Gene loci information

Transcript annotation

  • This transcript has been annotated as Bifunctional glutamate/proline–tRNA ligase.

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_3 g3833 g3833.t10 isoform g3833.t10 28288680 28291097
chr_3 g3833 g3833.t10 exon g3833.t10.exon1 28288680 28289941
chr_3 g3833 g3833.t10 cds g3833.t10.CDS1 28288688 28289941
chr_3 g3833 g3833.t10 exon g3833.t10.exon2 28290006 28291097
chr_3 g3833 g3833.t10 cds g3833.t10.CDS2 28290006 28291097
chr_3 g3833 g3833.t10 TTS g3833.t10 28291200 28291200
chr_3 g3833 g3833.t10 TSS g3833.t10 NA NA

Sequences

>g3833.t10 Gene=g3833 Length=2354
GTCGTGGTATGACTGTTGAAGGTTTAAAACAATTCATTATTGCACAAGGTTCTAGTAAAG
CTGTTGTATTTATGGAATGGGATAAAATTTGGGCTTTCAACAAAAAAGTCATCGATCCAA
TTGCACCTAGATACATTGCATTAGAAAACGACAATCGTATAATTGTCAAAGTTAATAATG
CAATATTACAAGCTCTTGAAGTTCCAAGACATCCCAAAAATAATGAAGTTGGCACAAAAA
CTATTTGGGTTGGCCCAGAAATTTATATTGACTATGCTGATGCTGAATCCTTAAAAGAAG
GTGAAAATGCAACATTTATAAATTGGGGTAATTTAAGAATCAAAAAGATTCATAAAGAAA
GTGAAAAAATTACTTCTATCGATGCTGAATTGAATTTGAGTGATACCGATTTCAAAAAGA
CATTAAAACTGACATGGCTTTGTAAACAGGATCCTTCAGAATATCCAACAACTTATTGCG
TTTATTTCGATCATATAATTAGCAAAGCTGTTCTTGGTAAAAATGAAGACTTTAAAGCAT
ATATCGGACATGAGACTAGAAAAGAAACAAAAATGTTGGCTGATCCTGAATTGAAAAAAT
GTCAGAAAGGCGATATCATTCAACTACAACGGCGCGGATTTTTCAAAGTTGATCAAGCTT
ATGCTCCAGCTAGCGAAATTTCAGGATCAGAACGTCCAATTGTATTGTACTTTATTCCTG
ATGGTCACAAAAAAGAAATACCCACATCTGGTCTTTCAAAGAAACCTTCATGCTCCGAAA
AAAAACAAAAATCCAAAAAAGTTACAACCGAGTCAAAAGACGAGAGCCCAAGATTGAAAA
AACAAACTCGATTGGGTTTGGAAGCTAAGAAAGAAGAGAATTTAGCTGATTGGTATTCTC
AAGTAATTACAAAGGGCGAAATGATTGAATATTATGATGTATCTGGATGTTATATTCTTC
GTCCATGGGCATTTGCAATCTGGAAGAATATTAAAAAATTTTTCGATGCCAAAATTACTG
ATATGGGAGTAAAAGAATGCTATTTTCCAATGTTTGTTTCAAAAGCTGCTTTGGAAAAAG
AAAAAGATCATATCGCTGATTTTGCACCCGAAGTTGCTTGGGTTACAAAATCAGGTGAAT
CAGATTTGGCTGAGCCAATTGCTGTACGTCCAACTTCAGAAACTGTCATGTATCCGGCAT
ATTCTAAATGGATCCAATCTTATCGCGATTTGCCAATTCGTTTGAATCAATGGAACAATG
TTCGTTGGGAATTTAAACATCCACAACCATTCATAAGAACTCGTGAATTTTTATGGCAAG
AAGGTCACACTGCATTTGCAACATCAAAAGAGGCTCAGGAAGAAGTTTACGAAATTCTGG
AATTATACAAACAAATTTATACTGATTTGTTAGCAATTCCAGTTGTAAAAGGACGTAAGA
CCGAGAAAGAAAAGTTTCCTGGTGGTGATTTTACAACAACAGTTGAAGCTTTTATTTCTG
CAAGTGGTCGCGGAATTCAAGGTGCAACCAGTCACTTTCTTGGTCAAAACTTTTCAAAAA
TGTTTGACATTATTTTCGAGAATCCAGAAACTCAAGAAAAGGAATATGTTTATCAGAATT
CATGGGGAATTAGCACTAGAACTATTGGTGTAATGGTAATGGTGCATGCTGATAATCAAG
GAATTGTTTTGCCACCTCGAGTGGCTTATACACAAGTTATTATAGTTCCTTGCGGTATCA
CTGCCACAACATCGAATACTGATCGTAAAACTCTTATTGATAGTTGCAAAGAATTGGAAA
AGCAATTGCAAGCATGCAATATTCGTATAGATGGAGATTATCGTGACAATTACTCTCCTG
GTTGGAAATATAATCATTGGGAATTAAAAGGTGTCCCAATTCGCATCGAATTGGGACCAA
AAGATTTGAAGGCTCAACAATTTGTTGCAGTACGACGTGATAATTTTGAAAAGTTGACCA
TCAGTAGAAGTAAAGCTTCAACAGATATTCCAGAATTACTTGAAAAGATTCATCAAAATA
TGTTAACAAAAGCAACAAAAGATTTAACCGATCACTTAAAAACAACAAAAAATTGGAAAG
AATTTACATCATTTTTGGATTCAAAATATATTATTATGGCTCCATTCTGTGGAGACATTC
TTTGTGAAGAAAAGATCAAGACAGATAGTGCACGTGAAGAGACCGATGAAGCTGTTCAAG
GACCTGCAATGGGAGCAAAATCCTTGTGTATTCCATTTGAACAGCCAGCTGAAATTCAAG
AAAGCGACAAATGCATTCATCCAGAGTGCAACAACAAACCGAAGTTCTACACACTTTTCG
GAAGAAGCTACTAA

