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.t2 TSS g5978.t2 13154443 13154443
chr_2 g5978 g5978.t2 isoform g5978.t2 13155350 13158067
chr_2 g5978 g5978.t2 exon g5978.t2.exon1 13155350 13155681
chr_2 g5978 g5978.t2 cds g5978.t2.CDS1 13155350 13155681
chr_2 g5978 g5978.t2 exon g5978.t2.exon2 13155743 13155992
chr_2 g5978 g5978.t2 cds g5978.t2.CDS2 13155743 13155992
chr_2 g5978 g5978.t2 exon g5978.t2.exon3 13156055 13156295
chr_2 g5978 g5978.t2 cds g5978.t2.CDS3 13156055 13156295
chr_2 g5978 g5978.t2 exon g5978.t2.exon4 13156351 13156848
chr_2 g5978 g5978.t2 cds g5978.t2.CDS4 13156351 13156848
chr_2 g5978 g5978.t2 exon g5978.t2.exon5 13156905 13157361
chr_2 g5978 g5978.t2 cds g5978.t2.CDS5 13156905 13157361
chr_2 g5978 g5978.t2 exon g5978.t2.exon6 13157558 13157620
chr_2 g5978 g5978.t2 cds g5978.t2.CDS6 13157558 13157620
chr_2 g5978 g5978.t2 exon g5978.t2.exon7 13157938 13158067
chr_2 g5978 g5978.t2 cds g5978.t2.CDS7 13157938 13158067
chr_2 g5978 g5978.t2 TTS g5978.t2 13158181 13158181

Sequences

>g5978.t2 Gene=g5978 Length=1971
ATGGTTGCTTCATCGATTGCATCAGTGTCGTCATCAAATTTATTAAGAAGAAATGTTAGA
ATTTTACTAATTGGTGATCCGGGAGTTGGAAAAACCTCATTGATTCTTTCACTTGTTAGT
GAAGAATTTCCTGAAGAAGTGCCATCAAAAGCAGAAGAAATCACAATTCCAGCTGATGTA
ACACCAGAACATGTGCCCACAAATATCGTTGATTATTCGGCATTGGAACAGAGTGAAGAA
AATTTAATTGAAGAACTTCAGAAAGCTCATGTTGTATGTGTTGTTTATTCAGTGGACGAT
GAAAATTCGCTTGATCGAATCAGTTCATACTGGCTACCATTCATCCGCGAACACAATCAA
GGTGAAAATCGCAAACCCGTGGTACTTGTTGGAAATAAAATTGATTTAGTGGACTATTCA
ACGATTGATCATGTTCTCACTATCATGGAAGATTTCAATGAGATTGAAAGTTGTGTTGAA
TGCTCAGCAAAGACACTTCATAATATTTCCGAAATGTTTTATTATGCACAAAAAGCTGTT
TTGCATCCTACAGCACCGCTTTATATCATGGAAGAGCAAGATTTGACAGAAAAGTGTAAG
AAAGCACTTATAAGAATATTTAAAGTTTGTGATATTGATGGTGATGGATTGCTTAATGAT
TATGAATTAAATCACTTTCAAAGGCGATGCTTTAATGCGCCATTACAGCCAACAGTTCTC
GATGAGGTTAAAGCAGTTTTGATGAAAAATACACCGGATGGAATAAGAGATGATTGTGTT
ACACTCAGTGGATTTCTTTTTCTCCACTGCCTTTTTATTCAACGTGGACGTAATGAAACA
ACTTGGGCTGTTTTGAGACGATTTGGTTACAATGAAAATTTAGAAATGAGTAAAGATTAT
TTATGTCCATCAATAAAAATTCCTCCAGGTTCAAGTACAGAATTATCGCATCGCGGTCAA
CAATTTTTGATGGCATTATTTGAGAGAAGTGATAAAGATAATGATGGAGCTCTTTCACCA
GATGAATTCAAACGTGTGTTTAGTGCTTGTCCATCACCTCCATTTTCGAGTGATATAAAA
AGAACTGTTCCAACTAATGATAAAGGATGGCCCACTCAGCATGGTTGGATTTGTCGATGG
ACACTTCAAACATTCATTGAACTTCCAAAAACCCTTGAGTATCTTGCCTATCTCGGTTTT
AATGTACACGAAAATGAATCGCAATTGACAGCAATTCATGTAACACGTGAGCGACGAATT
GATTTGGCAAAGAAACAAAGTAGCAGAACGACATATATGTGCCATGTAATCGGAATGAAA
GGTGCTGGAAAGACTGCATTGTGTCGAGCATTTTTAGTCGATGATATGAAAAAGTTGAAG
GACAAAGATTTGCGTGGAAATAACCAGTACTGTATTAATACAGTTCAAGTTTATGGACAA
GAAAAATATTTGATACTTCGTGATATAGATGTCCGACAAGTTCTCGATCCGCTTCAACCA
CAAGAAGTGTTGTGTGATGTCGCGTGCTTAGTTTATGATATTAGTGATCCAAAATCATTT
GAGTATATTGCAAGGATATACATAAAATACTTTGCTGAAAGTAAAATTCCAGTGCTTATA
GTGGGAGCGAAAGGCGATATGGAGGAAAAGAGACAAGACTATCTTCTCCAGCCTGCTGAA
TTTTGCCAAAAATATAAATTATTACCACCTCAGTACTTTAGTTTCAAGCACAATAAACGT
GATCTTTATATTAAACTTGGAACAATGGCATCATTTCCGAGATTTCAACCAGCTTGGATT
TTGTTTTATAAACACAGGTTCGTTCAACTGTGGGAGGAGACTCAACTTAAGCATTTTGGA
TTAATGACCAATGACCCGACGTTGTGGTGGAAAACAGTATTAGGCATAGCAACATGCTCA
GTTTTGGGATTCTTCGTAGTTCGCGCTCTCCATTCAGCTACAACACGATGA

