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.t2 TSS g7731.t2 25591251 25591251
chr_2 g7731 g7731.t2 isoform g7731.t2 25591504 25592591
chr_2 g7731 g7731.t2 exon g7731.t2.exon1 25591504 25591552
chr_2 g7731 g7731.t2 exon g7731.t2.exon2 25591699 25591797
chr_2 g7731 g7731.t2 cds g7731.t2.CDS1 25591757 25591797
chr_2 g7731 g7731.t2 exon g7731.t2.exon3 25591922 25592043
chr_2 g7731 g7731.t2 cds g7731.t2.CDS2 25591922 25592043
chr_2 g7731 g7731.t2 exon g7731.t2.exon4 25592118 25592314
chr_2 g7731 g7731.t2 cds g7731.t2.CDS3 25592118 25592314
chr_2 g7731 g7731.t2 exon g7731.t2.exon5 25592460 25592591
chr_2 g7731 g7731.t2 cds g7731.t2.CDS4 25592460 25592591
chr_2 g7731 g7731.t2 TTS g7731.t2 NA NA

Sequences

>g7731.t2 Gene=g7731 Length=599
ATGGAAAGCACACCCGAATGCAGAATATGTCGAACGGAAGCAACAGCAGACCGTCCACTA
TTTTTTCCATGCATATGTACAGGCAGTATCAAATACATTCATCAAGAATGTTTATTGCAA
TGGATGAGATACAGCAGAAAAGAAGTACTTTTACACCGATTTATTCTCCAGATATGCCGA
AAGTCTTGCCTCTTCGTGTGGTAGCTGGTGGTCTGTTAAGTTCGATAGCTACAGCTGTGA
AATATTGGCTTCATTACACATTAGTTGCTGTTGCATGGCTTGGTATTGTCCCTCTCACTG
CTTATCGCACATATCGATTTTTCTTTTCCGGATCGCTTGATATGCTAGTTTCACTTCCAT
TCGATATGTTTTCAACAGAGAATTTAGCTGCTGATGTCTTTCGTGGTTGTTTTGTTGTCA
CATGTACATTATTTGCTTTCATTGGTTTAGTGTGGCTAAGAGAGCAGATTCTTCATGGAG
GTGGACCAGATTGGTTAGAAAGAGATGAAGGAAACAATGTTAATGAAGATATTCCAAGAG
CTGCACCACCACCACAAGCAGATAATTTACAGGAACCACTTGATGATGAAAATGGCAAT

>g7731.t2 Gene=g7731 Length=164
MFIAMDEIQQKRSTFTPIYSPDMPKVLPLRVVAGGLLSSIATAVKYWLHYTLVAVAWLGI
VPLTAYRTYRFFFSGSLDMLVSLPFDMFSTENLAADVFRGCFVVTCTLFAFIGLVWLREQ
ILHGGGPDWLERDEGNNVNEDIPRAAPPPQADNLQEPLDDENGN

Protein features from InterProScan

Transcript Database ID Name Start End E.value
5 g7731.t2 MobiDBLite mobidb-lite consensus disorder prediction 133 164 -
1 g7731.t2 PANTHER PTHR13145:SF0 E3 UBIQUITIN-PROTEIN LIGASE MARCH6 10 157 3.2E-46
2 g7731.t2 PANTHER PTHR13145 SSM4 PROTEIN 10 157 3.2E-46
8 g7731.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 1 26 -
12 g7731.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 27 48 -
7 g7731.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 49 54 -
10 g7731.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 55 77 -
9 g7731.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 78 96 -
11 g7731.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 97 117 -
6 g7731.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 118 164 -
4 g7731.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 47 69 -
3 g7731.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 95 117 -

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. There were no conditions that were differentially expressed