Gene loci information

Transcript annotation

  • This transcript has been annotated as Valine–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_2 g7483 g7483.t1 TSS g7483.t1 23967942 23967942
chr_2 g7483 g7483.t1 isoform g7483.t1 23967966 23970930
chr_2 g7483 g7483.t1 exon g7483.t1.exon1 23967966 23968068
chr_2 g7483 g7483.t1 cds g7483.t1.CDS1 23967966 23968068
chr_2 g7483 g7483.t1 exon g7483.t1.exon2 23968118 23970930
chr_2 g7483 g7483.t1 cds g7483.t1.CDS2 23968118 23970930
chr_2 g7483 g7483.t1 TTS g7483.t1 23968458 23968458

Sequences

>g7483.t1 Gene=g7483 Length=2916
ATGATCTTTAAATATCAAAATTTTAACATTACTAAAAATAAAGTAAAAACTATTACACGA
CGGTGTTCAAATTCTTCTTTGCAAAAAGATGTATTTATAAACAAGCAACTTAAAATTGCC
GCATATCAACCTAAATTAATTGAAAACAAAAATGTCTGGAATATTAGAAATATTCGATCA
ACATCTAAAGAGAAGTTTTCAATGATTTTTCCACCGCCAAATGTGACAGGAAATATTCAT
TTAGGACATGCATTAACAGCAACAATTCAAGATGTAATAATTCGATGGAAGAGAAAGCAA
AATTTCGACACACAGTGGATATTTGGAACTGATCATGCTGGAATAGCTACTCAATTAATT
TTGGAAAAGATTTTATTCAAACGAGAGAACAAAACGAGACATGAAATTGGTAGAGAGCAA
TTTTTAAAAGAAACATGGAATTGGAAAAATGAAAAAAATTCAAGTATAAAAAACGATTTA
AAAAGATTGGGTTCAACTTTTAATTGGGAAAAAGAGTACTTCACAATGGATCAAAATCTA
AGTGAGGCAGTAAATGAAGCTTTTATAAGACTTTTTGATAAAGGACTCATTTATAGAGAA
AATTCATTAGTAAATTGGTGTTGCTCGTTAGAATCCGCAATATCGGATGTTGAAATTGAA
AGCCTTGAAGTTGATGGCAAAACGTCTATATCTATTCCGAATTATGAAAAAAATATAACT
GTAGGAATTCTAACCGAATTTGCTTACAAAATTGTTGATTCAGATGAAGAAATTGTAGTG
TCAACGACGCGACCAGAAACTATGCTTGCAGATTCAGCTGTTGCTGTCAATCCAAACGAT
CCTCGTTACTCTCATCTTAATAATATTAAATTGCATCATCCATACAGAAATGAAAGTATT
CCTCTAATATTTGATGAATCAGTAGATGTTAATTTTGGCACTGGTGCAGTAAAAATTACT
CCAGCTCATGATAAGAATGATTTTGAAGTGGGAAAGAGACATGATTTGCAATTTATTCAA
TTGATTACTGAAAACGGTTTGATTAGAGATAGTTTTGAAGGATTTTCTGGACTTGGAAGA
TTCGACGCTCGAGAAAAGATTCTCAATAGTTTGGTTGACTTAAACTTACTGCGTGGATCA
AAATCTCACAAAATGATTTTACCTATATGTTCACGATCAAAAGATATCATTGAATTCATG
ATAAAACCTCAATGGTTTGTAAAATGTAATGATCTCTCAAAACAAGCTGTTGAAGCAGTT
GAAACTGGTCAATTGAAAATTAATCCACAAATATTTGAAAAAGAATGGTTTAGATGGTTA
ACAAATTGCCGCGATTGGTGCATTTCTCGACAACTTTGGTGGGGTCATCAAATTCCTGCT
TATAAATTTCAACAAGAAAATGAAGAAATATGGATTGCAGCTAAATCACAAGAAGAGGCA
GAAAAGAGATTTAAAAAGATGCATCCAGATAAAAATGAATATTTAATTACGCGAGATCAA
GATGTATTAGATACATGGTTTTCTTCAGCACTTTTACCGTTTTCGGTATACAACTGGCCG
AATATTGATGCAAATTTTAACAAATATTTTCCATTGAATTTAATGGAAACTGGTCATGAT
ATACTTTTCTTTTGGGTTGCAAGAATGGTTATGCTTTCACTTGAATTAACAGGTAAGATT
CCTTTTAAAGAAGTTCTTCTTCACGGAATAGTATGTGATGCACATGGCAGAAAAATGTCT
AAAAGTCTTGGAAATGTCATATTACCTGAACAAATAATAAATGGAATAACTTTAGAAGAA
CTTCAAAATGAAACTTTGTCATCAGTTGAAAAAGGAATAATTAGCAAATCAGAATTAGAA
AAATCACTTGATGGACAGAAAAAAATGTTTCCAAATGGTATTCAAGAATGTGGCGTTGAT
GCATTACGTTTTACTCTTTGTTCACAAAATATCAAACAACATGTTATCAATTTTGATATC
AATGATTGTATTACAAATAAGCTCTTTTTCAACAAAATATGGCAAGCATCAAAATTTGCC
ATCAATTATGCAGAAACTAAAAATTTAAAAATATATGATATGAAGAATTTAAAAGGAATT
GAGCTTTCAGAGATTGATTTCTGGATTTTAAGCAGATTAGGCAATACAATTGAAACAGTA
TCAAAATCTATTGAAAACTATAATTTTCATTTTGCAACTGCAGCGTTAAAAACGTTTTTT
TATAACAATTTCTGTGATGTTTACTTAGAAACAACTAAAGAGCATTTAAAAAATGACACT
TCTCGAGGATTTACATGTGCGCACGTGCTTAATTTGTGTCTTTCAATAGGATTAAGTCAT
ATGGAAATTTTTACACCTTATTTAGCTAAAGAACTTTTTAATTATCTCCCAATCATTGAA
AATCTTGAAACAGGCAGATTCATTAACAATGAACTCGAAAAGAAAATAGAAAATTTATTG
GATATCTGTGCTAGCATAAGGGAAGTTAAAGCACATTTAGGAGTTACTAAAAAGACTGAT
GCATGTTTGAAAATTTTAATTAAATTAAAGGATCATGAAGACTTCTTTAATAAACATCTT
AATCATATAAGACATCTGACATTTAGTAATAATGTTGAATTGCTAACAAATGCTACAGAT
TTCGAGAAAGAAAATTTAACTGCATCATCGACCGCAAGCCATATGTGTTCATTTGGAATA
AGTATTAAAAATTTTGAAAAGCAAAACAATAGTAATGAGACTCTTAATAGAAAAAAACTA
CTTAAATTAGAACAAGAATTAACTAATTTGTTAAATGTAGTTAATAAAGAAGGATATAAA
GAAAAAGCAAAGAGAAGTGTACAACAGAAGCATGATGAAAAAATTCAAAAATTGAAATTA
GAGATTAATCATATTAAACAACTAAGAAATGAATGA

