Gene loci information

Transcript annotation

  • This transcript has been annotated as Alanine–tRNA ligase, mitochondrial.

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 g6507 g6507.t1 isoform g6507.t1 17324058 17327170
chr_2 g6507 g6507.t1 exon g6507.t1.exon1 17324058 17326035
chr_2 g6507 g6507.t1 cds g6507.t1.CDS1 17324058 17326035
chr_2 g6507 g6507.t1 exon g6507.t1.exon2 17326099 17326898
chr_2 g6507 g6507.t1 cds g6507.t1.CDS2 17326099 17326898
chr_2 g6507 g6507.t1 exon g6507.t1.exon3 17326958 17327170
chr_2 g6507 g6507.t1 cds g6507.t1.CDS3 17326958 17327170
chr_2 g6507 g6507.t1 TSS g6507.t1 NA NA
chr_2 g6507 g6507.t1 TTS g6507.t1 NA NA

Sequences

>g6507.t1 Gene=g6507 Length=2991
ATGATACTTAACAAAAATATTTTACTAAATACAACAAGATTAAAAGTGATAACATGCAGA
AATTATTCAACAAAATATCGATCATCAAAAGTCATACGACAGCAATTTCTTGACTATTTT
GTTAAAGATAATGATCATAATTTTGTTCGAAGTTCATCAGTAATTCCATTTTGTGATCCT
ACATTATCGTTTACGAATGCTGGAATGAATCAATTTAAGAATATATTTCTTGGAAATCAA
CAACCGAAATATACTCGAGTAGCAAATACACAAAAATGCATTAGAGTAGGAGGTAAACAT
AATGATCTCTCAGTTGTTGGAACAGATGGCTATCATCACACTTTCTTTGAAATGCTTGGA
AATTGGTCATTTGGTGATTACTTTAAGAAAGAAGCATGTGAAATGGCTTGGAATTTACTA
ACAAAAGTCTATGAAATTCCACCTGAGCGACTTTATGTAACTTATTTTAAAGGCGATCAA
ACATTAGGTTTAAAACCTGATATTGAATGTCGAGATATTTGGCTTGAAATTGGTGTACCA
ATTAATCGAATTGTGGCATGTGATGCAAAAGATAATTTTTGGGAAATGGGAAAAACAGGC
CCTTGTGGAGGATGCACTGAAATTCATGTTGATCACTTACCAAGCTATAGAAAAGTCAAT
AGAGCTAAGGATGTTAACAAGGATAAGCATGATTTAACTGAACTCTGGAATATTGTATTC
ATTGAAAACTTTAGGAAAAGTGATGGCACAATTGAGCATTTACAACAAAAACATGTTGAT
ACTGGCATGGGTTTTGAAAGACTTGTTGCCTTTCTTCAAGATAAGAGAAGTAACTATGAT
ACCGATCTTTTTATACCTCTTTTTGAGAAAATTCAGAGAATTACAAGAAAGCCTCCTTAT
CTCGGATCATTTAGTGGTGATGATTTTAAACGTGACATGTCTTATCGAGTTATTGCTGAC
CATAGCAGAATGATTGCAATTGCTTTAGCTGATGGAATGTTTCCAGAAGAAAATAAAAAA
TTAAGAAGAATTTTAAGGAAGTGCCTTAATGTGTCTGTTAAAGTTTTTAGTCATGAAAAT
TTACTAACTGAAACAATACCAGTTGTAGCAAATATTCTTGGTGACACATTTCCTGAACTT
CATCAAAAACTTTTCACATCACTTGATATCGTCAAATATGAGGATGAATATTACAAGTCA
CTAAAAAGTTCACTTTCAAAAGGCATTAAAGATATTCTCGAAAAAAATCCACAATTGATG
GATCTTGATTTATATGAGTATCCAGGATTTGTTCAAGCATATAATGAATTCAAAAGATAT
AAAAAATCAAATCCATATGAAATTTCTGGTGATATGATGATTCAACTTTACTCAAATTTT
GGCTTAGACTTGGATTTTATTGAAAGATTAGCAGAGATTGAAAGAATGACATTAGATATT
AATGGATTTGAAAATCGTATGGAAGCAATGAAAGGGAAATCTCTTGAGAATTTTAAAGTA
GACAACGATATAGTGATGCGATTAGATGGTTCGATACCAGCAACTAATAATGATTCAAAA
TATAACTATGAGTATGATCCAAGCAGTAATTTGTACAAAATTAAACCAGTCAAGACGAAA
ATTCTTGCAATTTTTGATACCAATGGGCAGTCTTTAAAAAGCACAAATGAATCTACAACA
TCTTATGTCAAAATTGTAACGAAAGACAGTCCGATATATGTTGAATCAGGTGGACAAGAG
TCTGATGTTGGATATTTGGAGCAGAATGGAACAATTTTTAATATTGAGTCAGTTAGTTCA
AAGCAAAATATAATATTTCACAAAATTAAAACAAATCAAAGCGCAAACTTGAATGTTGGT
GATGAAGTAGAACTGTCAATTGATAATGAGAAAAGAACATCATGCATTCGAAATCATACA
GCAACTCATATTTTGAATGCTGCCATTAGAAACATTAAAAATCTTCCCACTTATCAAAAA
TCAAGCACAGTTACGAGCGAAAACTTGAAAATTGAACTCGCAATGATAGGACCAAAATTG
AATGAATCAGAAATTGATGAAATAGAAAAATTAGTAAGAAGACATATAAAAGAATTACCT
TTGCAACAAACAACTGAAGTTATAAATTCACAAGAGTTGCAAAGTAAAAATAATGTAATA
ATGGTGCCAGGCGAAGTATATCCTGATGAAGATATTCATGTTGTGTCGTTTGATGATTTT
TCACATGAATTATGCTGCGGTACACATGCTAACAGTACAAGTGAAATTTTAGATTTTACA
TTTTTGAGTGTGAAGTCGACTGGTCGAGTAAGTTATCTCTTCAATGCAGTGACAGGAAAT
AAAGCCATTGAAGCTATCAAAAAAGGTGACGAGTTAATTAGTCAAATAAAATCTTTAAGT
GAAAATGATGAAATTGAAAAGTTCACAGTAATTTTAAGTCATTTAAGAAAGATTGCTTCA
AAATTACATGACAACGAAATTTCATATCTCAAAAAAATTCAATGTCAAAAACTTATAACT
GATATGAAAGAGACAATTAAATATAAGAGCAGGGATGTTGTAAGTGAACTTTTGGATATA
GAAATGAAGTCAGTTATTGAACAAAATGAGCCATTTATCGTTCATTTTCTTGCATGCTCA
GATCTAATGCAATCAGTTTCATTGCTAAAAGCAACAAGACTAGTAAGCGATGATAAACCA
GTCATCATCATATCACTTGTTGATAATGAAGTTAAAGCAAGATGTTGTGTGCCAAAAGAA
ATGATAAATGAAAATTTTAATGCTGAAAAGTGGCTGACGCATTTCGCTAAAATCTTCAAC
TCGACAGTTAAACCTCCAAAAGGACAAGATCCACTCGAAGTTTGTCTCATGAAAGGCAAA
AAAGTGAAATCTGAAGAATTCAATACCATGCTGGAACAAGCAATTGCAGCAGCAAAATCA
TTTGCAAATAGTAATATTTTAGATGAAACTAGATTTGTTAAAAAGAATTAG

