Gene loci information

Transcript annotation

  • This transcript has been annotated as Mitochondrial Rho GTPase.

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 g5978 g5978.t5 TSS g5978.t5 13154443 13154443
chr_2 g5978 g5978.t5 isoform g5978.t5 13155350 13156060
chr_2 g5978 g5978.t5 exon g5978.t5.exon1 13155350 13155681
chr_2 g5978 g5978.t5 cds g5978.t5.CDS1 13155350 13155681
chr_2 g5978 g5978.t5 exon g5978.t5.exon2 13155743 13155992
chr_2 g5978 g5978.t5 cds g5978.t5.CDS2 13155743 13155992
chr_2 g5978 g5978.t5 exon g5978.t5.exon3 13156055 13156060
chr_2 g5978 g5978.t5 cds g5978.t5.CDS3 13156055 13156060
chr_2 g5978 g5978.t5 TTS g5978.t5 NA NA

Sequences

>g5978.t5 Gene=g5978 Length=588
ATGGTTGCTTCATCGATTGCATCAGTGTCGTCATCAAATTTATTAAGAAGAAATGTTAGA
ATTTTACTAATTGGTGATCCGGGAGTTGGAAAAACCTCATTGATTCTTTCACTTGTTAGT
GAAGAATTTCCTGAAGAAGTGCCATCAAAAGCAGAAGAAATCACAATTCCAGCTGATGTA
ACACCAGAACATGTGCCCACAAATATCGTTGATTATTCGGCATTGGAACAGAGTGAAGAA
AATTTAATTGAAGAACTTCAGAAAGCTCATGTTGTATGTGTTGTTTATTCAGTGGACGAT
GAAAATTCGCTTGATCGAATCAGTTCATACTGGCTACCATTCATCCGCGAACACAATCAA
GGTGAAAATCGCAAACCCGTGGTACTTGTTGGAAATAAAATTGATTTAGTGGACTATTCA
ACGATTGATCATGTTCTCACTATCATGGAAGATTTCAATGAGATTGAAAGTTGTGTTGAA
TGCTCAGCAAAGACACTTCATAATATTTCCGAAATGTTTTATTATGCACAAAAAGCTGTT
TTGCATCCTACAGCACCGCTTTATATCATGGAAGAGCAAGATTTGACA

>g5978.t5 Gene=g5978 Length=196
MVASSIASVSSSNLLRRNVRILLIGDPGVGKTSLILSLVSEEFPEEVPSKAEEITIPADV
TPEHVPTNIVDYSALEQSEENLIEELQKAHVVCVVYSVDDENSLDRISSYWLPFIREHNQ
GENRKPVVLVGNKIDLVDYSTIDHVLTIMEDFNEIESCVECSAKTLHNISEMFYYAQKAV
LHPTAPLYIMEEQDLT

Protein features from InterProScan

Transcript Database ID Name Start End E.value
9 g5978.t5 CDD cd01893 Miro1 17 183 0.0000000
8 g5978.t5 Gene3D G3DSA:3.40.50.300 - 16 186 0.0000000
2 g5978.t5 PANTHER PTHR24072:SF124 MITOCHONDRIAL RHO GTPASE 1 16 195 0.0000000
3 g5978.t5 PANTHER PTHR24072 RHO FAMILY GTPASE 16 195 0.0000000
4 g5978.t5 PRINTS PR00449 Transforming protein P21 ras signature 19 40 0.0000000
6 g5978.t5 PRINTS PR00449 Transforming protein P21 ras signature 123 136 0.0000000
5 g5978.t5 PRINTS PR00449 Transforming protein P21 ras signature 158 180 0.0000000
1 g5978.t5 Pfam PF00071 Ras family 20 180 0.0000000
14 g5978.t5 ProSiteProfiles PS51423 Miro domain profile. 12 196 15.4030000
10 g5978.t5 SMART SM00173 ras_sub_4 16 183 0.0000023
11 g5978.t5 SMART SM00175 rab_sub_5 19 183 0.0000001
12 g5978.t5 SMART SM00174 rho_sub_3 21 183 0.0000000
7 g5978.t5 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 16 190 0.0000000
13 g5978.t5 TIGRFAM TIGR00231 small_GTP: small GTP-binding protein domain 18 176 0.0000000

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

Data is missing for g5978/g5978.t5; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5978.t5.fa.iupred3.txt does not exist

GO terms from InterProScan

GOID TERM ONTOLOGY
GO:0047497 mitochondrion transport along microtubule BP
GO:0031307 integral component of mitochondrial outer membrane CC
GO:0005525 GTP binding MF
GO:0003924 GTPase activity MF

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