General information for g2508.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Protein-S-isoprenylcysteine O-methyltransferase.
Parent gene
- The parent gene g2508 is located on chr_3: 18335879..18337750 (+ 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 | g2508 | g2508.t1 | TSS | g2508.t1 | 18333862 | 18333862 |
| chr_3 | g2508 | g2508.t1 | isoform | g2508.t1 | 18334439 | 18337010 |
| chr_3 | g2508 | g2508.t1 | exon | g2508.t1.exon1 | 18334439 | 18334560 |
| chr_3 | g2508 | g2508.t1 | cds | g2508.t1.CDS1 | 18334439 | 18334560 |
| chr_3 | g2508 | g2508.t1 | exon | g2508.t1.exon2 | 18334616 | 18335460 |
| chr_3 | g2508 | g2508.t1 | cds | g2508.t1.CDS2 | 18334616 | 18335460 |
| chr_3 | g2508 | g2508.t1 | exon | g2508.t1.exon3 | 18335809 | 18335816 |
| chr_3 | g2508 | g2508.t1 | cds | g2508.t1.CDS3 | 18335809 | 18335816 |
| chr_3 | g2508 | g2508.t1 | exon | g2508.t1.exon4 | 18335881 | 18336327 |
| chr_3 | g2508 | g2508.t1 | cds | g2508.t1.CDS4 | 18335881 | 18336327 |
| chr_3 | g2508 | g2508.t1 | exon | g2508.t1.exon5 | 18336707 | 18336739 |
| chr_3 | g2508 | g2508.t1 | cds | g2508.t1.CDS5 | 18336707 | 18336739 |
| chr_3 | g2508 | g2508.t1 | exon | g2508.t1.exon6 | 18336828 | 18337010 |
| chr_3 | g2508 | g2508.t1 | cds | g2508.t1.CDS6 | 18336828 | 18337010 |
| chr_3 | g2508 | g2508.t1 | TTS | g2508.t1 | NA | NA |
Sequences
>g2508.t1 Gene=g2508 Length=1638
ATGATTTTTAGGAATTTTTGTCATAAAATAAAATGGAAATATTTAGAATTATCTCGTAAT
TATTCACATAAAATTTTATTTTTCGGAACAGATAATTTCTCACTTCCATCATTAAAATTA
ATAACTAAACAAAATGATCTATATTCACGTCTTGAGGTTGTCACTTCTTTTAAATCAAAG
AAAAATCCAATAAAAGACTTTGCTAACGAACAAAAATTACCTGTGCATGATTGGGAAAGT
CTTAAAAACGATTTAAAAATATTTAGTGAATTTGACATAGGTTTAGTTGTTTCTTTTGGT
CATTTAATTCCTGAAAATATTATTAATAATTTTCATAAAGGGATGCTAAATGTACATGCA
AGTCTACTGCCAAAATATCGAGGTGCGAGTCCTATAATTTACGCTATAAAAAATCATGAA
ACTATAACAGGTGTATCAATAATGAAAATCAAGGCAAAAAAGTTTGATGTAGGGGATGTA
CTTGCGATGAAAGAAGTATCTATAACAGATGACATTCTTATGTCAGAATTACACGACCAA
TTAGCTAATTTAGGAGCACAATTATTAATCGATTGTCTCAAACATTTAGAAGAATGTAAG
CCAATAAAGCAAGACGAGAGCCAAGCATCATACGCACCTAAAATTGATAAAGAATTTTGC
AAAGTAAGATGGAATGAAATGAGTGCACGTGAGATTTATGATTTATACAGAGCACTCTAT
TCTTACAAGCATGTGTTGACAACATTTAAAAATGAACCGGTTAAGTTGTTAGAATTAAAA
AAATCTAATGAAGTCATTGAATATAACATTGCTGGACATTTAAAATTTTGTAAAAAAACG
AAAAAACTATTAGTGCATTGTGTTGATGGTGAATGTATAGAAATTAATAAATTACTGATA
GCTAAAAAAGTGATGAGTGCATCAGATTTTAATAATGGATTCTTAAAAAACATAAATGAT
TTTGAAAACTTTCAGATTGCTATTCGAGCTGGAATTTTAGGGTATTTTTTTGGCATTGCT
CTTTTTATTTCAATTACAATGGAGGATAAATACAAGTCTTTTGGAATTTATTTGGCTTTT
TTAACATTCTTTCATTACTCGGAGTATTTTGTAATTTCGTTAAGTCATCCAGAATCATTG
ACACTTGATTCTTTTATGCTTAATCATTCAATTCAATATGAATTTGCGGCTATAATTAGT
TGGATAGAATATTTCGTTGAAGTTTATTATTATCCTGAAATGAAAAAGTGCAAAACAATT
TGGATAATAGGTTCTACTATTTGCTTAAGTGGTGAAATTTTGAGAAAGGTTGCAATGTTA
ACAGCCAAAAAAAGTTTCCATCATTTAGTGCAATTTCAGCAAGCCGATGATCATAAATTA
ATAACGATAGGAGTTTATAGTTGGTTTCGACATCCTGCTTATGTGGGATGGTTTTATTGG
TCTATAGCTACTCAGCTAATAATGGCAAACCCAATTTGTTTTGTTCTCTATCTCATTGCA
AGCTGGCTTTTTTTCAAAGAGAGAATCCATACTGAAGAGATCACTTTACTCAATTTCTTT
GGACAAGAATATGTTCAATATCAGCAAAGAACAAAGACTGGTTTACCATTCATAAATGGA
TATATTACAACAAACTAA
>g2508.t1 Gene=g2508 Length=545
MIFRNFCHKIKWKYLELSRNYSHKILFFGTDNFSLPSLKLITKQNDLYSRLEVVTSFKSK
KNPIKDFANEQKLPVHDWESLKNDLKIFSEFDIGLVVSFGHLIPENIINNFHKGMLNVHA
SLLPKYRGASPIIYAIKNHETITGVSIMKIKAKKFDVGDVLAMKEVSITDDILMSELHDQ
LANLGAQLLIDCLKHLEECKPIKQDESQASYAPKIDKEFCKVRWNEMSAREIYDLYRALY
SYKHVLTTFKNEPVKLLELKKSNEVIEYNIAGHLKFCKKTKKLLVHCVDGECIEINKLLI
AKKVMSASDFNNGFLKNINDFENFQIAIRAGILGYFFGIALFISITMEDKYKSFGIYLAF
LTFFHYSEYFVISLSHPESLTLDSFMLNHSIQYEFAAIISWIEYFVEVYYYPEMKKCKTI
WIIGSTICLSGEILRKVAMLTAKKSFHHLVQFQQADDHKLITIGVYSWFRHPAYVGWFYW