>g6507.t1 Gene=g6507 Length=996
MILNKNILLNTTRLKVITCRNYSTKYRSSKVIRQQFLDYFVKDNDHNFVRSSSVIPFCDP
TLSFTNAGMNQFKNIFLGNQQPKYTRVANTQKCIRVGGKHNDLSVVGTDGYHHTFFEMLG
NWSFGDYFKKEACEMAWNLLTKVYEIPPERLYVTYFKGDQTLGLKPDIECRDIWLEIGVP
INRIVACDAKDNFWEMGKTGPCGGCTEIHVDHLPSYRKVNRAKDVNKDKHDLTELWNIVF
IENFRKSDGTIEHLQQKHVDTGMGFERLVAFLQDKRSNYDTDLFIPLFEKIQRITRKPPY
LGSFSGDDFKRDMSYRVIADHSRMIAIALADGMFPEENKKLRRILRKCLNVSVKVFSHEN
LLTETIPVVANILGDTFPELHQKLFTSLDIVKYEDEYYKSLKSSLSKGIKDILEKNPQLM
DLDLYEYPGFVQAYNEFKRYKKSNPYEISGDMMIQLYSNFGLDLDFIERLAEIERMTLDI
NGFENRMEAMKGKSLENFKVDNDIVMRLDGSIPATNNDSKYNYEYDPSSNLYKIKPVKTK
ILAIFDTNGQSLKSTNESTTSYVKIVTKDSPIYVESGGQESDVGYLEQNGTIFNIESVSS
KQNIIFHKIKTNQSANLNVGDEVELSIDNEKRTSCIRNHTATHILNAAIRNIKNLPTYQK
SSTVTSENLKIELAMIGPKLNESEIDEIEKLVRRHIKELPLQQTTEVINSQELQSKNNVI
MVPGEVYPDEDIHVVSFDDFSHELCCGTHANSTSEILDFTFLSVKSTGRVSYLFNAVTGN
KAIEAIKKGDELISQIKSLSENDEIEKFTVILSHLRKIASKLHDNEISYLKKIQCQKLIT
DMKETIKYKSRDVVSELLDIEMKSVIEQNEPFIVHFLACSDLMQSVSLLKATRLVSDDKP
VIIISLVDNEVKARCCVPKEMINENFNAEKWLTHFAKIFNSTVKPPKGQDPLEVCLMKGK
KVKSEEFNTMLEQAIAAAKSFANSNILDETRFVKKN

