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_4 g17015 g17015.t14 TSS g17015.t14 12161055 12161055
chr_4 g17015 g17015.t14 isoform g17015.t14 12161643 12163690
chr_4 g17015 g17015.t14 exon g17015.t14.exon1 12161643 12162539
chr_4 g17015 g17015.t14 cds g17015.t14.CDS1 12161787 12162539
chr_4 g17015 g17015.t14 exon g17015.t14.exon2 12162599 12163690
chr_4 g17015 g17015.t14 cds g17015.t14.CDS2 12162599 12163690
chr_4 g17015 g17015.t14 TTS g17015.t14 12163773 12163773

Sequences

>g17015.t14 Gene=g17015 Length=1989
GACATTGTAAGAAATTTGAAGAGCCAAAAGGCAGCAAAGCAAGACATTGACGCAGCAGTA
AAAATTCTATTGGAATTAAAAGCAGAATATAAGAAAGTGACAGGAAAAGATTGGAAACCA
GAAACTAATCAAAATAAAGAAAACATGGTTCCACCAACCGAAAAGCCTTCTGATTCAAAG
AAAGATGAACTCACGAAGAAAATCAATGATCAAGGAAATATTGTCCGTTCATTGAAATCA
AATAAAGCAACTCCAAAAACTGAAATTGATGGAGCTGTTCAAGTTCTTTTATCGCTTAAA
GCTGAATATAAAGAATTGACTGGTGAAGATTTTCCAGTTGCTGGACGACAACAACAACCA
GCTAAAGAAAAAACAGCAAAACCAACCGAAAAGGCAACAAAACCAACCGAAAAGAAGCAA
GAACCGAAAAAAGTTGCAGTTGAATCAAAAGATGAAAGCTCAGGATTGAAGAAGCAAACT
CGATTAGGTTTGGAAGCGAAAAAGGAAGAAAATTTGCCTGATTGGTATTCACAAGTAATC
ACAAAGGGCGAAATGATTGAATATTACGATGTATCTGGATGTTATATTCTTCGTCCATGG
GCATTTGCAATTTGGAAAAATATCAAGAAATTTTTCGATGCAAAAATTACTGACATGGGA
GTAAAAGAATGCTATTTTCCAATGTTTGTTTCAAAAGCTGCTTTGGAAAAAGAGAAAGAT
CATATTGCAGATTTTGCACCAGAAGTTGCTTGGGTAACAAAATCAGGTGAATCAGATTTA
GCTGAACCAATTGCTGTTCGTCCAACATCAGAAACTGTCATGTATCCAGCATATGCCAAA
TGGGTTCAATCATATCGTGATTTGCCAATTCGTTTAAATCAATGGAACAATGTTGTTCGT
TGGGAATTTAAACATCCACAACCATTTTTAAGAACTCGTGAATTTTTATGGCAAGAAGGT
CATACTGCATTTGCAACATCAAAAGAAGCTCAAGAAGAAGTTTATGAAATTCTTGAATTG
TACAAACAAATTTATACAGATTTGCTGGCAATTCCAGTTGTAAAAGGACGTAAGACCGAG
AAGGAAAAGTTTGCTGGTGGTGATTTTACAACAACAGTTGAAGCTTTTATTTCTGCAAGT
GGTCGTGGAATTCAAGGTGCTACAAGTCACTTCCTTGGTCAAAACTTTTCAAAAATGTTT
GAAATCATCTTTGAAAATCCAGAAACACAAGAAAAGGAATATGTTTATCAAAATTCATGG
GGAATTACTACCAGAACTATTGGTGTGATGGTGATGGTCCATGCTGATAATCAAGGTCTT
GTTTTGCCACCTCGAGTTGCTTATACTCAAGTTGTTATAGTTCCATGCGGTATTACTGCC
ACAACATCAGATACCGATCGTAAAAATCTCATTGACAGTTGTAAAGAATTGGAAAAGCAA
CTGCAAGCATGCAATATTCGTGTTGAAGGTGATTATCGTGACAATTACTCTCCTGGTTGG
AAATATAATCATTGGGAATTGAAAGGTGTTCCAATTCGCATTGAATTGGGACCAAAAGAT
TTGAAAGCTCAACAATTTGTTGCTGTACGTCGCGATAATTCTGAAAAATTGACCATCAGT
CGAAGCAAAGCTTCAACAGATATCCCAGAATTACTTGAAAAAATTCATCAAAATATGTTG
GCAAAAGCAACAAAAGATTTAACCGAACATTTAAAAACAACAAAAGATTGGAAAGAATTT
ACATCATTTTTGGATACAAAAAATATTATAATGGCTCCATTCTGTGGTGATATTCCTTGT
GAGGAAAAGATCAAGGCAGATAGTGCACGTGAAGAAACTGATGAAGCTGTTCAAGGACCT
GCAATGGGAGCAAAATCCTTGTGCATTCCATTTGAACAACCAGCTGAAATTCAAGCAAAC
GACAAATGCATTCATCCACAGTGCAACAACAAACCGAAATTCTACACACTTTTTGGAAGA
AGCTACTAA

