General information for g3833.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Bifunctional glutamate/proline–tRNA ligase.
Parent gene
- The parent gene g3833 is located on chr_3: 28290022..28291097 (+ 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 | g3833 | g3833.t1 | TSS | g3833.t1 | 28287301 | 28287301 |
| chr_3 | g3833 | g3833.t1 | isoform | g3833.t1 | 28287380 | 28291097 |
| chr_3 | g3833 | g3833.t1 | exon | g3833.t1.exon1 | 28287380 | 28287422 |
| chr_3 | g3833 | g3833.t1 | cds | g3833.t1.CDS1 | 28287380 | 28287422 |
| chr_3 | g3833 | g3833.t1 | exon | g3833.t1.exon2 | 28287528 | 28288203 |
| chr_3 | g3833 | g3833.t1 | cds | g3833.t1.CDS2 | 28287528 | 28288203 |
| chr_3 | g3833 | g3833.t1 | exon | g3833.t1.exon3 | 28288260 | 28288522 |
| chr_3 | g3833 | g3833.t1 | cds | g3833.t1.CDS3 | 28288260 | 28288522 |
| chr_3 | g3833 | g3833.t1 | exon | g3833.t1.exon4 | 28288671 | 28289944 |
| chr_3 | g3833 | g3833.t1 | cds | g3833.t1.CDS4 | 28288671 | 28289944 |
| chr_3 | g3833 | g3833.t1 | exon | g3833.t1.exon5 | 28290006 | 28291097 |
| chr_3 | g3833 | g3833.t1 | cds | g3833.t1.CDS5 | 28290006 | 28291097 |
| chr_3 | g3833 | g3833.t1 | TTS | g3833.t1 | 28291200 | 28291200 |
Sequences
>g3833.t1 Gene=g3833 Length=3348
ATGCCAATTAAAGTAAATAGTGATTTAAAGAATCCACCAACCGATGGTGTGGATACCGCT
GAAAATTTTTCATCTCTTCCAAAAGACGCTAACTCTACAAAATCAAATAAACAAGAATCT
CCAACAGCACTTGATGTTGACGATAGAAAGCAAGAAGGTAAATTTGTCGATCTTCCAGGA
GCTGAAATGGGCAAAGTTATTGTTCGCTTTCCTCCTGAAGCATCAGGATATTTGCACATT
GGTCATGCTAAAGCAGCTCTTTTAAATCAATATTATCAACAAGCATTTAATGGAAAACTG
ATTATGAGATTTGACGACACTAATCCAGCTAAAGAAAATGTTCACTTTGAAAACGTTATT
TTAGAGGATTTAGAAATGCTTCAAATTAAACCAGATTTATTCACTTATACATCAGATTAT
TTTGAGCTCATGTTAAAGTATTGTGAACAATTAATGAAAGAGAGAAAAGCATATGCTGAC
GATACTGATCCTGAACTGATGAAGCAAGAACGTGAACAGAGAGTTGAGTCTAAAAACAGA
AACAACTCAATCGAAAAGAATTTTGAAATGTGGAATGAAATGTTAGCTGGCACAGAAAAA
GGACAGAAATGTTGTATCCGAGCGAAAATCGACATGTCTTCTCCAAATGGATGCCTTCGT
GATCCAACAATTTATCGTTGCAAAAATGAGCCACATCCACGTACTGGAACTAAATACAAA
GTTTATCCAACTTATGATTTTGCATGTCCAATTGTTGATGCAATTGAAAATGTAACTCAT
ACTCTTCGTACAATGGAATATCACGATCGTGATGATCAATTTTATTGGTTTATTGATGCA
TTAAAACTTCGTAAACCATATATTTGGGAATATTCTCGTTTAAATATGACTAACACAGTA
TTATCAAAACGTAAATTAACTTGGTTTGTTGAAAACGGTCTTGTTGATGGTTGGGATGAT
CCTCGCTTTCCTACAGTTCGAGGTATTTTACGTCGTGGTATGACTGTTGAAGGTTTAAAA
CAATTCATTATTGCACAAGGTTCTAGTAAAGCTGTTGTATTTATGGAATGGGATAAAATT
TGGGCTTTCAACAAAAAAGTCATCGATCCAATTGCACCTAGATACATTGCATTAGAAAAC
GACAATCGTATAATTGTCAAAGTTAATAATGCAATATTACAAGCTCTTGAAGTTCCAAGA
CATCCCAAAAATAATGAAGTTGGCACAAAAACTATTTGGGTTGGCCCAGAAATTTATATT
