 102 -
4 g2628.t4 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 129 151 -

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:0005524 ATP binding 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