General information for g5883.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Alanine–tRNA ligase, cytoplasmic.
Parent gene
- The parent gene g5883 is located on chr_2: 12576087..12578032 (+ strand)
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 | g5883 | g5883.t1 | isoform | g5883.t1 | 12574761 | 12578032 |
| chr_2 | g5883 | g5883.t1 | exon | g5883.t1.exon1 | 12574761 | 12574804 |
| chr_2 | g5883 | g5883.t1 | cds | g5883.t1.CDS1 | 12574761 | 12574804 |
| chr_2 | g5883 | g5883.t1 | TSS | g5883.t1 | 12574792 | 12574792 |
| chr_2 | g5883 | g5883.t1 | exon | g5883.t1.exon2 | 12574925 | 12574934 |
| chr_2 | g5883 | g5883.t1 | cds | g5883.t1.CDS2 | 12574925 | 12574934 |
| chr_2 | g5883 | g5883.t1 | exon | g5883.t1.exon3 | 12575058 | 12576018 |
| chr_2 | g5883 | g5883.t1 | cds | g5883.t1.CDS3 | 12575058 | 12576018 |
| chr_2 | g5883 | g5883.t1 | exon | g5883.t1.exon4 | 12576087 | 12578032 |
| chr_2 | g5883 | g5883.t1 | cds | g5883.t1.CDS4 | 12576087 | 12578032 |
| chr_2 | g5883 | g5883.t1 | TTS | g5883.t1 | 12578134 | 12578134 |
Sequences
>g5883.t1 Gene=g5883 Length=2961
ATGTCGAGTATGAATAGAGAAATAATTTTCATAGTGACTCACATTGAAATTAAGGAAAAA
ATGGATACCACGCTGACAGCAAATCAAATTCGTAAGCTCTTTTTGGATTTCTTTGAAGAG
CAAAAACATATTTATGTTCATTCATCATCAACAATTCCTCTCGATGATCCAACATTGCTC
TTTGCAAATGCTGGAATGAATCAATTCAAGCCAATTTTCTTGGGAACTGCCGATCCAAAT
TCTGAAATGTCAAAATGGGTAAGAGTTGCAAACACTCAAAAGTGCATTCGTGCTGGAGGC
AAGCACAACGATTTAGATGATGTTGGAAAAGATGTTTATCATCACACTTTCTTTGAAATG
CTTGGCAACTGGTCATTTGGTGACTATTTCAAAAAAGAAATCTGTACATGGGCTTGGGAA
TTCTTGACTGGTCGCCTTAAACTGCCAAAAGATCGACTCTATGTAACATATTTTGGTGGT
GATAAAGATGCCGGCTTAGAACCAGATTTGGAATGCAAACAAATCTGGACAGATTTGGGA
GTTTTACCAGCTCACATTTTACCTGGTTCAATGAAAGACAATTTCTGGGAAATGGGTGAA
ACAGGACCTTGTGGACCTTGCAGTGAATTACATTTTGATCGAATTGGCGGAAGAAGCGTG
CCAGAGTTAGTAAATATGGATGATCCCGATGTACTTGAAATTTGGAATCTTGTGTTTATT
CAATTTAATCGTGAAGCTGATTCATCACTCAAGTTACTGCCAAAGAAACATATTGACTGT
GGCATGGGCTTTGAACGTCTTGTATCAGTTATTCAAAACAAGAGATCAAATTATGATACT
GACATATTTGTACCACTTTTTGATGCTATTCAAAAAGGAACTGGAGCTCGTGCTTACACT
GGTAAAGTTGGAGCAGAAGATGTTGATGGAGTTGATATGGCTTATCGTGTACTCGCTGAT
CATGCTCGTACAATCACAATTGCATTAGCTGATGGCGGATTTCCTGATAGCACTGGTCGT
GGATATGTTTTGCGTAGAATTTTAAGACGTGCTGTTCGCTATGCAACTGAAAAATTAAAT
GCTAAGCCGGGATTCTTTGCTACCCTCGTAACTACAGTAGTTGAATTGCTTGGCGATACT
TTCCCTGAATTAAGAAAAGATCCACTGCACACAATGAATATTATCAATGAAGAGGAACAA
CAATTTTTGAAGACACTTTCAAGAGGCAGAAATTTACTAAATCGAACAATTGCTAAGCTG
AAGGATAACGTCTTACCAGGTGATGTTGCCTGGCGCTTATATGATACATATGGTTTCCCT
ATTGATTTAACGCATTTGATGGTAGAAGAAAGAAATTTATCAATTGATATGGTCGCTTAT
GAAGAAGCTAAACACAAAAGTTACATTGCATCACAAGGAAAAACAGCAAGTACTTTAGAT
ACTGTCAATCTTGATGTCCATGCTATTTCAGAGTTACAAGAGAAAGGTGTTCCAACTACA