>g7483.t1 Gene=g7483 Length=971
MIFKYQNFNITKNKVKTITRRCSNSSLQKDVFINKQLKIAAYQPKLIENKNVWNIRNIRS
TSKEKFSMIFPPPNVTGNIHLGHALTATIQDVIIRWKRKQNFDTQWIFGTDHAGIATQLI
LEKILFKRENKTRHEIGREQFLKETWNWKNEKNSSIKNDLKRLGSTFNWEKEYFTMDQNL
SEAVNEAFIRLFDKGLIYRENSLVNWCCSLESAISDVEIESLEVDGKTSISIPNYEKNIT
VGILTEFAYKIVDSDEEIVVSTTRPETMLADSAVAVNPNDPRYSHLNNIKLHHPYRNESI
PLIFDESVDVNFGTGAVKITPAHDKNDFEVGKRHDLQFIQLITENGLIRDSFEGFSGLGR
FDAREKILNSLVDLNLLRGSKSHKMILPICSRSKDIIEFMIKPQWFVKCNDLSKQAVEAV
ETGQLKINPQIFEKEWFRWLTNCRDWCISRQLWWGHQIPAYKFQQENEEIWIAAKSQEEA
EKRFKKMHPDKNEYLITRDQDVLDTWFSSALLPFSVYNWPNIDANFNKYFPLNLMETGHD
ILFFWVARMVMLSLELTGKIPFKEVLLHGIVCDAHGRKMSKSLGNVILPEQIINGITLEE
LQNETLSSVEKGIISKSELEKSLDGQKKMFPNGIQECGVDALRFTLCSQNIKQHVINFDI
NDCITNKLFFNKIWQASKFAINYAETKNLKIYDMKNLKGIELSEIDFWILSRLGNTIETV
SKSIENYNFHFATAALKTFFYNNFCDVYLETTKEHLKNDTSRGFTCAHVLNLCLSIGLSH
MEIFTPYLAKELFNYLPIIENLETGRFINNELEKKIENLLDICASIREVKAHLGVTKKTD
ACLKILIKLKDHEDFFNKHLNHIRHLTFSNNVELLTNATDFEKENLTASSTASHMCSFGI
SIKNFEKQNNSNETLNRKKLLKLEQELTNLLNVVNKEGYKEKAKRSVQQKHDEKIQKLKL
EINHIKQLRNE

