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.t1 TSS g17015.t1 12156272 12156272
chr_4 g17015 g17015.t1 isoform g17015.t1 12156363 12163690
chr_4 g17015 g17015.t1 exon g17015.t1.exon1 12156363 12156405
chr_4 g17015 g17015.t1 cds g17015.t1.CDS1 12156363 12156405
chr_4 g17015 g17015.t1 exon g17015.t1.exon2 12156511 12157603
chr_4 g17015 g17015.t1 cds g17015.t1.CDS2 12156511 12157603
chr_4 g17015 g17015.t1 TTS g17015.t1 12156983 12156983
chr_4 g17015 g17015.t1 exon g17015.t1.exon3 12157660 12157922
chr_4 g17015 g17015.t1 cds g17015.t1.CDS3 12157660 12157922
chr_4 g17015 g17015.t1 exon g17015.t1.exon4 12160076 12160863
chr_4 g17015 g17015.t1 cds g17015.t1.CDS4 12160076 12160863
chr_4 g17015 g17015.t1 exon g17015.t1.exon5 12161139 12162539
chr_4 g17015 g17015.t1 cds g17015.t1.CDS5 12161139 12162539
chr_4 g17015 g17015.t1 exon g17015.t1.exon6 12162599 12163690
chr_4 g17015 g17015.t1 cds g17015.t1.CDS6 12162599 12163690

Sequences

>g17015.t1 Gene=g17015 Length=4680
ATGCCAATCAAAGTAATTTGTGATTTAAAGAATCCACCAATTGGTGCTTTGGTTGTTGCC
GAAATTATTAAATCAACTGATCCAGTTGTAATTGAATGGAGCGATAAAGAAGCATCTATC
AATTTTGGTAACAATTCACTTTCATGTGTGAGCAACAACGACCTTTTAAGAGCTCTAGCT
CGACAAGCCGGAAGTTATCAGCTTTATGGAAAAACTCCGATTGAAAGAACTCAAATTGAT
CATTGGTTGACTTACTGCCTCAATTATGATGCTCATATTGATGAAGCAATTCAATATTTG
AATAAATGTTTAGCTCCATTGACTTATTTAGTGTCAAATAAGCTGACAATTGCTGATTTA
GCTGTGTTCAATGAATTTTTTGTCAAGTATGATCTTTTGAAGAAATCTGGTTTGCCTAGT
CATGTTCAACGCTGGTATAACCTCATCAGTTCATTGCCAACAGTTCAAACTGTGCTTTCA
TCACTTCCAAAAGATGGTAAATCTACAAAATCAAAGAAACAAGAAAAACAAGAATTTTCA
GCAGCTCTTGGTGTTGGCGATAGAAAGCAAGAAGGAAAATTTGTCGATCTTCCAGGAGCT
GAAATGGGAAAAGTTGTTGTTCGCTTTCCTCCTGAAGCATCAGGGTATTTGCACATTGGT
CATGCTAAAGCAGCTCTTTTAAATCAATATTATCAGCAAGCATTTGATGGAAAATTGATT
ATGAGATTTGATGACACCAATCCAGCTAAAGAAAATGTTCATTTTGAGGAAGTCATTTTG
GAAGATGTAGAAATGCTTCAAATTAAACCTGATGCATTCACTTACACCTCAGATTATTTT
GATATCATGCTTAAATATTGTGAGCAATTAATGAAAGAAGGAAAAGCATATGCTGATGAT
ACTGATCCTGAATTGATGAAACAAGAACGTGAACAGAAAGTTGAGTCAAAGAACCGAAAT
AATTCGGTTGAAAAGAATTTTGAAATGTGGAAAGAAATGTTGGCTGGCACAGAAAAAGGA
CAAAAATGTTGTATTCGAGCAAAAATTGACATGTCATCACCAAATGGATGCCTTCGTGAT
