General information for g5978.t4
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Mitochondrial Rho GTPase.
Parent gene
- The parent gene g5978 is located on chr_2: 13156357..13158067 (+ strand)
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.t4 | TSS | g5978.t4 | 13154443 | 13154443 |
| chr_2 | g5978 | g5978.t4 | isoform | g5978.t4 | 13154444 | 13155748 |
| chr_2 | g5978 | g5978.t4 | exon | g5978.t4.exon1 | 13154444 | 13154629 |
| chr_2 | g5978 | g5978.t4 | exon | g5978.t4.exon2 | 13155271 | 13155681 |
| chr_2 | g5978 | g5978.t4 | cds | g5978.t4.CDS1 | 13155350 | 13155681 |
| chr_2 | g5978 | g5978.t4 | exon | g5978.t4.exon3 | 13155743 | 13155748 |
| chr_2 | g5978 | g5978.t4 | cds | g5978.t4.CDS2 | 13155743 | 13155746 |
| chr_2 | g5978 | g5978.t4 | TTS | g5978.t4 | NA | NA |
Sequences
>g5978.t4 Gene=g5978 Length=603
CATAGAGAACAAAAATAAAGTGTGTAGTTTATTATAATTTTTAAGAAATCAAGACTAAAA
GACCAACGGAGATAAAATACAGCATCTGTTCTAGACACGAGTTTTGGCGCGTTGTTAGCA
GTAGTGTGTTGGAAGTGATTGCAAGAATTAATCGAGAAATTAAAGTGAAATGTGGAAAAA
GTGAATATTTTTTTTGCACGAAAGGAAAACAAACTCAACAGATTTGAGACAGTAGCGAAG
TGGAATATTTAATTAAATTAGCATCATGGTTGCTTCATCGATTGCATCAGTGTCGTCATC
AAATTTATTAAGAAGAAATGTTAGAATTTTACTAATTGGTGATCCGGGAGTTGGAAAAAC
CTCATTGATTCTTTCACTTGTTAGTGAAGAATTTCCTGAAGAAGTGCCATCAAAAGCAGA
AGAAATCACAATTCCAGCTGATGTAACACCAGAACATGTGCCCACAAATATCGTTGATTA
TTCGGCATTGGAACAGAGTGAAGAAAATTTAATTGAAGAACTTCAGAAAGCTCATGTTGT
ATGTGTTGTTTATTCAGTGGACGATGAAAATTCGCTTGATCGAATCAGTTCATACTGGCT
ACC
>g5978.t4 Gene=g5978 Length=112
MVASSIASVSSSNLLRRNVRILLIGDPGVGKTSLILSLVSEEFPEEVPSKAEEITIPADV
TPEHVPTNIVDYSALEQSEENLIEELQKAHVVCVVYSVDDENSLDRISSYWL
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 5 | g5978.t4 | Gene3D | G3DSA:3.40.50.300 | - | 6 | 112 | 0.000 |
| 2 | g5978.t4 | PANTHER | PTHR24072:SF124 | MITOCHONDRIAL RHO GTPASE 1 | 16 | 112 | 0.000 |
| 3 | g5978.t4 | PANTHER | PTHR24072 | RHO FAMILY GTPASE | 16 | 112 | 0.000 |
| 1 | g5978.t4 | Pfam | PF00071 | Ras family | 20 | 111 | 0.000 |
| 6 | g5978.t4 | ProSiteProfiles | PS51423 | Miro domain profile. | 12 | 112 | 11.932 |
| 4 | g5978.t4 | SUPERFAMILY | SSF52540 | P-loop containing nucleoside triphosphate hydrolases | 18 | 111 | 0.000 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5978/g5978.t4; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5978.t4.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.