>g17015.t14 Gene=g17015 Length=614
MVPPTEKPSDSKKDELTKKINDQGNIVRSLKSNKATPKTEIDGAVQVLLSLKAEYKELTG
EDFPVAGRQQQPAKEKTAKPTEKATKPTEKKQEPKKVAVESKDESSGLKKQTRLGLEAKK
EENLPDWYSQVITKGEMIEYYDVSGCYILRPWAFAIWKNIKKFFDAKITDMGVKECYFPM
FVSKAALEKEKDHIADFAPEVAWVTKSGESDLAEPIAVRPTSETVMYPAYAKWVQSYRDL
PIRLNQWNNVVRWEFKHPQPFLRTREFLWQEGHTAFATSKEAQEEVYEILELYKQIYTDL
LAIPVVKGRKTEKEKFAGGDFTTTVEAFISASGRGIQGATSHFLGQNFSKMFEIIFENPE
TQEKEYVYQNSWGITTRTIGVMVMVHADNQGLVLPPRVAYTQVVIVPCGITATTSDTDRK
NLIDSCKELEKQLQACNIRVEGDYRDNYSPGWKYNHWELKGVPIRIELGPKDLKAQQFVA
VRRDNSEKLTISRSKASTDIPELLEKIHQNMLAKATKDLTEHLKTTKDWKEFTSFLDTKN
IIMAPFCGDIPCEEKIKADSAREETDEAVQGPAMGAKSLCIPFEQPAEIQANDKCIHPQC
NNKPKFYTLFGRSY

Protein features from InterProScan

Transcript Database ID Name Start End E.value
21 g17015.t14 CDD cd00936 WEPRS_RNA 16 64 1.37239E-16
22 g17015.t14 CDD cd00778 ProRS_core_arch_euk 123 385 2.47079E-171
23 g17015.t14 CDD cd00862 ProRS_anticodon_zinc 391 614 2.56629E-84
20 g17015.t14 Coils Coil Coil 419 439 -
18 g17015.t14 Gene3D G3DSA:1.10.287.10 - 4 64 1.2E-18
19 g17015.t14 Gene3D G3DSA:3.30.930.10 Bira Bifunctional Protein; Domain 2 116 395 1.2E-116
17 g17015.t14 Gene3D G3DSA:3.40.50.800 - 396 521 4.6E-44
16 g17015.t14 Gene3D G3DSA:3.30.110.30 - 523 613 5.4E-33
7 g17015.t14 Hamap MF_01571 Proline–tRNA ligase [proS]. 117 614 37.026218
29 g17015.t14 MobiDBLite mobidb-lite consensus disorder prediction 1 41 -
28 g17015.t14 MobiDBLite mobidb-lite consensus disorder prediction 7 21 -
30 g17015.t14 MobiDBLite mobidb-lite consensus disorder prediction 22 36 -
27 g17015.t14 MobiDBLite mobidb-lite consensus disorder prediction 60 114 -
26 g17015.t14 MobiDBLite mobidb-lite consensus disorder prediction 75 114 -
5 g17015.t14 PANTHER PTHR43382 PROLYL-TRNA SYNTHETASE 7 614 0.0
6 g17015.t14 PANTHER PTHR43382:SF2 BIFUNCTIONAL GLUTAMATE/PROLINE–TRNA LIGASE 7 614 0.0
9 g17015.t14 PRINTS PR01046 Prolyl-tRNA synthetase signature 175 193 5.3E-12
11 g17015.t14 PRINTS PR01046 Prolyl-tRNA synthetase signature 216 227 5.3E-12
8 g17015.t14 PRINTS PR01046 Prolyl-tRNA synthetase signature 246 254 5.3E-12
10 g17015.t14 PRINTS PR01046 Prolyl-tRNA synthetase signature 256 267 5.3E-12
3 g17015.t14 Pfam PF00458 WHEP-TRS domain 16 63 1.3E-18
2 g17015.t14 Pfam PF00587 tRNA synthetase class II core domain (G, H, P, S and T) 214 383 3.7E-18
4 g17015.t14 Pfam PF03129 Anticodon binding domain 402 500 4.2E-19
1 g17015.t14 Pfam PF09180 Prolyl-tRNA synthetase, C-terminal 529 614 1.4E-22
32 g17015.t14 ProSiteProfiles PS51185 WHEP-TRS domain profile. 12 69 12.479
33 g17015.t14 ProSiteProfiles PS50862 Aminoacyl-transfer RNA synthetases class-II family profile. 156 395 21.344
24 g17015.t14 SMART SM00991 WHEP_TRS_a_2_a_3_a 16 73 9.5E-19
25 g17015.t14 SMART SM00946 ProRS_C_1_2 529 614 4.2E-31
15 g17015.t14 SUPERFAMILY SSF47060 S15/NS1 RNA-binding domain 16 65 2.12E-11
12 g17015.t14 SUPERFAMILY SSF55681 Class II aaRS and biotin synthetases 121 388 6.02E-76
14 g17015.t14 SUPERFAMILY SSF52954 Class II aaRS ABD-related 391 521 7.85E-31
13 g17015.t14 SUPERFAMILY SSF64586 C-terminal domain of ProRS 525 614 3.53E-17
31 g17015.t14 TIGRFAM TIGR00408 proS_fam_I: proline–tRNA ligase 118 614 9.6E-182

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:0006418 tRNA aminoacylation for protein translation BP
GO:0000166 nucleotide binding MF
GO:0004812 aminoacyl-tRNA ligase activity MF
GO:0005737 cytoplasm CC
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