>g3833.t10 Gene=g3833 Length=781
MTVEGLKQFIIAQGSSKAVVFMEWDKIWAFNKKVIDPIAPRYIALENDNRIIVKVNNAIL
QALEVPRHPKNNEVGTKTIWVGPEIYIDYADAESLKEGENATFINWGNLRIKKIHKESEK
ITSIDAELNLSDTDFKKTLKLTWLCKQDPSEYPTTYCVYFDHIISKAVLGKNEDFKAYIG
HETRKETKMLADPELKKCQKGDIIQLQRRGFFKVDQAYAPASEISGSERPIVLYFIPDGH
KKEIPTSGLSKKPSCSEKKQKSKKVTTESKDESPRLKKQTRLGLEAKKEENLADWYSQVI
TKGEMIEYYDVSGCYILRPWAFAIWKNIKKFFDAKITDMGVKECYFPMFVSKAALEKEKD
HIADFAPEVAWVTKSGESDLAEPIAVRPTSETVMYPAYSKWIQSYRDLPIRLNQWNNVRW
EFKHPQPFIRTREFLWQEGHTAFATSKEAQEEVYEILELYKQIYTDLLAIPVVKGRKTEK
EKFPGGDFTTTVEAFISASGRGIQGATSHFLGQNFSKMFDIIFENPETQEKEYVYQNSWG
ISTRTIGVMVMVHADNQGIVLPPRVAYTQVIIVPCGITATTSNTDRKTLIDSCKELEKQL
QACNIRIDGDYRDNYSPGWKYNHWELKGVPIRIELGPKDLKAQQFVAVRRDNFEKLTISR
SKASTDIPELLEKIHQNMLTKATKDLTDHLKTTKNWKEFTSFLDSKYIIMAPFCGDILCE
EKIKTDSAREETDEAVQGPAMGAKSLCIPFEQPAEIQESDKCIHPECNNKPKFYTLFGRS
Y