Protein features from InterProScan

Transcript Database ID Name Start End E.value
20 g6507.t1 CDD cd00673 AlaRS_core 32 275 1.6222E-111
19 g6507.t1 Coils Coil Coil 473 493 -
18 g6507.t1 Coils Coil Coil 996 996 -
16 g6507.t1 Gene3D G3DSA:3.30.930.10 Bira Bifunctional Protein; Domain 2 27 276 7.4E-107
17 g6507.t1 Gene3D G3DSA:2.40.30.130 - 520 627 3.4E-8
15 g6507.t1 Gene3D G3DSA:3.30.980.10 - 628 791 3.4E-30
6 g6507.t1 Hamap MF_00036_B Alanine–tRNA ligase [alaS]. 28 986 89.038689
4 g6507.t1 PANTHER PTHR11777:SF8 ALANINE–TRNA LIGASE, MITOCHONDRIAL 17 984 9.4E-291
5 g6507.t1 PANTHER PTHR11777 ALANYL-TRNA SYNTHETASE 17 984 9.4E-291
9 g6507.t1 PRINTS PR00980 Alanyl-tRNA synthetase signature 101 112 2.8E-15
10 g6507.t1 PRINTS PR00980 Alanyl-tRNA synthetase signature 233 244 2.8E-15
8 g6507.t1 PRINTS PR00980 Alanyl-tRNA synthetase signature 260 273 2.8E-15
7 g6507.t1 PRINTS PR00980 Alanyl-tRNA synthetase signature 316 332 2.8E-15
2 g6507.t1 Pfam PF01411 tRNA synthetases class II (A) 32 408 5.8E-133
1 g6507.t1 Pfam PF01411 tRNA synthetases class II (A) 444 630 3.7E-24
3 g6507.t1 Pfam PF07973 Threonyl and Alanyl tRNA synthetase second additional domain 733 767 8.5E-7
23 g6507.t1 ProSiteProfiles PS50860 Alanyl-transfer RNA synthetases family profile. 27 788 84.452
21 g6507.t1 SMART SM00863 tRNA_SAD_4 732 771 3.9E-4
11 g6507.t1 SUPERFAMILY SSF55681 Class II aaRS and biotin synthetases 29 279 2.65E-90
13 g6507.t1 SUPERFAMILY SSF101353 Putative anticodon-binding domain of alanyl-tRNA synthetase (AlaRS) 280 502 7.45E-36
14 g6507.t1 SUPERFAMILY SSF50447 Translation proteins 559 627 7.06E-7
12 g6507.t1 SUPERFAMILY SSF55186 ThrRS/AlaRS common domain 632 781 2.49E-26
22 g6507.t1 TIGRFAM TIGR00344 alaS: alanine–tRNA ligase 32 940 5.6E-183

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:0005737 cytoplasm CC
GO:0003676 nucleic acid binding MF
GO:0000166 nucleotide binding MF
GO:0043039 tRNA aminoacylation BP
GO:0004812 aminoacyl-tRNA ligase activity MF
GO:0006419 alanyl-tRNA aminoacylation BP
GO:0004813 alanine-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