General information for g12287.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Elongation factor 2.
Parent gene
- The parent gene g12287 is located on chr_1: 22172800..22173568 (+ 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_1 | g12287 | g12287.t1 | TSS | g12287.t1 | 22169311 | 22169311 |
| chr_1 | g12287 | g12287.t1 | isoform | g12287.t1 | 22169380 | 22173107 |
| chr_1 | g12287 | g12287.t1 | exon | g12287.t1.exon1 | 22169380 | 22169382 |
| chr_1 | g12287 | g12287.t1 | cds | g12287.t1.CDS1 | 22169380 | 22169382 |
| chr_1 | g12287 | g12287.t1 | exon | g12287.t1.exon2 | 22169830 | 22170044 |
| chr_1 | g12287 | g12287.t1 | cds | g12287.t1.CDS2 | 22169830 | 22170044 |
| chr_1 | g12287 | g12287.t1 | exon | g12287.t1.exon3 | 22170108 | 22170301 |
| chr_1 | g12287 | g12287.t1 | cds | g12287.t1.CDS3 | 22170108 | 22170301 |
| chr_1 | g12287 | g12287.t1 | exon | g12287.t1.exon4 | 22170545 | 22171575 |
| chr_1 | g12287 | g12287.t1 | cds | g12287.t1.CDS4 | 22170545 | 22171575 |
| chr_1 | g12287 | g12287.t1 | exon | g12287.t1.exon5 | 22171753 | 22172190 |
| chr_1 | g12287 | g12287.t1 | cds | g12287.t1.CDS5 | 22171753 | 22172190 |
| chr_1 | g12287 | g12287.t1 | exon | g12287.t1.exon6 | 22172261 | 22172432 |
| chr_1 | g12287 | g12287.t1 | cds | g12287.t1.CDS6 | 22172261 | 22172432 |
| chr_1 | g12287 | g12287.t1 | exon | g12287.t1.exon7 | 22172626 | 22173107 |
| chr_1 | g12287 | g12287.t1 | cds | g12287.t1.CDS7 | 22172626 | 22173107 |
| chr_1 | g12287 | g12287.t1 | TTS | g12287.t1 | 22173564 | 22173564 |
Sequences
>g12287.t1 Gene=g12287 Length=2535
ATGGTCAACTTTACTGTCGACGAAATCCGTGCTATGATGGACAAGAAGAAGAACATCCGT
AATATGTCTGTCATTGCTCATGTCGATCACGGAAAATCTACTTTAACTGATTCGTTGGTT
TCAAAAGCTGGTATTATTGCTGGTGCAAAAGCTGGTGAAACAAGATTCACAGACACACGC
AAGGATGAACAAGAAAGATGTATCACAATTAAGTCAACTGCTATCTCTATGTTCTTTGAG
TTAGAAGACAAAGATTTGGTTTTCATTACAAATCCTGATCAACGTGACAAAGAAGAAAAA
GGTTTCTTGATTAATTTGATTGACTCACCCGGTCACGTTGATTTCTCATCAGAAGTCACA
GCCGCTCTTCGTGTTACTGATGGTGCTCTTGTTGTTGTCGATTGCGTATCAGGTGTTTGT
GTACAAACTGAGACTGTATTGCGTCAAGCTATTGCCGAACGTATTAAGCCAGTTTTGTTC
ATGAACAAGATGGACCGTGCTTTGTTGGAATTGCAATTGGATGCTGAAGATTTGTACCAA
ACATTCCAACGTATCGTCGAAAACGTCAACGTTATCATCGCCACTTACAGCGATGACGAT
GGTCCAATGGGAGAAGTTCGTGTTGATCCATCAAAGGGTTCAGTCGGTTTCGGTTCCGGC
TTGCACGGATGGGCTTTCACTCTCAAACAATTTTCGGAAATGTATGCAGCTAAATTCAAG
ATCGATGTCGTTAAACTCATGAATCGCTTATGGGGTGAAAATTTCTTCAATGCAAAGACC
AAGAAATGGGCAAAGACAAAGGACGATGATAACAAGCGTTCATTTGTCATGTATGTATTG
GATCCAATTTATAAGGTATTCGATGTCATTATGAATTACAAGAAAGAAGAAATTCCTGGC
TTATTGGAGAAAATCGGAGTCACACTCAAGCACGAAGACAAAGATAAGGATGGTAAACAA
TTATTGAAAGTTGTCATGCGCTCATGGTTGCCAGCTGGTGAAGCTTTACTTCAAATGATT
GCTATTCACTTGCCTTCACCAGTCGTCGCTCAAAAATACCGTATGGAAATGTTGTATGAG
GGACCACTCGATGACGAGGCTGCCGTTGCTGTCAAGAACTGCGATCCAAATGGTCCATTG
ATGATGTACGTCTCAAAAATGGTACCAACCAGTGACAAGGGTCGTTTCTATGCTTTCGGA
CGTGTGTTCTCCGGAAAAGTTCAAACTGGTCAAAAATGCCGTATAATGGGACCAAATTAC
