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.t7 isoform g5978.t7 13156357 13158067
chr_2 g5978 g5978.t7 exon g5978.t7.exon1 13156357 13156848
chr_2 g5978 g5978.t7 cds g5978.t7.CDS1 13156413 13156848
chr_2 g5978 g5978.t7 exon g5978.t7.exon2 13156905 13157361
chr_2 g5978 g5978.t7 cds g5978.t7.CDS2 13156905 13157361
chr_2 g5978 g5978.t7 exon g5978.t7.exon3 13157558 13157620
chr_2 g5978 g5978.t7 cds g5978.t7.CDS3 13157558 13157620
chr_2 g5978 g5978.t7 exon g5978.t7.exon4 13157938 13158067
chr_2 g5978 g5978.t7 cds g5978.t7.CDS4 13157938 13158067
chr_2 g5978 g5978.t7 TTS g5978.t7 13158181 13158181
chr_2 g5978 g5978.t7 TSS g5978.t7 NA NA

Sequences

>g5978.t7 Gene=g5978 Length=1142
GTAATGAAACAACTTGGGCTGTTTTGAGACGATTTGGTTACAATGAAAATTTAGAAATGA
GTAAAGATTATTTATGTCCATCAATAAAAATTCCTCCAGGTTCAAGTACAGAATTATCGC
ATCGCGGTCAACAATTTTTGATGGCATTATTTGAGAGAAGTGATAAAGATAATGATGGAG
CTCTTTCACCAGATGAATTCAAACGTGTGTTTAGTGCTTGTCCATCACCTCCATTTTCGA
GTGATATAAAAAGAACTGTTCCAACTAATGATAAAGGATGGCCCACTCAGCATGGTTGGA
TTTGTCGATGGACACTTCAAACATTCATTGAACTTCCAAAAACCCTTGAGTATCTTGCCT
ATCTCGGTTTTAATGTACACGAAAATGAATCGCAATTGACAGCAATTCATGTAACACGTG
AGCGACGAATTGATTTGGCAAAGAAACAAAGTAGCAGAACGACATATATGTGCCATGTAA
TCGGAATGAAAGGTGCTGGAAAGACTGCATTGTGTCGAGCATTTTTAGTCGATGATATGA
AAAAGTTGAAGGACAAAGATTTGCGTGGAAATAACCAGTACTGTATTAATACAGTTCAAG
TTTATGGACAAGAAAAATATTTGATACTTCGTGATATAGATGTCCGACAAGTTCTCGATC
CGCTTCAACCACAAGAAGTGTTGTGTGATGTCGCGTGCTTAGTTTATGATATTAGTGATC
CAAAATCATTTGAGTATATTGCAAGGATATACATAAAATACTTTGCTGAAAGTAAAATTC
CAGTGCTTATAGTGGGAGCGAAAGGCGATATGGAGGAAAAGAGACAAGACTATCTTCTCC
AGCCTGCTGAATTTTGCCAAAAATATAAATTATTACCACCTCAGTACTTTAGTTTCAAGC
ACAATAAACGTGATCTTTATATTAAACTTGGAACAATGGCATCATTTCCGAGATTTCAAC
CAGCTTGGATTTTGTTTTATAAACACAGGTTCGTTCAACTGTGGGAGGAGACTCAACTTA
AGCATTTTGGATTAATGACCAATGACCCGACGTTGTGGTGGAAAACAGTATTAGGCATAG
CAACATGCTCAGTTTTGGGATTCTTCGTAGTTCGCGCTCTCCATTCAGCTACAACACGAT
GA

>g5978.t7 Gene=g5978 Length=361
MSKDYLCPSIKIPPGSSTELSHRGQQFLMALFERSDKDNDGALSPDEFKRVFSACPSPPF
SSDIKRTVPTNDKGWPTQHGWICRWTLQTFIELPKTLEYLAYLGFNVHENESQLTAIHVT
RERRIDLAKKQSSRTTYMCHVIGMKGAGKTALCRAFLVDDMKKLKDKDLRGNNQYCINTV
QVYGQEKYLILRDIDVRQVLDPLQPQEVLCDVACLVYDISDPKSFEYIARIYIKYFAESK
IPVLIVGAKGDMEEKRQDYLLQPAEFCQKYKLLPPQYFSFKHNKRDLYIKLGTMASFPRF
QPAWILFYKHRFVQLWEETQLKHFGLMTNDPTLWWKTVLGIATCSVLGFFVVRALHSATT
R

Protein features from InterProScan

Transcript Database ID Name Start End E.value
12 g5978.t7 CDD cd01892 Miro2 134 310 1.01236E-69
8 g5978.t7 Gene3D G3DSA:1.10.238.10 - 1 194 4.0E-65
7 g5978.t7 Gene3D G3DSA:3.40.50.300 - 195 296 6.3E-28
3 g5978.t7 PANTHER PTHR24072:SF311 MITOCHONDRIAL RHO GTPASE 2 2 163 1.0E-30
4 g5978.t7 PANTHER PTHR24072 RHO FAMILY GTPASE 2 163 1.0E-30
2 g5978.t7 Pfam PF08355 EF hand associated 62 131 3.3E-23
1 g5978.t7 Pfam PF00071 Ras family 141 271 4.5E-8
10 g5978.t7 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 1 332 -
11 g5978.t7 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 333 355 -
9 g5978.t7 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 356 361 -
14 g5978.t7 ProSitePatterns PS00018 EF-hand calcium-binding domain. 36 48 -
16 g5978.t7 ProSiteProfiles PS50222 EF-hand calcium-binding domain profile. 23 58 11.835
17 g5978.t7 ProSiteProfiles PS51423 Miro domain profile. 130 282 15.871
15 g5978.t7 SMART SM00054 efh_1 27 55 0.0096
6 g5978.t7 SUPERFAMILY SSF47473 EF-hand 17 111 3.42E-9
5 g5978.t7 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 134 285 1.61E-20
13 g5978.t7 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 333 355 -

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

Data is missing for g5978/g5978.t7; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5978.t7.fa.iupred3.txt does not exist

GO terms from InterProScan

GOID TERM ONTOLOGY
GO:0005509 calcium ion binding MF
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