GACTATGCTGATGCTGAATCCTTAAAAGAAGGTGAAAATGCAACATTTATAAATTGGGGT
AATTTAAGAATCAAAAAGATTCATAAAGAAAGTGAAAAAATTACTTCTATCGATGCTGAA
TTGAATTTGAGTGATACCGATTTCAAAAAGACATTAAAACTGACATGGCTTTGTAAACAG
GATCCTTCAGAATATCCAACAACTTATTGCGTTTATTTCGATCATATAATTAGCAAAGCT
GTTCTTGGTAAAAATGAAGACTTTAAAGCATATATCGGACATGAGACTAGAAAAGAAACA
AAAATGTTGGCTGATCCTGAATTGAAAAAATGTCAGAAAGGCGATATCATTCAACTACAA
CGGCGCGGATTTTTCAAAGTTGATCAAGCTTATGCTCCAGCTAGCGAAATTTCAGGATCA
GAACGTCCAATTGTATTGTACTTTATTCCTGATGGTCACAAAAAAGAAATACCCACATCT
GGTCTTTCAAAGAAACCTTCATGCTCCGAAAAAAAACAAAAATCCAAAAAAGTTACAACC
GAGTCAAAAGACGAGAGCCCAAGATTGAAAAAACAAACTCGATTGGGTTTGGAAGCTAAG
AAAGAAGAGAATTTAGCTGATTGGTATTCTCAAGTAATTACAAAGGGCGAAATGATTGAA
TATTATGATGTATCTGGATGTTATATTCTTCGTCCATGGGCATTTGCAATCTGGAAGAAT
ATTAAAAAATTTTTCGATGCCAAAATTACTGATATGGGAGTAAAAGAATGCTATTTTCCA
ATGTTTGTTTCAAAAGCTGCTTTGGAAAAAGAAAAAGATCATATCGCTGATTTTGCACCC
GAAGTTGCTTGGGTTACAAAATCAGGTGAATCAGATTTGGCTGAGCCAATTGCTGTACGT
CCAACTTCAGAAACTGTCATGTATCCGGCATATTCTAAATGGATCCAATCTTATCGCGAT
TTGCCAATTCGTTTGAATCAATGGAACAATGTTGTGCGTTGGGAATTTAAACATCCACAA
CCATTCATAAGAACTCGTGAATTTTTATGGCAAGAAGGTCACACTGCATTTGCAACATCA
AAAGAGGCTCAGGAAGAAGTTTACGAAATTCTGGAATTATACAAACAAATTTATACTGAT
TTGTTAGCAATTCCAGTTGTAAAAGGACGTAAGACCGAGAAAGAAAAGTTTCCTGGTGGT
GATTTTACAACAACAGTTGAAGCTTTTATTTCTGCAAGTGGTCGCGGAATTCAAGGTGCA
ACCAGTCACTTTCTTGGTCAAAACTTTTCAAAAATGTTTGACATTATTTTCGAGAATCCA
GAAACTCAAGAAAAGGAATATGTTTATCAGAATTCATGGGGAATTAGCACTAGAACTATT
GGTGTAATGGTAATGGTGCATGCTGATAATCAAGGAATTGTTTTGCCACCTCGAGTGGCT
TATACACAAGTTATTATAGTTCCTTGCGGTATCACTGCCACAACATCGAATACTGATCGT
AAAACTCTTATTGATAGTTGCAAAGAATTGGAAAAGCAATTGCAAGCATGCAATATTCGT
ATAGATGGAGATTATCGTGACAATTACTCTCCTGGTTGGAAATATAATCATTGGGAATTA
AAAGGTGTCCCAATTCGCATCGAATTGGGACCAAAAGATTTGAAGGCTCAACAATTTGTT
GCAGTACGACGTGATAATTTTGAAAAGTTGACCATCAGTAGAAGTAAAGCTTCAACAGAT
ATTCCAGAATTACTTGAAAAGATTCATCAAAATATGTTAACAAAAGCAACAAAAGATTTA
ACCGATCACTTAAAAACAACAAAAAATTGGAAAGAATTTACATCATTTTTGGATTCAAAA
TATATTATTATGGCTCCATTCTGTGGAGACATTCTTTGTGAAGAAAAGATCAAGACAGAT
AGTGCACGTGAAGAGACCGATGAAGCTGTTCAAGGACCTGCAATGGGAGCAAAATCCTTG
TGTATTCCATTTGAACAGCCAGCTGAAATTCAAGAAAGCGACAAATGCATTCATCCAGAG
TGCAACAACAAACCGAAGTTCTACACACTTTTCGGAAGAAGCTACTAA
>g3833.t1 Gene=g3833 Length=1115
MPIKVNSDLKNPPTDGVDTAENFSSLPKDANSTKSNKQESPTALDVDDRKQEGKFVDLPG
AEMGKVIVRFPPEASGYLHIGHAKAALLNQYYQQAFNGKLIMRFDDTNPAKENVHFENVI
LEDLEMLQIKPDLFTYTSDYFELMLKYCEQLMKERKAYADDTDPELMKQEREQRVESKNR
NNSIEKNFEMWNEMLAGTEKGQKCCIRAKIDMSSPNGCLRDPTIYRCKNEPHPRTGTKYK
VYPTYDFACPIVDAIENVTHTLRTMEYHDRDDQFYWFIDALKLRKPYIWEYSRLNMTNTV
LSKRKLTWFVENGLVDGWDDPRFPTVRGILRRGMTVEGLKQFIIAQGSSKAVVFMEWDKI