CCAACAATTTATCGTTGCAAAAATGAACCACATCCACGTACTGGAACTAATTACAAAGTT
TATCCAACTTATGATTTTGCTTGTCCTATTGTTGATGCAATTGAAAATGTGACTCATACT
CTTCGTACAATGGAATATCACGATCGTGATGATCAATTTTATTGGTTTATTGATGCATTG
AAACTTCGTAAACCATACATTTGGGAATATTCACGTTTAAATATGACTAACACTGTTCTA
TCTAAACGTAAATTGACTTGGTTTGTTGAAAACGGTCTGGTTGATGGCTGGGATGATCCT
CGTTTTCCTACAGTTCGAGGTGTTTTACGTCGTGGTATGACTGTTGAAGGTCTAAAACAA
TTCATTATTGCACAAGGTTCTAGTAAAGCTGTAGTATTTATGGAATGGGATAAAATTTGG
GCTTTCAATAAGAAAGTCATTGATCCAATTGCACCTAGATATACAGCATTAGAAAATGAC
AATCGTATTATTGTTAAAGTCGCTAATGCAAAATTGCAAGCACTTGAAGTTCCAAAACAT
CCCAAAAATGAGGAAGTTGGCACAAAAACTATTTGGGTTGGTCCAGAAATTTATATTGAC
TATGCTGATGCTGAATGTTTAAAAGAAGGTGAAAATGCGACATTTATAAATTGGGGTAAT
TTGAGAATCAAGAAAATTCATAAAGAAGGAGAAAAAATTACTTCAGTCGATGCTGAATTG
AATTTGGGTGACACTGATTTCAAAAAGACGTTAAAACTTACATGGCTTTGTAAACAAGAT
CCATCAGAATATCCACCAACTTATTGTGTTTATTTTGATCATATTATAAACAAATCTGTT
CTTGGTAAAGATGAAGACTTTAAATCATACATCGGACATGAGACTAGAAAAGAAACAAAA
ATGTTTGGTGATCCTGAATTGAAAAAATGTCAAAAAGGCGACATCATTCAACTACAACGA
CGTGGATTTTTCAAAGTTGATCAAGCTTATGCTCCAGCTAGTGAAATTTCAGGAGTTGAA
CGTCCAATTGTTTTGTTCTTTATTCCTGATGGTCATAAAAAAGAAATGCCCACGTCTGGT
CTTTCAAAGAAACTTCAAGCAGCAGAGGAAAAATCAAACAACAGTGCATCAGTGATTAAA
AAATCATCATCTGTTGGACAAGTAAGTGACATTAATGAAAAAATAAACAAACAAGGTGAC
GTTGTAAGAAATTTGAAGAGCCAAAAGGCAGCAAAGCAAGACATTGACGCAGCAGTAAAA
ATTCTATTGGAATTAAAAGCAGAATATAAAACAGCAACTGGTCAAGATTGGAAACCAGGT
GCTACTCCTGTTAAAACTGAAACAAAATCTACTCCATCAATCGGGCAAGTCAGTGACATT
AACGAAAAAATTGTTCAGCAAGGCGACATTGTCAGAAATTTGAAGAGCCAAAAGGCAGCA
AAGCAAGACATTGACGCAGCAGTGAAAATTCTGTTAGAATTAAAAGCAGAATATAAAACA
GCAACTGGTCAAGATTGGAAACCAGGTGCTACTCCTGTTAAAACTGAAACAAAAGCTGCT
CCATCAGTTGGACAAGTCAGTGACATCAATGAAAAAATTGTTCAGCAAGGCGACATTGTA
AGAAATTTGAAGAGCCAAAAGGCAGCAAAGCAAGACATTGACGCAGCAGTAAAAATTCTA
TTGGAATTAAAAGCAGAATATAAGAAAGTGACAGGAAAAGATTGGAAACCAGAAACTAAT
CAAAATAAAGAAAACATGGTTCCACCAACCGAAAAGCCTTCTGATTCAAAGAAAGATGAA
CTCACGAAGAAAATCAATGATCAAGGAAATATTGTCCGTTCATTGAAATCAAATAAAGCA
ACTCCAAAAACTGAAATTGATGGAGCTGTTCAAGTTCTTTTATCGCTTAAAGCTGAATAT
AAAGAATTGACTGGTGAAGATTTTCCAGTTGCTGGACGACAACAACAACCAGCTAAAGAA
AAAACAGCAAAACCAACCGAAAAGGCAACAAAACCAACCGAAAAGAAGCAAGAACCGAAA