ACACCTGGCAAGAAGGAAGACTTGTACGAAAAATCAATTCAACGTACTATTTTGATGATG
GGTCGTTATGTTGAAGCCATTGAAGATGTTCCATGCGGTAACATTTGCGGTTTGGTTGGT
GTTGATCAATTCTTGGTCAAGACTGGAACAATCACAACATTCAAAGATGCCCATAACATG
AAGGTCATGAAATTTTCAGTTTCACCTGTCGTGCGTGTTGCTGTCGAGCCTAAAAATCCA
GCTGATTTGCCCAAACTCGTCGAAGGTCTTAAGCGTTTGGCTAAATCCGATCCTATGGTA
CAATGTATCATTGAAGAATCTGGCGAACATATTATTGCTGGTGCTGGTGAATTGCATTTG
GAAATTTGCTTGAAGGACTTGGAAGAAGATCACGCTTGTATCCCATTGAAGAAATCCGAT
CCAGTTGTATCGTATCGTGAAACAGTCTCTGATGAATCATCCATGATGTGTTTATCAAAA
TCACCAAACAAGCATAATCGTCTTTTCATGAAGGCCATGCCTATGCCTGATGGTCTTGCT
GAAGATATTGATGGAGGTGCAGTTAATGCTCGTGACGATTTCAAGATTCGTGCACGTTAC
TTGGCTGAGAAATACGAATGGGATGTTACAGAAGCTCGTAAGATTTGGTGTTTCGGTCCA
GACGGTACAGGTCCAAATGTAATTGTTGACGTCACTAAGGGTGTACAATATTTGAATGAA
ATCAAGGACTCTGTTGTTGCTGGCTTCCAATGGGCTACAAAAGAAGGTGTCTTGGCTGAA
GAGAACATGAGAGCTGTTCGTTTCAACATTTATGATGTTACACTGCATGCTGACGCTATC
CATCGTGGAGGTGGTCAAATCATTCCAACAACTCGTCGTTGCTTGTATGCATCATACATC
ACAGCTTCTCCACGTTTGATGGAGCCAGTTTATTTGTGTGAAATTCAATGTCCAGAAGTT
GCTGTCGGTGGTATTTATGGTGTGCTTAATCGTCGTCGTGGTCATGTCTTTGAAGAATCA
CAAGTTGCCGGTACACCTATGTTCGTTGTCAAAGCTTATTTGCCTGTAAATGAATCATTT
GGATTCACTGCTGATTTGCGCTCAAATACTGGAGGTCAAGCTTTCCCACAATGTGTATTT
GACCATTGGCAGATCTTCCCAGGTGACCCTAACGAACCATCATCAAAACCATACCAGATT
GTGCAAGATACAAGAAAACGTAAAGGTCTCAAAGAAGGTTTACCAGATTTGAACCAATAC
TATGATAAAATGTAA
>g12287.t1 Gene=g12287 Length=844
MVNFTVDEIRAMMDKKKNIRNMSVIAHVDHGKSTLTDSLVSKAGIIAGAKAGETRFTDTR
KDEQERCITIKSTAISMFFELEDKDLVFITNPDQRDKEEKGFLINLIDSPGHVDFSSEVT
AALRVTDGALVVVDCVSGVCVQTETVLRQAIAERIKPVLFMNKMDRALLELQLDAEDLYQ
TFQRIVENVNVIIATYSDDDGPMGEVRVDPSKGSVGFGSGLHGWAFTLKQFSEMYAAKFK
IDVVKLMNRLWGENFFNAKTKKWAKTKDDDNKRSFVMYVLDPIYKVFDVIMNYKKEEIPG
LLEKIGVTLKHEDKDKDGKQLLKVVMRSWLPAGEALLQMIAIHLPSPVVAQKYRMEMLYE
GPLDDEAAVAVKNCDPNGPLMMYVSKMVPTSDKGRFYAFGRVFSGKVQTGQKCRIMGPNY
TPGKKEDLYEKSIQRTILMMGRYVEAIEDVPCGNICGLVGVDQFLVKTGTITTFKDAHNM
KVMKFSVSPVVRVAVEPKNPADLPKLVEGLKRLAKSDPMVQCIIEESGEHIIAGAGELHL
EICLKDLEEDHACIPLKKSDPVVSYRETVSDESSMMCLSKSPNKHNRLFMKAMPMPDGLA
EDIDGGAVNARDDFKIRARYLAEKYEWDVTEARKIWCFGPDGTGPNVIVDVTKGVQYLNE
IKDSVVAGFQWATKEGVLAEENMRAVRFNIYDVTLHADAIHRGGGQIIPTTRRCLYASYI
TASPRLMEPVYLCEIQCPEVAVGGIYGVLNRRRGHVFEESQVAGTPMFVVKAYLPVNESF
GFTADLRSNTGGQAFPQCVFDHWQIFPGDPNEPSSKPYQIVQDTRKRKGLKEGLPDLNQY
YDKM
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 28 | g12287.t1 | CDD | cd01885 | EF2 | 20 | 236 | 1.88115E-120 |
| 27 | g12287.t1 | CDD | cd03700 | EF2_snRNP_like_II | 380 | 474 | 4.45524E-54 |
| 26 | g12287.t1 | CDD | cd16261 | EF2_snRNP_III | 489 | 560 | 7.87641E-43 |
| 25 | g12287.t1 | CDD | cd01681 | aeEF2_snRNP_like_IV | 560 | 732 | 1.12441E-105 |
| 24 | g12287.t1 | CDD | cd04096 | eEF2_snRNP_like_C | 728 | 807 | 1.25918E-49 |
| 18 | g12287.t1 | Gene3D | G3DSA:3.40.50.300 | - | 13 | 346 | 2.2E-189 |
| 22 | g12287.t1 | Gene3D | G3DSA:2.40.30.10 | Translation factors | 49 | 473 | 2.2E-189 |