WAFNKKVIDPIAPRYIALENDNRIIVKVNNAILQALEVPRHPKNNEVGTKTIWVGPEIYI
DYADAESLKEGENATFINWGNLRIKKIHKESEKITSIDAELNLSDTDFKKTLKLTWLCKQ
DPSEYPTTYCVYFDHIISKAVLGKNEDFKAYIGHETRKETKMLADPELKKCQKGDIIQLQ
RRGFFKVDQAYAPASEISGSERPIVLYFIPDGHKKEIPTSGLSKKPSCSEKKQKSKKVTT
ESKDESPRLKKQTRLGLEAKKEENLADWYSQVITKGEMIEYYDVSGCYILRPWAFAIWKN
IKKFFDAKITDMGVKECYFPMFVSKAALEKEKDHIADFAPEVAWVTKSGESDLAEPIAVR
PTSETVMYPAYSKWIQSYRDLPIRLNQWNNVVRWEFKHPQPFIRTREFLWQEGHTAFATS
KEAQEEVYEILELYKQIYTDLLAIPVVKGRKTEKEKFPGGDFTTTVEAFISASGRGIQGA
TSHFLGQNFSKMFDIIFENPETQEKEYVYQNSWGISTRTIGVMVMVHADNQGIVLPPRVA
YTQVIIVPCGITATTSNTDRKTLIDSCKELEKQLQACNIRIDGDYRDNYSPGWKYNHWEL
KGVPIRIELGPKDLKAQQFVAVRRDNFEKLTISRSKASTDIPELLEKIHQNMLTKATKDL
TDHLKTTKNWKEFTSFLDSKYIIMAPFCGDILCEEKIKTDSAREETDEAVQGPAMGAKSL
CIPFEQPAEIQESDKCIHPECNNKPKFYTLFGRSY
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 30 | g3833.t1 | CDD | cd00807 | GlnRS_core | 65 | 374 | 1.72992E-135 |
| 28 | g3833.t1 | CDD | cd00778 | ProRS_core_arch_euk | 624 | 886 | 1.08879E-166 |
| 29 | g3833.t1 | CDD | cd00862 | ProRS_anticodon_zinc | 892 | 1115 | 5.14837E-78 |
| 26 | g3833.t1 | Coils | Coil | Coil | 167 | 187 | - |
| 27 | g3833.t1 | Coils | Coil | Coil | 920 | 940 | - |
| 22 | g3833.t1 | Gene3D | G3DSA:3.40.50.620 | HUPs | 35 | 374 | 6.6E-129 |
| 24 | g3833.t1 | Gene3D | G3DSA:2.40.240.10 | Ribosomal Protein L25; Chain P | 375 | 551 | 7.4E-22 |
| 25 | g3833.t1 | Gene3D | G3DSA:2.40.240.10 | Ribosomal Protein L25; Chain P | 380 | 482 | 7.4E-22 |
| 23 | g3833.t1 | Gene3D | G3DSA:3.30.930.10 | Bira Bifunctional Protein; Domain 2 | 617 | 896 | 3.4E-116 |
| 21 | g3833.t1 | Gene3D | G3DSA:3.40.50.800 | - | 897 | 1022 | 3.6E-42 |
| 20 | g3833.t1 | Gene3D | G3DSA:3.30.110.30 | - | 1024 | 1114 | 2.9E-32 |
| 9 | g3833.t1 | Hamap | MF_02076 | Glutamate–tRNA ligase [gltX]. | 4 | 569 | 30.728867 |
| 8 | g3833.t1 | Hamap | MF_01571 | Proline–tRNA ligase [proS]. | 618 | 1115 | 36.969841 |
| 36 | g3833.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 51 | - |
| 35 | g3833.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 17 | 40 | - |
| 34 | g3833.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 578 | 614 | - |
| 33 | g3833.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 587 | 614 | - |
| 7 | g3833.t1 | PANTHER | PTHR43382 | PROLYL-TRNA SYNTHETASE | 35 | 602 | 0.0 |
| 6 | g3833.t1 | PANTHER | PTHR43382 | PROLYL-TRNA SYNTHETASE | 585 | 1115 | 0.0 |
| 11 | g3833.t1 | PRINTS | PR00987 | Glutamyl-tRNA synthetase signature | 69 | 81 | 5.9E-16 |
| 14 | g3833.t1 | PRINTS | PR00987 | Glutamyl-tRNA synthetase signature | 83 | 94 | 5.9E-16 |