Protein features from InterProScan

Transcript Database ID Name Start End E.value
23 g3833.t10 CDD cd00778 ProRS_core_arch_euk 291 552 5.49575E-167
24 g3833.t10 CDD cd00862 ProRS_anticodon_zinc 558 781 4.01609E-79
22 g3833.t10 Coils Coil Coil 586 606 -
20 g3833.t10 Gene3D G3DSA:2.40.240.10 Ribosomal Protein L25; Chain P 40 218 4.2E-22
21 g3833.t10 Gene3D G3DSA:2.40.240.10 Ribosomal Protein L25; Chain P 47 149 4.2E-22
19 g3833.t10 Gene3D G3DSA:3.30.930.10 Bira Bifunctional Protein; Domain 2 284 562 9.9E-114
18 g3833.t10 Gene3D G3DSA:3.40.50.800 - 563 688 2.1E-42
17 g3833.t10 Gene3D G3DSA:3.30.110.30 - 690 780 1.8E-32
9 g3833.t10 Hamap MF_01571 Proline–tRNA ligase [proS]. 285 781 36.193081
27 g3833.t10 MobiDBLite mobidb-lite consensus disorder prediction 245 281 -
26 g3833.t10 MobiDBLite mobidb-lite consensus disorder prediction 254 281 -
5 g3833.t10 PANTHER PTHR43382 PROLYL-TRNA SYNTHETASE 1 268 0.0
7 g3833.t10 PANTHER PTHR43382:SF2 BIFUNCTIONAL GLUTAMATE/PROLINE–TRNA LIGASE 1 268 0.0
6 g3833.t10 PANTHER PTHR43382 PROLYL-TRNA SYNTHETASE 252 781 0.0
8 g3833.t10 PANTHER PTHR43382:SF2 BIFUNCTIONAL GLUTAMATE/PROLINE–TRNA LIGASE 252 781 0.0
10 g3833.t10 PRINTS PR01046 Prolyl-tRNA synthetase signature 343 361 2.9E-9
11 g3833.t10 PRINTS PR01046 Prolyl-tRNA synthetase signature 384 395 2.9E-9
12 g3833.t10 PRINTS PR01046 Prolyl-tRNA synthetase signature 423 434 2.9E-9
3 g3833.t10 Pfam PF03950 tRNA synthetases class I (E and Q), anti-codon binding domain 39 215 8.0E-32
2 g3833.t10 Pfam PF00587 tRNA synthetase class II core domain (G, H, P, S and T) 382 550 2.7E-16
4 g3833.t10 Pfam PF03129 Anticodon binding domain 569 667 1.8E-17
1 g3833.t10 Pfam PF09180 Prolyl-tRNA synthetase, C-terminal 696 781 2.4E-21
29 g3833.t10 ProSiteProfiles PS50862 Aminoacyl-transfer RNA synthetases class-II family profile. 324 562 17.666
25 g3833.t10 SMART SM00946 ProRS_C_1_2 696 781 3.0E-29
15 g3833.t10 SUPERFAMILY SSF50715 Ribosomal protein L25-like 39 241 4.13E-43
13 g3833.t10 SUPERFAMILY SSF55681 Class II aaRS and biotin synthetases 290 555 7.19E-73
16 g3833.t10 SUPERFAMILY SSF52954 Class II aaRS ABD-related 558 688 2.62E-29
14 g3833.t10 SUPERFAMILY SSF64586 C-terminal domain of ProRS 692 781 2.16E-16
28 g3833.t10 TIGRFAM TIGR00408 proS_fam_I: proline–tRNA ligase 286 781 2.3E-177

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:0000166 nucleotide binding MF
GO:0006418 tRNA aminoacylation for protein translation BP
GO:0006412 translation BP
GO:0004812 aminoacyl-tRNA ligase activity MF
GO:0004827 proline-tRNA ligase 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