Protein features from InterProScan

Transcript Database ID Name Start End E.value
21 g7483.t1 CDD cd00817 ValRS_core 64 658 9.00234E-176
20 g7483.t1 CDD cd07962 Anticodon_Ia_Val 658 796 2.91139E-33
19 g7483.t1 Coils Coil Coil 809 829 -
18 g7483.t1 Coils Coil Coil 948 971 -
13 g7483.t1 Gene3D G3DSA:3.40.50.620 HUPs 37 244 1.1E-53
17 g7483.t1 Gene3D G3DSA:3.90.740.10 - 245 285 1.1E-5
16 g7483.t1 Gene3D G3DSA:3.90.740.10 - 286 376 6.7E-21
14 g7483.t1 Gene3D G3DSA:3.40.50.620 HUPs 377 607 4.2E-63
15 g7483.t1 Gene3D G3DSA:1.10.730.10 - 608 836 8.3E-44
3 g7483.t1 PANTHER PTHR11946:SF62 RE41093P 38 968 0.0
4 g7483.t1 PANTHER PTHR11946 VALYL-TRNA SYNTHETASES 38 968 0.0
6 g7483.t1 PRINTS PR00986 Valyl-tRNA synthetase signature 66 77 9.2E-29
8 g7483.t1 PRINTS PR00986 Valyl-tRNA synthetase signature 277 294 9.2E-29
5 g7483.t1 PRINTS PR00986 Valyl-tRNA synthetase signature 392 405 9.2E-29
9 g7483.t1 PRINTS PR00986 Valyl-tRNA synthetase signature 499 520 9.2E-29
7 g7483.t1 PRINTS PR00986 Valyl-tRNA synthetase signature 530 548 9.2E-29
1 g7483.t1 Pfam PF00133 tRNA synthetases class I (I, L, M and V) 49 652 1.3E-187
2 g7483.t1 Pfam PF08264 Anticodon-binding domain of tRNA ligase 706 841 6.0E-23
22 g7483.t1 ProSitePatterns PS00178 Aminoacyl-transfer RNA synthetases class-I signature. 73 84 -
10 g7483.t1 SUPERFAMILY SSF52374 Nucleotidylyl transferase 42 661 1.85E-124
12 g7483.t1 SUPERFAMILY SSF50677 ValRS/IleRS/LeuRS editing domain 240 387 3.14E-50
11 g7483.t1 SUPERFAMILY SSF47323 Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases 670 882 3.92E-33
23 g7483.t1 TIGRFAM TIGR00422 valS: valine–tRNA ligase 45 955 1.6E-255

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:0005524 ATP binding MF
GO:0004832 valine-tRNA ligase activity MF
GO:0002161 aminoacyl-tRNA editing activity MF
GO:0006418 tRNA aminoacylation for protein translation BP
GO:0000166 nucleotide binding MF
GO:0006438 valyl-tRNA aminoacylation BP
GO:0004812 aminoacyl-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