>g5978.t2 Gene=g5978 Length=656
MVASSIASVSSSNLLRRNVRILLIGDPGVGKTSLILSLVSEEFPEEVPSKAEEITIPADV
TPEHVPTNIVDYSALEQSEENLIEELQKAHVVCVVYSVDDENSLDRISSYWLPFIREHNQ
GENRKPVVLVGNKIDLVDYSTIDHVLTIMEDFNEIESCVECSAKTLHNISEMFYYAQKAV
LHPTAPLYIMEEQDLTEKCKKALIRIFKVCDIDGDGLLNDYELNHFQRRCFNAPLQPTVL
DEVKAVLMKNTPDGIRDDCVTLSGFLFLHCLFIQRGRNETTWAVLRRFGYNENLEMSKDY
LCPSIKIPPGSSTELSHRGQQFLMALFERSDKDNDGALSPDEFKRVFSACPSPPFSSDIK
RTVPTNDKGWPTQHGWICRWTLQTFIELPKTLEYLAYLGFNVHENESQLTAIHVTRERRI
DLAKKQSSRTTYMCHVIGMKGAGKTALCRAFLVDDMKKLKDKDLRGNNQYCINTVQVYGQ
EKYLILRDIDVRQVLDPLQPQEVLCDVACLVYDISDPKSFEYIARIYIKYFAESKIPVLI
VGAKGDMEEKRQDYLLQPAEFCQKYKLLPPQYFSFKHNKRDLYIKLGTMASFPRFQPAWI
LFYKHRFVQLWEETQLKHFGLMTNDPTLWWKTVLGIATCSVLGFFVVRALHSATTR

Protein features from InterProScan

Transcript Database ID Name Start End E.value
22 g5978.t2 CDD cd01893 Miro1 17 183 3.51584E-89
21 g5978.t2 CDD cd01892 Miro2 429 605 1.31316E-66
13 g5978.t2 Gene3D G3DSA:3.40.50.300 - 16 186 2.9E-32
16 g5978.t2 Gene3D G3DSA:1.10.238.10 - 189 294 2.0E-39
15 g5978.t2 Gene3D G3DSA:1.10.238.10 - 296 489 1.5E-64
14 g5978.t2 Gene3D G3DSA:3.40.50.300 - 490 591 1.7E-27
5 g5978.t2 PANTHER PTHR24072:SF311 MITOCHONDRIAL RHO GTPASE 2 16 458 3.2E-167
6 g5978.t2 PANTHER PTHR24072 RHO FAMILY GTPASE 16 458 3.2E-167
20 g5978.t2 PIRSF PIRSF037488 Miro 15 639 2.9E-208
7 g5978.t2 PRINTS PR00449 Transforming protein P21 ras signature 19 40 2.5E-15
9 g5978.t2 PRINTS PR00449 Transforming protein P21 ras signature 123 136 2.5E-15
8 g5978.t2 PRINTS PR00449 Transforming protein P21 ras signature 158 180 2.5E-15
2 g5978.t2 Pfam PF00071 Ras family 20 180 2.3E-20
3 g5978.t2 Pfam PF08356 EF hand associated 234 319 3.2E-32
4 g5978.t2 Pfam PF08355 EF hand associated 357 426 8.0E-23
1 g5978.t2 Pfam PF00071 Ras family 436 566 1.4E-7
18 g5978.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 1 627 -
19 g5978.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 628 650 -
17 g5978.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 651 656 -
30 g5978.t2 ProSitePatterns PS00018 EF-hand calcium-binding domain. 211 223 -
29 g5978.t2 ProSitePatterns PS00018 EF-hand calcium-binding domain. 331 343 -
35 g5978.t2 ProSiteProfiles PS51423 Miro domain profile. 12 191 14.885
32 g5978.t2 ProSiteProfiles PS50222 EF-hand calcium-binding domain profile. 198 233 7.651
33 g5978.t2 ProSiteProfiles PS50222 EF-hand calcium-binding domain profile. 318 353 11.835
34 g5978.t2 ProSiteProfiles PS51423 Miro domain profile. 425 577 15.871
24 g5978.t2 SMART SM00173 ras_sub_4 16 183 2.3E-6
27 g5978.t2 SMART SM00175 rab_sub_5 19 183 1.1E-7
28 g5978.t2 SMART SM00174 rho_sub_3 21 183 4.2E-10
26 g5978.t2 SMART SM00054 efh_1 202 230 3.3
25 g5978.t2 SMART SM00054 efh_1 322 350 0.0096
11 g5978.t2 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 16 216 3.81E-35
12 g5978.t2 SUPERFAMILY SSF47473 EF-hand 183 382 9.76E-20
10 g5978.t2 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 429 579 5.8E-20
31 g5978.t2 TIGRFAM TIGR00231 small_GTP: small GTP-binding protein domain 18 176 3.7E-12
23 g5978.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 628 650 -

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

Data is missing for g5978/g5978.t2; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5978.t2.fa.iupred3.txt does not exist

GO terms from InterProScan

GOID TERM ONTOLOGY
GO:0031307 integral component of mitochondrial outer membrane CC
GO:0005509 calcium ion binding MF
GO:0005525 GTP binding MF
GO:0007005 mitochondrion organization BP
GO:0003924 GTPase activity MF

KEGG

Orthology

Pathway

  • This transcript belongs to the following pathways

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