| 23 | g12287.t1 | Gene3D | G3DSA:3.90.1430.10 | Yeast translation eEF2 (G’ domain) | 228 | 330 | 2.2E-189 |
| 20 | g12287.t1 | Gene3D | G3DSA:3.30.70.870 | Elongation Factor G (Translational Gtpase) | 487 | 564 | 1.5E-38 |
| 21 | g12287.t1 | Gene3D | G3DSA:3.30.70.240 | - | 566 | 830 | 5.6E-127 |
| 19 | g12287.t1 | Gene3D | G3DSA:3.30.230.10 | - | 572 | 832 | 5.6E-127 |
| 6 | g12287.t1 | PANTHER | PTHR42908:SF24 | EUKARYOTIC TRANSLATION ELONGATION FACTOR 2, GENE 2 | 1 | 844 | 0.0 |
| 7 | g12287.t1 | PANTHER | PTHR42908 | TRANSLATION ELONGATION FACTOR-RELATED | 1 | 844 | 0.0 |
| 12 | g12287.t1 | PRINTS | PR00315 | GTP-binding elongation factor signature | 21 | 34 | 4.5E-13 |
| 11 | g12287.t1 | PRINTS | PR00315 | GTP-binding elongation factor signature | 65 | 73 | 4.5E-13 |
| 10 | g12287.t1 | PRINTS | PR00315 | GTP-binding elongation factor signature | 105 | 115 | 4.5E-13 |
| 9 | g12287.t1 | PRINTS | PR00315 | GTP-binding elongation factor signature | 121 | 132 | 4.5E-13 |
| 8 | g12287.t1 | PRINTS | PR00315 | GTP-binding elongation factor signature | 157 | 166 | 4.5E-13 |
| 4 | g12287.t1 | Pfam | PF00009 | Elongation factor Tu GTP binding domain | 17 | 345 | 8.4E-67 |
| 3 | g12287.t1 | Pfam | PF03144 | Elongation factor Tu domain 2 | 397 | 471 | 3.7E-13 |
| 1 | g12287.t1 | Pfam | PF14492 | Elongation Factor G, domain III | 489 | 550 | 1.6E-13 |
| 2 | g12287.t1 | Pfam | PF03764 | Elongation factor G, domain IV | 608 | 722 | 1.6E-31 |
| 5 | g12287.t1 | Pfam | PF00679 | Elongation factor G C-terminus | 725 | 811 | 5.0E-22 |
| 29 | g12287.t1 | ProSitePatterns | PS00301 | Translational (tr)-type guanine nucleotide-binding (G) domain signature. | 58 | 73 | - |
| 33 | g12287.t1 | ProSiteProfiles | PS51722 | Translational (tr)-type guanine nucleotide-binding (G) domain profile. | 17 | 348 | 54.195 |
| 30 | g12287.t1 | SMART | SM00889 | EFG_IV_2 | 607 | 723 | 1.3E-27 |
| 31 | g12287.t1 | SMART | SM00838 | EFG_C_a | 725 | 814 | 2.6E-19 |
| 14 | g12287.t1 | SUPERFAMILY | SSF52540 | P-loop containing nucleoside triphosphate hydrolases | 4 | 345 | 1.66E-110 |
| 17 | g12287.t1 | SUPERFAMILY | SSF50447 | Translation proteins | 346 | 483 | 6.19E-45 |
| 16 | g12287.t1 | SUPERFAMILY | SSF54980 | EF-G C-terminal domain-like | 486 | 561 | 9.71E-21 |
| 13 | g12287.t1 | SUPERFAMILY | SSF54211 | Ribosomal protein S5 domain 2-like | 563 | 727 | 2.53E-70 |
| 15 | g12287.t1 | SUPERFAMILY | SSF54980 | EF-G C-terminal domain-like | 728 | 842 | 6.23E-34 |
| 32 | g12287.t1 | TIGRFAM | TIGR00231 | small_GTP: small GTP-binding protein domain | 19 | 168 | 4.4E-18 |
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:0005525 | GTP binding | MF |
| GO:0003924 | GTPase activity | MF |
KEGG
Orthology
- This transcript has been annotated with K03234 (elongation factor 2)
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.