SIATQLIMANPICFVLYLIASWLFFKERIHTEEITLLNFFGQEYVQYQQRTKTGLPFING
YITTN
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 23 | g2508.t1 | CDD | cd08646 | FMT_core_Met-tRNA-FMT_N | 24 | 215 | 1.87228E-77 |
| 22 | g2508.t1 | CDD | cd08704 | Met_tRNA_FMT_C | 218 | 307 | 3.66628E-11 |
| 8 | g2508.t1 | Gene3D | G3DSA:3.40.50.170 | Formyltransferase | 18 | 216 | 3.6E-56 |
| 10 | g2508.t1 | Gene3D | G3DSA:3.10.25.10 | - | 217 | 322 | 2.3E-10 |
| 9 | g2508.t1 | Gene3D | G3DSA:1.20.120.1630 | - | 354 | 538 | 1.3E-29 |
| 4 | g2508.t1 | PANTHER | PTHR11138 | METHIONYL-TRNA FORMYLTRANSFERASE | 18 | 320 | 5.7E-89 |
| 5 | g2508.t1 | PANTHER | PTHR11138:SF0 | METHIONYL-TRNA FORMYLTRANSFERASE, MITOCHONDRIAL | 18 | 320 | 5.7E-89 |
| 1 | g2508.t1 | Pfam | PF00551 | Formyl transferase | 58 | 191 | 4.1E-21 |
| 3 | g2508.t1 | Pfam | PF02911 | Formyl transferase, C-terminal domain | 214 | 314 | 2.5E-14 |
| 2 | g2508.t1 | Pfam | PF04140 | Isoprenylcysteine carboxyl methyltransferase (ICMT) family | 427 | 516 | 2.0E-27 |
| 16 | g2508.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 1 | 325 | - |
| 17 | g2508.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 326 | 347 | - |
| 11 | g2508.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 348 | 353 | - |
| 21 | g2508.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 354 | 372 | - |
| 14 | g2508.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 373 | 391 | - |
| 20 | g2508.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 392 | 412 | - |
| 12 | g2508.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 413 | 418 | - |
| 19 | g2508.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 419 | 438 | - |
| 15 | g2508.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 439 | 476 | - |
| 18 | g2508.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 477 | 505 | - |
| 13 | g2508.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 506 | 545 | - |
| 29 | g2508.t1 | ProSiteProfiles | PS51564 | Protein-S-isoprenylcysteine O-methyltransferase (EC 2.1.1.100) family profile. | 227 | 545 | 32.991 |
| 6 | g2508.t1 | SUPERFAMILY | SSF53328 | Formyltransferase | 24 | 217 | 9.81E-41 |
| 7 | g2508.t1 | SUPERFAMILY | SSF50486 | FMT C-terminal domain-like | 215 | 314 | 9.03E-11 |
| 30 | g2508.t1 | TIGRFAM | TIGR00460 | fmt: methionyl-tRNA formyltransferase | 24 | 322 | 6.9E-67 |
| 25 | g2508.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 325 | 347 | - |
| 24 | g2508.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 354 | 376 | - |
| 28 | g2508.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 391 | 413 | - |
| 26 | g2508.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 420 | 442 | - |
| 27 | g2508.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 477 | 499 | - |
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:0005783 | endoplasmic reticulum | CC |
| GO:0003824 | catalytic activity | MF |
| GO:0071951 | conversion of methionyl-tRNA to N-formyl-methionyl-tRNA | BP |
| GO:0009058 | biosynthetic process | BP |
| GO:0006481 | C-terminal protein methylation | BP |
| GO:0016021 | integral component of membrane | CC |
| GO:0016742 | hydroxymethyl-, formyl- and related transferase activity | MF |
| GO:0004671 | protein C-terminal S-isoprenylcysteine carboxyl O-methyltransferase activity | MF |
| GO:0004479 | methionyl-tRNA formyltransferase activity | MF |
KEGG
Orthology
- This transcript has been annotated with K00604 (methionyl-tRNA formyltransferase)
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.
