Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative E3 ubiquitin-protein ligase MARCHF6.

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 g7731 g7731.t4 isoform g7731.t4 25594152 25594988
chr_2 g7731 g7731.t4 exon g7731.t4.exon1 25594152 25594988
chr_2 g7731 g7731.t4 cds g7731.t4.CDS1 25594419 25594988
chr_2 g7731 g7731.t4 TTS g7731.t4 25595592 25595592
chr_2 g7731 g7731.t4 TSS g7731.t4 NA NA

Sequences

>g7731.t4 Gene=g7731 Length=837
GGTAGCGGAATTGGAAATAATGCAAATATTGGAGATATTAGTGGAGATAATGAGACTGTA
ACATCGACTGTAGTAGCTGTATCAACTTCAAAACCTCATGAACTTTATACAGCAGCAATT
GGCATATACTTGTGTTGGCTCATATCAAAAGGAATAGCATTGGCTGTAAATTTGTTTCCA
CAAGGACGCACAGCAATAATTGAGAAATTTAAACATTGGTGTTCAGTCGCAATTAGTTAT
GGACTTGCTGCAATAATATTTGTTTTGATGCTTGGTTTAGTTCCACTAATGTTCGGTCTT
CTGCTTGAACTAGTTGTTGTTGTACCACTGCGAGTACCATTGAATCAGACGCCAGTACTC
TTTTTGTGGCAAGATTGGGCTTTAGGTTGTCTCTATACAAAAATAACAGTCGCACTTTTA
TTCATGGGTCCAGATTTTCGATTAAAACGCGCCATCGAGCAAGCTTATCGTGATGGTTTG
AGAGAAATGAATTTAAAATTCATCATAAGAGAACTAGCAATACCTGTGATTTCAGCGTTC
GGTTTAGCGTTAGCGGTTCCTTATGTCATCGCACACTCCATCATGCCAATATTTTTCACA
AATCAAATGACTCGTGTCTTAATCTCTCGTCGCATCTATCCATTCTTCCTTATTGTCATC
ATTGTCTGTGCAATAATCGTTTTTCAAATTAAACAATTTAAGAAGCTGTATATTGCCATC
AAAAATGATAAATATCTTGTTGGAAAGCGTTTAGTAAATTATGATCAGCATCAACGTCAG
AAGCTGCTTAATCAACAGCAACAACAACAACAAGCTGAAGTTAGAGCTGAGCTGTGA

>g7731.t4 Gene=g7731 Length=189
MLGLVPLMFGLLLELVVVVPLRVPLNQTPVLFLWQDWALGCLYTKITVALLFMGPDFRLK
RAIEQAYRDGLREMNLKFIIRELAIPVISAFGLALAVPYVIAHSIMPIFFTNQMTRVLIS
RRIYPFFLIVIIVCAIIVFQIKQFKKLYIAIKNDKYLVGKRLVNYDQHQRQKLLNQQQQQ
QQAEVRAEL

Protein features from InterProScan

Transcript Database ID Name Start End E.value
1 g7731.t4 PANTHER PTHR13145:SF0 E3 UBIQUITIN-PROTEIN LIGASE MARCH6 2 170 3.9E-55
2 g7731.t4 PANTHER PTHR13145 SSM4 PROTEIN 2 170 3.9E-55
11 g7731.t4 Phobius SIGNAL_PEPTIDE Signal peptide region 1 18 -
12 g7731.t4 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide. 1 1 -
13 g7731.t4 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide. 2 13 -
17 g7731.t4 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide. 14 18 -
9 g7731.t4 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 19 36 -
15 g7731.t4 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 37 57 -
8 g7731.t4 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 58 77 -
16 g7731.t4 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 78 102 -
10 g7731.t4 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 103 121 -
14 g7731.t4 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 122 141 -
7 g7731.t4 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 142 189 -
3 g7731.t4 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 2 21 -
4 g7731.t4 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 31 53 -
6 g7731.t4 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 83 102 -
5 g7731.t4 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 117 139 -

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

GO terms from InterProScan

There are no GO annotations for this transcript.

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