AAAGTTGCAGTTGAATCAAAAGATGAAAGCTCAGGATTGAAGAAGCAAACTCGATTAGGT
TTGGAAGCGAAAAAGGAAGAAAATTTGCCTGATTGGTATTCACAAGTAATCACAAAGGGC
GAAATGATTGAATATTACGATGTATCTGGATGTTATATTCTTCGTCCATGGGCATTTGCA
ATTTGGAAAAATATCAAGAAATTTTTCGATGCAAAAATTACTGACATGGGAGTAAAAGAA
TGCTATTTTCCAATGTTTGTTTCAAAAGCTGCTTTGGAAAAAGAGAAAGATCATATTGCA
GATTTTGCACCAGAAGTTGCTTGGGTAACAAAATCAGGTGAATCAGATTTAGCTGAACCA
ATTGCTGTTCGTCCAACATCAGAAACTGTCATGTATCCAGCATATGCCAAATGGGTTCAA
TCATATCGTGATTTGCCAATTCGTTTAAATCAATGGAACAATGTTGTTCGTTGGGAATTT
AAACATCCACAACCATTTTTAAGAACTCGTGAATTTTTATGGCAAGAAGGTCATACTGCA
TTTGCAACATCAAAAGAAGCTCAAGAAGAAGTTTATGAAATTCTTGAATTGTACAAACAA
ATTTATACAGATTTGCTGGCAATTCCAGTTGTAAAAGGACGTAAGACCGAGAAGGAAAAG
TTTGCTGGTGGTGATTTTACAACAACAGTTGAAGCTTTTATTTCTGCAAGTGGTCGTGGA
ATTCAAGGTGCTACAAGTCACTTCCTTGGTCAAAACTTTTCAAAAATGTTTGAAATCATC
TTTGAAAATCCAGAAACACAAGAAAAGGAATATGTTTATCAAAATTCATGGGGAATTACT
ACCAGAACTATTGGTGTGATGGTGATGGTCCATGCTGATAATCAAGGTCTTGTTTTGCCA
CCTCGAGTTGCTTATACTCAAGTTGTTATAGTTCCATGCGGTATTACTGCCACAACATCA
GATACCGATCGTAAAAATCTCATTGACAGTTGTAAAGAATTGGAAAAGCAACTGCAAGCA
TGCAATATTCGTGTTGAAGGTGATTATCGTGACAATTACTCTCCTGGTTGGAAATATAAT
CATTGGGAATTGAAAGGTGTTCCAATTCGCATTGAATTGGGACCAAAAGATTTGAAAGCT
CAACAATTTGTTGCTGTACGTCGCGATAATTCTGAAAAATTGACCATCAGTCGAAGCAAA
GCTTCAACAGATATCCCAGAATTACTTGAAAAAATTCATCAAAATATGTTGGCAAAAGCA
ACAAAAGATTTAACCGAACATTTAAAAACAACAAAAGATTGGAAAGAATTTACATCATTT
TTGGATACAAAAAATATTATAATGGCTCCATTCTGTGGTGATATTCCTTGTGAGGAAAAG
ATCAAGGCAGATAGTGCACGTGAAGAAACTGATGAAGCTGTTCAAGGACCTGCAATGGGA
GCAAAATCCTTGTGCATTCCATTTGAACAACCAGCTGAAATTCAAGCAAACGACAAATGC
ATTCATCCACAGTGCAACAACAAACCGAAATTCTACACACTTTTTGGAAGAAGCTACTAA

>g17015.t1 Gene=g17015 Length=1559
MPIKVICDLKNPPIGALVVAEIIKSTDPVVIEWSDKEASINFGNNSLSCVSNNDLLRALA
RQAGSYQLYGKTPIERTQIDHWLTYCLNYDAHIDEAIQYLNKCLAPLTYLVSNKLTIADL
AVFNEFFVKYDLLKKSGLPSHVQRWYNLISSLPTVQTVLSSLPKDGKSTKSKKQEKQEFS
AALGVGDRKQEGKFVDLPGAEMGKVVVRFPPEASGYLHIGHAKAALLNQYYQQAFDGKLI
MRFDDTNPAKENVHFEEVILEDVEMLQIKPDAFTYTSDYFDIMLKYCEQLMKEGKAYADD
TDPELMKQEREQKVESKNRNNSVEKNFEMWKEMLAGTEKGQKCCIRAKIDMSSPNGCLRD
PTIYRCKNEPHPRTGTNYKVYPTYDFACPIVDAIENVTHTLRTMEYHDRDDQFYWFIDAL
