General information for g3703.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Elongation factor Tu, mitochondrial.
Parent gene
- The parent gene g3703 is located on chr_3: 27561217..27563392 (+ 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_3 | g3703 | g3703.t1 | TSS | g3703.t1 | 27559298 | 27559298 |
| chr_3 | g3703 | g3703.t1 | isoform | g3703.t1 | 27559446 | 27561217 |
| chr_3 | g3703 | g3703.t1 | exon | g3703.t1.exon1 | 27559446 | 27559485 |
| chr_3 | g3703 | g3703.t1 | cds | g3703.t1.CDS1 | 27559446 | 27559485 |
| chr_3 | g3703 | g3703.t1 | exon | g3703.t1.exon2 | 27559554 | 27559676 |
| chr_3 | g3703 | g3703.t1 | cds | g3703.t1.CDS2 | 27559554 | 27559676 |
| chr_3 | g3703 | g3703.t1 | exon | g3703.t1.exon3 | 27559735 | 27559779 |
| chr_3 | g3703 | g3703.t1 | cds | g3703.t1.CDS3 | 27559735 | 27559779 |
| chr_3 | g3703 | g3703.t1 | exon | g3703.t1.exon4 | 27559835 | 27560014 |
| chr_3 | g3703 | g3703.t1 | cds | g3703.t1.CDS4 | 27559835 | 27560014 |
| chr_3 | g3703 | g3703.t1 | exon | g3703.t1.exon5 | 27560072 | 27560596 |
| chr_3 | g3703 | g3703.t1 | cds | g3703.t1.CDS5 | 27560072 | 27560596 |
| chr_3 | g3703 | g3703.t1 | exon | g3703.t1.exon6 | 27560672 | 27560767 |
| chr_3 | g3703 | g3703.t1 | cds | g3703.t1.CDS6 | 27560672 | 27560767 |
| chr_3 | g3703 | g3703.t1 | exon | g3703.t1.exon7 | 27560820 | 27561217 |
| chr_3 | g3703 | g3703.t1 | cds | g3703.t1.CDS7 | 27560820 | 27561217 |
| chr_3 | g3703 | g3703.t1 | TTS | g3703.t1 | 27561360 | 27561360 |
Sequences
>g3703.t1 Gene=g3703 Length=1407
ATGTCGGCTTTAGTAGCTGTTAAACAAGCATTATCGCCAGCTCTTCGCTCCACATTCAGA
CAATTTCTGTTAAATACCAATGTTAAGTCATCAGGTTGCATTTCTGTATCGCCATTTATC
ATTTCAAAAAGATATTTTGCAGAGAAAAAAGTTTTCCAAAGAACTAAACCTCATTGCAAT
ATTGGCACAATTGGGCATGTAGATCACGGCAAAACGACATTGACAGCTGCTATAACAAAA
GTATTGGCTGAAAAAGATTTAGCTGAAAGTAAAGCATATTCTGATATAGATAATGCACCA
GAAGAAAAAGCTCGTGGAATCACAATCAATGTAGCTCATATTGAATATCAAACAGATAAT
CGTCATTATGGACATACAGATTGCCCTGGACATGCTGATTATATTAAAAACATGATTACG
GGTACTGCACAAATGGATGGAGCTATTTTAGTCGTCGCTGCAACGGATGGAGCTATGCCT
CAAACTAGAGAACATCTCTTATTGGCTAAACAAATTGGAGTTAATGATATTGTTGTATTT
ATTAATAAAGTAGACGCTGCTGATGCTGAAATGGTTGAACTTGTTGAGATGGAAATTCGT
GAACTCATGACAGAAATGGGCTATGATGGCGATAAAGTTCCTATTATTAAAGGTTCAGCA
TTGTGCGCATTAGAAGAGAAAAATCCAGATATCGGTCAAAAAGCAATTTTGGAACTTCTT
GATACTGTTGATAAGACAATTCCTACTCCAGTTAGAGAGTTAGATAAACCATTCCTATTA
CCTGTTGAAAATGTCTATAGCATTCAAGGTCGCGGTACAGTTGTGTCGGGAAGATTAGAA
CGAGGTGTTTTAAAGAAGGGAGCTGAATGTGAATTTGTTGGATATAACAAAGTATTGAAA
TCAACTGTTACAGGAGTTGAAATGTTCCATCAAATTCTCGAAGAAGCTCAAGCAGGTGAT
CAACTTGGTGCATTAGTCAGAGGAGTGAAGCGTGACGATATTAAAAGAGGTATGGTAATG
TGTAAACCTGGATCATGCAAAGCAATTGATCAAGTTGAAGCCCAAGTTTACATTTTAAGC
AAAGAAGAAGGCGGTCGAACAAAACCTTTTACAAGCTTCTTCCAATTACAAATGTTCTCA
CGTACATGGGACTGTGCTGCTGTTTGTATAATACCTGGAAAAGAAATGTGTATGCCAGGT
GAAGATACAAGTCTTCAATTGAAACTTTTTAGACCAATGGTTCTTGAACAAGGACAGAGA
TTCACACTTAGAGATGGCAAAATTACACTTGGAACTGGCGTTGTAACTAAAATTTTACCA
CCATTATCTGAAATAGAACGACAAGAATTGACAGAAGGTAAGAAAGGACGTGAAAAGAAA
GAGAAAAAGAACAAGAAAACAGTTTAA
>g3703.t1 Gene=g3703 Length=468
MSALVAVKQALSPALRSTFRQFLLNTNVKSSGCISVSPFIISKRYFAEKKVFQRTKPHCN
IGTIGHVDHGKTTLTAAITKVLAEKDLAESKAYSDIDNAPEEKARGITINVAHIEYQTDN
RHYGHTDCPGHADYIKNMITGTAQMDGAILVVAATDGAMPQTREHLLLAKQIGVNDIVVF
INKVDAADAEMVELVEMEIRELMTEMGYDGDKVPIIKGSALCALEEKNPDIGQKAILELL
DTVDKTIPTPVRELDKPFLLPVENVYSIQGRGTVVSGRLERGVLKKGAECEFVGYNKVLK
STVTGVEMFHQILEEAQAGDQLGALVRGVKRDDIKRGMVMCKPGSCKAIDQVEAQVYILS