AATGATTCATTCAAATATCGCTATCGTGCCGAATCAATTGATTCAAAGGCAGAGTACATT
TTTGAAGGATGTAAAGGAAAAATTTTAGCAATTCGTTTCAATAATCAATTTGTCGATGAA
GTCACAAGCGGACAAGAATGTGGCTTGATTTTGGATCAAACCAATTTTTATGCTGAATCA
GGTGGACAAATTTACGATCAAGGGTTCTTTGTCAAATTAACGGATGAAGCAACAGAATTT
TCAGTAAGAACAGTTTACAATAAAGGCGGTTATATCTTACATATTGGTGTCGTTGAGGGA
ACATTGAAAGTTGGCGATGAACTTGAATTACATTTAGACACTGTTCGTCGCTCATTAACA
ATGAAAAATCATTCTGCCACACATGCTTTGAATCACTCACTGCTCAAAGTTCTTGGTAAT
GATACAGAACAACGTGGCTCATTAGTTATTCCTGAAAAATTGCGATTTGATTTTACCAGC
AAAAATGCAATGACAGTGCAACAAGTTTCTGATACTGAAAAGCGCACTCAAGATGTTGTT
CAAAAGAATATGCAGATTTATGCAAAGGAATCGAATTTAAAAGTTGCAAAATCAATCAAT
GGATTAAGATCTGTCTTTGACGAAGTTTATCCCGATCCTGTAAGAGTTATTTCATTTGGC
GTTCCCGTTGAAACACTAGAAAAGAATCCAGAAGGAGAGGAAGGTGTTGAAACATCTGTT
GAATTTTGTGGAGGAACACATTTACATCAATCTGGTCATATTGTTGATTTTATAATCACA
AATGAAGAAGCAATTGCAAAAGGCATTCGAAGAATTGTAGCTCTTACTGGACCTGAAGCC
GAAAAAGCACGTCAAAAGACAGCTCTTTTAGAAAATGATTTGAACAAACTTAAATCAAAA
ATCGATGCTGCCGGTGATAATGTGAATATTAAAGAAGTAACAAGAGAAATTGTTGCTCTT
ACTGAAGACGTTTCGCAAGCTACAATTTCATATGTTAAAAAGGATGAAATGCGTAATATT
TTGAATGGTCTCAAGAAGGCTCTTGGTGATAAGGAGCGTGCAATGAAAGCAGCTGTTGTA
AATGTCGTTTCTGAGCAAGCAAAACAACTTGTTGAACAAAATAAGGATGCTAAATTTTTA
GTTCATCGCTTTGAAGCATACAATAATACAAAAGCACTCGATGCAGCTTTGAAACAGGTA
CAAAAAGTTAGCCCTGATGCTTCAGCTCTATTTGTTACAGTTGATGAAGATTCGAAAAAG
ATTTTCTGTTTGGCTAATGCATCAAAGTCTGCTATTGAAAAAGGACTCAAAGCTAATGAA
TGGGTACAACAAGTTCAATCATTGATGAATGGAAAAGGAGGTGGTAAACCAGAATCCGCA
CAAGCTTCAGGCAGCAATTATGAAAAGGTTGATGAAATAATTGCTTTAGCGAAATCATTT
GCTAACTCTAAATTGGAGTAA
>g5883.t1 Gene=g5883 Length=986
MSSMNREIIFIVTHIEIKEKMDTTLTANQIRKLFLDFFEEQKHIYVHSSSTIPLDDPTLL
FANAGMNQFKPIFLGTADPNSEMSKWVRVANTQKCIRAGGKHNDLDDVGKDVYHHTFFEM
LGNWSFGDYFKKEICTWAWEFLTGRLKLPKDRLYVTYFGGDKDAGLEPDLECKQIWTDLG
VLPAHILPGSMKDNFWEMGETGPCGPCSELHFDRIGGRSVPELVNMDDPDVLEIWNLVFI
QFNREADSSLKLLPKKHIDCGMGFERLVSVIQNKRSNYDTDIFVPLFDAIQKGTGARAYT
GKVGAEDVDGVDMAYRVLADHARTITIALADGGFPDSTGRGYVLRRILRRAVRYATEKLN
AKPGFFATLVTTVVELLGDTFPELRKDPLHTMNIINEEEQQFLKTLSRGRNLLNRTIAKL
KDNVLPGDVAWRLYDTYGFPIDLTHLMVEERNLSIDMVAYEEAKHKSYIASQGKTASTLD
TVNLDVHAISELQEKGVPTTNDSFKYRYRAESIDSKAEYIFEGCKGKILAIRFNNQFVDE
VTSGQECGLILDQTNFYAESGGQIYDQGFFVKLTDEATEFSVRTVYNKGGYILHIGVVEG
TLKVGDELELHLDTVRRSLTMKNHSATHALNHSLLKVLGNDTEQRGSLVIPEKLRFDFTS
KNAMTVQQVSDTEKRTQDVVQKNMQIYAKESNLKVAKSINGLRSVFDEVYPDPVRVISFG
VPVETLEKNPEGEEGVETSVEFCGGTHLHQSGHIVDFIITNEEAIAKGIRRIVALTGPEA
EKARQKTALLENDLNKLKSKIDAAGDNVNIKEVTREIVALTEDVSQATISYVKKDEMRNI
LNGLKKALGDKERAMKAAVVNVVSEQAKQLVEQNKDAKFLVHRFEAYNNTKALDAALKQV
QKVSPDASALFVTVDEDSKKIFCLANASKSAIEKGLKANEWVQQVQSLMNGKGGGKPESA
QASGSNYEKVDEIIALAKSFANSKLE