KLRKPYIWEYSRLNMTNTVLSKRKLTWFVENGLVDGWDDPRFPTVRGVLRRGMTVEGLKQ
FIIAQGSSKAVVFMEWDKIWAFNKKVIDPIAPRYTALENDNRIIVKVANAKLQALEVPKH
PKNEEVGTKTIWVGPEIYIDYADAECLKEGENATFINWGNLRIKKIHKEGEKITSVDAEL
NLGDTDFKKTLKLTWLCKQDPSEYPPTYCVYFDHIINKSVLGKDEDFKSYIGHETRKETK
MFGDPELKKCQKGDIIQLQRRGFFKVDQAYAPASEISGVERPIVLFFIPDGHKKEMPTSG
LSKKLQAAEEKSNNSASVIKKSSSVGQVSDINEKINKQGDVVRNLKSQKAAKQDIDAAVK
ILLELKAEYKTATGQDWKPGATPVKTETKSTPSIGQVSDINEKIVQQGDIVRNLKSQKAA
KQDIDAAVKILLELKAEYKTATGQDWKPGATPVKTETKAAPSVGQVSDINEKIVQQGDIV
RNLKSQKAAKQDIDAAVKILLELKAEYKKVTGKDWKPETNQNKENMVPPTEKPSDSKKDE
LTKKINDQGNIVRSLKSNKATPKTEIDGAVQVLLSLKAEYKELTGEDFPVAGRQQQPAKE
KTAKPTEKATKPTEKKQEPKKVAVESKDESSGLKKQTRLGLEAKKEENLPDWYSQVITKG
EMIEYYDVSGCYILRPWAFAIWKNIKKFFDAKITDMGVKECYFPMFVSKAALEKEKDHIA
DFAPEVAWVTKSGESDLAEPIAVRPTSETVMYPAYAKWVQSYRDLPIRLNQWNNVVRWEF
KHPQPFLRTREFLWQEGHTAFATSKEAQEEVYEILELYKQIYTDLLAIPVVKGRKTEKEK
FAGGDFTTTVEAFISASGRGIQGATSHFLGQNFSKMFEIIFENPETQEKEYVYQNSWGIT
TRTIGVMVMVHADNQGLVLPPRVAYTQVVIVPCGITATTSDTDRKNLIDSCKELEKQLQA
CNIRVEGDYRDNYSPGWKYNHWELKGVPIRIELGPKDLKAQQFVAVRRDNSEKLTISRSK
ASTDIPELLEKIHQNMLAKATKDLTEHLKTTKDWKEFTSFLDTKNIIMAPFCGDIPCEEK
IKADSAREETDEAVQGPAMGAKSLCIPFEQPAEIQANDKCIHPQCNNKPKFYTLFGRSY

Protein features from InterProScan

Transcript Database ID Name Start End E.value
48 g17015.t1 CDD cd00807 GlnRS_core 204 513 7.80103E-136
43 g17015.t1 CDD cd00936 WEPRS_RNA 751 800 1.00071E-20
45 g17015.t1 CDD cd00936 WEPRS_RNA 820 869 1.74362E-20
44 g17015.t1 CDD cd00936 WEPRS_RNA 889 937 8.70135E-20
42 g17015.t1 CDD cd00936 WEPRS_RNA 961 1009 5.20482E-16
46 g17015.t1 CDD cd00778 ProRS_core_arch_euk 1068 1330 3.41176E-163
47 g17015.t1 CDD cd00862 ProRS_anticodon_zinc 1336 1559 1.02338E-80
40 g17015.t1 Coils Coil Coil 306 326 -
41 g17015.t1 Coils Coil Coil 1364 1384 -
39 g17015.t1 Gene3D G3DSA:1.20.1050.130 - 1 170 6.0E-39
31 g17015.t1 Gene3D G3DSA:3.40.50.620 HUPs 180 513 1.9E-130
38 g17015.t1 Gene3D G3DSA:2.40.240.10 Ribosomal Protein L25; Chain P 514 690 1.6E-22
37 g17015.t1 Gene3D G3DSA:2.40.240.10 Ribosomal Protein L25; Chain P 519 621 1.6E-22
32 g17015.t1 Gene3D G3DSA:1.10.287.10 - 748 803 8.7E-25