KEEGGRTKPFTSFFQLQMFSRTWDCAAVCIIPGKEMCMPGEDTSLQLKLFRPMVLEQGQR
FTLRDGKITLGTGVVTKILPPLSEIERQELTEGKKGREKKEKKNKKTV
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 24 | g3703.t1 | CDD | cd01884 | EF_Tu | 57 | 250 | 8.65286E-143 |
| 23 | g3703.t1 | CDD | cd03697 | EFTU_II | 258 | 344 | 3.47511E-49 |
| 22 | g3703.t1 | CDD | cd03706 | mtEFTU_III | 347 | 438 | 1.75481E-51 |
| 14 | g3703.t1 | Gene3D | G3DSA:3.40.50.300 | - | 48 | 250 | 8.8E-67 |
| 15 | g3703.t1 | Gene3D | G3DSA:2.40.30.10 | Translation factors | 253 | 347 | 5.2E-34 |
| 16 | g3703.t1 | Gene3D | G3DSA:2.40.30.10 | Translation factors | 350 | 448 | 2.5E-31 |
| 26 | g3703.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 446 | 468 | - |
| 4 | g3703.t1 | PANTHER | PTHR43721:SF22 | ELONGATION FACTOR TU, MITOCHONDRIAL | 47 | 439 | 4.5E-198 |
| 5 | g3703.t1 | PANTHER | PTHR43721 | ELONGATION FACTOR TU-RELATED | 47 | 439 | 4.5E-198 |
| 10 | g3703.t1 | PRINTS | PR00315 | GTP-binding elongation factor signature | 60 | 73 | 5.6E-24 |
| 7 | g3703.t1 | PRINTS | PR00315 | GTP-binding elongation factor signature | 104 | 112 | 5.6E-24 |
| 6 | g3703.t1 | PRINTS | PR00315 | GTP-binding elongation factor signature | 124 | 134 | 5.6E-24 |
| 9 | g3703.t1 | PRINTS | PR00315 | GTP-binding elongation factor signature | 140 | 151 | 5.6E-24 |
| 8 | g3703.t1 | PRINTS | PR00315 | GTP-binding elongation factor signature | 177 | 186 | 5.6E-24 |
| 3 | g3703.t1 | Pfam | PF00009 | Elongation factor Tu GTP binding domain | 56 | 248 | 7.3E-56 |
| 2 | g3703.t1 | Pfam | PF03144 | Elongation factor Tu domain 2 | 272 | 341 | 1.9E-15 |
| 1 | g3703.t1 | Pfam | PF03143 | Elongation factor Tu C-terminal domain | 346 | 438 | 2.2E-23 |
| 18 | g3703.t1 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 16 | - |
| 19 | g3703.t1 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 2 | - |
| 20 | g3703.t1 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 3 | 11 | - |
| 21 | g3703.t1 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 12 | 16 | - |
| 17 | g3703.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 17 | 468 | - |
| 25 | g3703.t1 | ProSitePatterns | PS00301 | Translational (tr)-type guanine nucleotide-binding (G) domain signature. | 97 | 112 | - |
| 29 | g3703.t1 | ProSiteProfiles | PS51722 | Translational (tr)-type guanine nucleotide-binding (G) domain profile. | 56 | 251 | 57.627 |
| 12 | g3703.t1 | SUPERFAMILY | SSF52540 | P-loop containing nucleoside triphosphate hydrolases | 55 | 273 | 8.46E-58 |
| 13 | g3703.t1 | SUPERFAMILY | SSF50447 | Translation proteins | 252 | 345 | 5.3E-27 |
| 11 | g3703.t1 | SUPERFAMILY | SSF50465 | EF-Tu/eEF-1alpha/eIF2-gamma C-terminal domain | 350 | 443 | 4.56E-31 |
| 27 | g3703.t1 | TIGRFAM | TIGR00485 | EF-Tu: translation elongation factor Tu | 49 | 439 | 5.0E-175 |
| 28 | g3703.t1 | TIGRFAM | TIGR00231 | small_GTP: small GTP-binding protein domain | 60 | 196 | 1.1E-11 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
GO terms from InterProScan
| GOID | TERM | ONTOLOGY |
|---|---|---|
| GO:0003746 | translation elongation factor activity | MF |
| GO:0006414 | translational elongation | BP |
| GO:0005525 | GTP binding | MF |
| GO:0003924 | GTPase activity | MF |
KEGG
Orthology
- This transcript has been annotated with K02358 (elongation factor Tu)
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.