| 13 | g3833.t1 | PRINTS | PR00987 | Glutamyl-tRNA synthetase signature | 98 | 111 | 5.9E-16 |
| 10 | g3833.t1 | PRINTS | PR00987 | Glutamyl-tRNA synthetase signature | 243 | 253 | 5.9E-16 |
| 12 | g3833.t1 | PRINTS | PR00987 | Glutamyl-tRNA synthetase signature | 259 | 267 | 5.9E-16 |
| 1 | g3833.t1 | Pfam | PF00749 | tRNA synthetases class I (E and Q), catalytic domain | 65 | 369 | 8.7E-117 |
| 4 | g3833.t1 | Pfam | PF03950 | tRNA synthetases class I (E and Q), anti-codon binding domain | 372 | 548 | 1.4E-31 |
| 3 | g3833.t1 | Pfam | PF00587 | tRNA synthetase class II core domain (G, H, P, S and T) | 715 | 884 | 8.1E-18 |
| 5 | g3833.t1 | Pfam | PF03129 | Anticodon binding domain | 903 | 1001 | 2.9E-17 |
| 2 | g3833.t1 | Pfam | PF09180 | Prolyl-tRNA synthetase, C-terminal | 1030 | 1115 | 3.9E-21 |
| 32 | g3833.t1 | ProSitePatterns | PS00178 | Aminoacyl-transfer RNA synthetases class-I signature. | 72 | 83 | - |
| 39 | g3833.t1 | ProSiteProfiles | PS50862 | Aminoacyl-transfer RNA synthetases class-II family profile. | 657 | 896 | 21.764 |
| 31 | g3833.t1 | SMART | SM00946 | ProRS_C_1_2 | 1030 | 1115 | 3.0E-29 |
| 16 | g3833.t1 | SUPERFAMILY | SSF52374 | Nucleotidylyl transferase | 65 | 377 | 1.58E-84 |
| 18 | g3833.t1 | SUPERFAMILY | SSF50715 | Ribosomal protein L25-like | 372 | 574 | 7.32E-43 |
| 15 | g3833.t1 | SUPERFAMILY | SSF55681 | Class II aaRS and biotin synthetases | 623 | 889 | 1.07E-75 |
| 19 | g3833.t1 | SUPERFAMILY | SSF52954 | Class II aaRS ABD-related | 892 | 1022 | 4.42E-29 |
| 17 | g3833.t1 | SUPERFAMILY | SSF64586 | C-terminal domain of ProRS | 1026 | 1115 | 3.53E-16 |
| 37 | g3833.t1 | TIGRFAM | TIGR00463 | gltX_arch: glutamate–tRNA ligase | 37 | 551 | 1.4E-148 |
| 38 | g3833.t1 | TIGRFAM | TIGR00408 | proS_fam_I: proline–tRNA ligase | 619 | 1115 | 1.9E-179 |
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:0006433 | prolyl-tRNA aminoacylation | BP |
| GO:0005524 | ATP binding | MF |
| GO:0005737 | cytoplasm | CC |
| GO:0004818 | glutamate-tRNA ligase activity | MF |
| GO:0000166 | nucleotide binding | MF |
| GO:0006418 | tRNA aminoacylation for protein translation | BP |
| GO:0043039 | tRNA aminoacylation | BP |
| GO:0006424 | glutamyl-tRNA aminoacylation | BP |
| GO:0006412 | translation | BP |
| GO:0004812 | aminoacyl-tRNA ligase activity | MF |
| GO:0004827 | proline-tRNA ligase activity | MF |
KEGG
Orthology
- This transcript has been annotated with K01881 (prolyl-tRNA synthetase)
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.