34 g17015.t1 Gene3D G3DSA:1.10.287.10 - 817 872 1.7E-24
35 g17015.t1 Gene3D G3DSA:1.10.287.10 - 886 940 2.7E-22
33 g17015.t1 Gene3D G3DSA:1.10.287.10 - 949 1009 3.7E-18
36 g17015.t1 Gene3D G3DSA:3.30.930.10 Bira Bifunctional Protein; Domain 2 1061 1340 7.4E-116
30 g17015.t1 Gene3D G3DSA:3.40.50.800 - 1341 1466 1.7E-43
29 g17015.t1 Gene3D G3DSA:3.30.110.30 - 1468 1558 1.9E-32
13 g17015.t1 Hamap MF_02076 Glutamate–tRNA ligase [gltX]. 106 708 31.802025
12 g17015.t1 Hamap MF_01571 Proline–tRNA ligase [proS]. 1062 1559 37.026218
60 g17015.t1 MobiDBLite mobidb-lite consensus disorder prediction 934 978 -
61 g17015.t1 MobiDBLite mobidb-lite consensus disorder prediction 950 966 -
59 g17015.t1 MobiDBLite mobidb-lite consensus disorder prediction 1007 1059 -
58 g17015.t1 MobiDBLite mobidb-lite consensus disorder prediction 1020 1059 -
10 g17015.t1 PANTHER PTHR43382 PROLYL-TRNA SYNTHETASE 15 880 0.0
11 g17015.t1 PANTHER PTHR43382 PROLYL-TRNA SYNTHETASE 882 1559 0.0
16 g17015.t1 PRINTS PR00987 Glutamyl-tRNA synthetase signature 208 220 2.9E-15
15 g17015.t1 PRINTS PR00987 Glutamyl-tRNA synthetase signature 222 233 2.9E-15
18 g17015.t1 PRINTS PR00987 Glutamyl-tRNA synthetase signature 237 250 2.9E-15
14 g17015.t1 PRINTS PR00987 Glutamyl-tRNA synthetase signature 382 392 2.9E-15
17 g17015.t1 PRINTS PR00987 Glutamyl-tRNA synthetase signature 398 406 2.9E-15
1 g17015.t1 Pfam PF00749 tRNA synthetases class I (E and Q), catalytic domain 204 508 3.2E-118
8 g17015.t1 Pfam PF03950 tRNA synthetases class I (E and Q), anti-codon binding domain 511 687 3.2E-31
7 g17015.t1 Pfam PF00458 WHEP-TRS domain 751 802 8.1E-23
4 g17015.t1 Pfam PF00458 WHEP-TRS domain 820 871 1.5E-22
5 g17015.t1 Pfam PF00458 WHEP-TRS domain 889 939 2.6E-21
6 g17015.t1 Pfam PF00458 WHEP-TRS domain 961 1008 4.1E-18
3 g17015.t1 Pfam PF00587 tRNA synthetase class II core domain (G, H, P, S and T) 1159 1328 1.6E-17
9 g17015.t1 Pfam PF03129 Anticodon binding domain 1347 1445 1.5E-18
2 g17015.t1 Pfam PF09180 Prolyl-tRNA synthetase, C-terminal 1474 1559 4.9E-22
