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.t6 TSS g5978.t6 13154443 13154443
chr_2 g5978 g5978.t6 isoform g5978.t6 13155350 13156357
chr_2 g5978 g5978.t6 exon g5978.t6.exon1 13155350 13155681
chr_2 g5978 g5978.t6 cds g5978.t6.CDS1 13155350 13155681
chr_2 g5978 g5978.t6 exon g5978.t6.exon2 13155743 13155992
chr_2 g5978 g5978.t6 cds g5978.t6.CDS2 13155743 13155992
chr_2 g5978 g5978.t6 exon g5978.t6.exon3 13156055 13156295
chr_2 g5978 g5978.t6 cds g5978.t6.CDS3 13156055 13156295
chr_2 g5978 g5978.t6 exon g5978.t6.exon4 13156351 13156357
chr_2 g5978 g5978.t6 cds g5978.t6.CDS4 13156351 13156355
chr_2 g5978 g5978.t6 TTS g5978.t6 NA NA

Sequences

>g5978.t6 Gene=g5978 Length=830
ATGGTTGCTTCATCGATTGCATCAGTGTCGTCATCAAATTTATTAAGAAGAAATGTTAGA
ATTTTACTAATTGGTGATCCGGGAGTTGGAAAAACCTCATTGATTCTTTCACTTGTTAGT
GAAGAATTTCCTGAAGAAGTGCCATCAAAAGCAGAAGAAATCACAATTCCAGCTGATGTA
ACACCAGAACATGTGCCCACAAATATCGTTGATTATTCGGCATTGGAACAGAGTGAAGAA
AATTTAATTGAAGAACTTCAGAAAGCTCATGTTGTATGTGTTGTTTATTCAGTGGACGAT
GAAAATTCGCTTGATCGAATCAGTTCATACTGGCTACCATTCATCCGCGAACACAATCAA
GGTGAAAATCGCAAACCCGTGGTACTTGTTGGAAATAAAATTGATTTAGTGGACTATTCA
ACGATTGATCATGTTCTCACTATCATGGAAGATTTCAATGAGATTGAAAGTTGTGTTGAA
TGCTCAGCAAAGACACTTCATAATATTTCCGAAATGTTTTATTATGCACAAAAAGCTGTT
TTGCATCCTACAGCACCGCTTTATATCATGGAAGAGCAAGATTTGACAGAAAAGTGTAAG
AAAGCACTTATAAGAATATTTAAAGTTTGTGATATTGATGGTGATGGATTGCTTAATGAT
TATGAATTAAATCACTTTCAAAGGCGATGCTTTAATGCGCCATTACAGCCAACAGTTCTC
GATGAGGTTAAAGCAGTTTTGATGAAAAATACACCGGATGGAATAAGAGATGATTGTGTT
ACACTCAGTGGATTTCTTTTTCTCCACTGCCTTTTTATTCAACGTGGACG

>g5978.t6 Gene=g5978 Length=276
MVASSIASVSSSNLLRRNVRILLIGDPGVGKTSLILSLVSEEFPEEVPSKAEEITIPADV
TPEHVPTNIVDYSALEQSEENLIEELQKAHVVCVVYSVDDENSLDRISSYWLPFIREHNQ
GENRKPVVLVGNKIDLVDYSTIDHVLTIMEDFNEIESCVECSAKTLHNISEMFYYAQKAV
LHPTAPLYIMEEQDLTEKCKKALIRIFKVCDIDGDGLLNDYELNHFQRRCFNAPLQPTVL
DEVKAVLMKNTPDGIRDDCVTLSGFLFLHCLFIQRG

Protein features from InterProScan

Transcript Database ID Name Start End E.value
12 g5978.t6 CDD cd01893 Miro1 17 183 5.93158E-90
10 g5978.t6 Gene3D G3DSA:3.40.50.300 - 16 186 4.1E-33
11 g5978.t6 Gene3D G3DSA:1.10.238.10 - 189 276 3.2E-29
3 g5978.t6 PANTHER PTHR24072:SF124 MITOCHONDRIAL RHO GTPASE 1 16 276 1.1E-114
4 g5978.t6 PANTHER PTHR24072 RHO FAMILY GTPASE 16 276 1.1E-114
5 g5978.t6 PRINTS PR00449 Transforming protein P21 ras signature 19 40 2.7E-16
7 g5978.t6 PRINTS PR00449 Transforming protein P21 ras signature 123 136 2.7E-16
6 g5978.t6 PRINTS PR00449 Transforming protein P21 ras signature 158 180 2.7E-16
1 g5978.t6 Pfam PF00071 Ras family 20 180 3.4E-21
2 g5978.t6 Pfam PF08356 EF hand associated 234 276 6.7E-10
13 g5978.t6 ProSitePatterns PS00018 EF-hand calcium-binding domain. 211 223 -
18 g5978.t6 ProSiteProfiles PS51423 Miro domain profile. 12 191 14.885
14 g5978.t6 SMART SM00173 ras_sub_4 16 183 2.3E-6
15 g5978.t6 SMART SM00175 rab_sub_5 19 183 1.1E-7
16 g5978.t6 SMART SM00174 rho_sub_3 21 183 4.2E-10
8 g5978.t6 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 16 216 6.81E-36
9 g5978.t6 SUPERFAMILY SSF47473 EF-hand 195 272 6.23E-9
17 g5978.t6 TIGRFAM TIGR00231 small_GTP: small GTP-binding protein domain 18 176 5.5E-13

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

Data is missing for g5978/g5978.t6; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5978.t6.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.

Raw TPM values