57 g17015.t1 ProSitePatterns PS00178 Aminoacyl-transfer RNA synthetases class-I signature. 211 222 -
55 g17015.t1 ProSitePatterns PS00762 WHEP-TRS domain signature. 758 786 -
56 g17015.t1 ProSitePatterns PS00762 WHEP-TRS domain signature. 827 855 -
54 g17015.t1 ProSitePatterns PS00762 WHEP-TRS domain signature. 896 924 -
66 g17015.t1 ProSiteProfiles PS51185 WHEP-TRS domain profile. 747 803 15.673
65 g17015.t1 ProSiteProfiles PS51185 WHEP-TRS domain profile. 816 872 15.527
64 g17015.t1 ProSiteProfiles PS51185 WHEP-TRS domain profile. 885 941 14.64
67 g17015.t1 ProSiteProfiles PS51185 WHEP-TRS domain profile. 957 1014 12.479
68 g17015.t1 ProSiteProfiles PS50862 Aminoacyl-transfer RNA synthetases class-II family profile. 1101 1340 21.344
49 g17015.t1 SMART SM00991 WHEP_TRS_a_2_a_3_a 751 813 1.8E-28
50 g17015.t1 SMART SM00991 WHEP_TRS_a_2_a_3_a 820 882 4.6E-28
52 g17015.t1 SMART SM00991 WHEP_TRS_a_2_a_3_a 889 950 4.8E-25
51 g17015.t1 SMART SM00991 WHEP_TRS_a_2_a_3_a 961 1018 9.5E-19
53 g17015.t1 SMART SM00946 ProRS_C_1_2 1474 1559 4.2E-31
23 g17015.t1 SUPERFAMILY SSF47616 GST C-terminal domain-like 54 157 1.03E-15
20 g17015.t1 SUPERFAMILY SSF52374 Nucleotidylyl transferase 204 516 6.17E-85
22 g17015.t1 SUPERFAMILY SSF50715 Ribosomal protein L25-like 511 713 7.85E-44
25 g17015.t1 SUPERFAMILY SSF47060 S15/NS1 RNA-binding domain 748 803 1.02E-16
28 g17015.t1 SUPERFAMILY SSF47060 S15/NS1 RNA-binding domain 817 872 1.26E-16
27 g17015.t1 SUPERFAMILY SSF47060 S15/NS1 RNA-binding domain 886 939 1.14E-15
26 g17015.t1 SUPERFAMILY SSF47060 S15/NS1 RNA-binding domain 961 1010 6.67E-11
19 g17015.t1 SUPERFAMILY SSF55681 Class II aaRS and biotin synthetases 1066 1333 3.4E-75
24 g17015.t1 SUPERFAMILY SSF52954 Class II aaRS ABD-related 1336 1466 3.11E-30
21 g17015.t1 SUPERFAMILY SSF64586 C-terminal domain of ProRS 1470 1559 1.24E-16
62 g17015.t1 TIGRFAM TIGR00463 gltX_arch: glutamate–tRNA ligase 168 690 3.2E-153
63 g17015.t1 TIGRFAM TIGR00408 proS_fam_I: proline–tRNA ligase 1063 1559 1.1E-180

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

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