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 23 | g5883.t1 | CDD | cd00673 | AlaRS_core | 27 | 274 | 2.02201E-129 |
| 22 | g5883.t1 | Coils | Coil | Coil | 403 | 423 | - |
| 21 | g5883.t1 | Coils | Coil | Coil | 780 | 807 | - |
| 18 | g5883.t1 | Gene3D | G3DSA:3.30.930.10 | Bira Bifunctional Protein; Domain 2 | 24 | 275 | 5.1E-119 |
| 19 | g5883.t1 | Gene3D | G3DSA:2.40.30.130 | - | 527 | 611 | 4.4E-10 |
| 17 | g5883.t1 | Gene3D | G3DSA:3.30.980.10 | - | 616 | 772 | 1.1E-40 |
| 20 | g5883.t1 | Gene3D | G3DSA:3.30.54.20 | - | 684 | 754 | 1.1E-40 |
| 16 | g5883.t1 | Gene3D | G3DSA:3.10.310.40 | - | 869 | 982 | 9.6E-16 |
| 6 | g5883.t1 | Hamap | MF_00036_B | Alanine–tRNA ligase [alaS]. | 1 | 985 | 134.134445 |
| 4 | g5883.t1 | PANTHER | PTHR11777:SF34 | ALANINE–TRNA LIGASE, CYTOPLASMIC | 21 | 985 | 0.0 |
| 5 | g5883.t1 | PANTHER | PTHR11777 | ALANYL-TRNA SYNTHETASE | 21 | 985 | 0.0 |
| 8 | g5883.t1 | PRINTS | PR00980 | Alanyl-tRNA synthetase signature | 103 | 114 | 7.4E-30 |
| 10 | g5883.t1 | PRINTS | PR00980 | Alanyl-tRNA synthetase signature | 232 | 243 | 7.4E-30 |
| 9 | g5883.t1 | PRINTS | PR00980 | Alanyl-tRNA synthetase signature | 259 | 272 | 7.4E-30 |
| 7 | g5883.t1 | PRINTS | PR00980 | Alanyl-tRNA synthetase signature | 316 | 332 | 7.4E-30 |
| 11 | g5883.t1 | PRINTS | PR00980 | Alanyl-tRNA synthetase signature | 340 | 353 | 7.4E-30 |
| 2 | g5883.t1 | Pfam | PF01411 | tRNA synthetases class II (A) | 29 | 614 | 5.0E-217 |
| 3 | g5883.t1 | Pfam | PF07973 | Threonyl and Alanyl tRNA synthetase second additional domain | 714 | 773 | 1.9E-14 |
| 1 | g5883.t1 | Pfam | PF02272 | DHHA1 domain | 836 | 980 | 3.0E-17 |
| 26 | g5883.t1 | ProSiteProfiles | PS50860 | Alanyl-transfer RNA synthetases family profile. | 25 | 786 | 116.081 |
| 24 | g5883.t1 | SMART | SM00863 | tRNA_SAD_4 | 714 | 773 | 5.7E-16 |
| 12 | g5883.t1 | SUPERFAMILY | SSF55681 | Class II aaRS and biotin synthetases | 26 | 278 | 1.57E-94 |
| 14 | g5883.t1 | SUPERFAMILY | SSF101353 | Putative anticodon-binding domain of alanyl-tRNA synthetase (AlaRS) | 279 | 490 | 2.75E-58 |
| 15 | g5883.t1 | SUPERFAMILY | SSF50447 | Translation proteins | 536 | 610 | 2.78E-15 |
| 13 | g5883.t1 | SUPERFAMILY | SSF55186 | ThrRS/AlaRS common domain | 616 | 780 | 8.24E-35 |
| 25 | g5883.t1 | TIGRFAM | TIGR00344 | alaS: alanine–tRNA ligase | 29 | 964 | 6.8E-252 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5883/g5883.t1; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5883.t1.fa.iupred3.txt does not exist
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
- This transcript has been annotated with K01872 (alanyl-tRNA synthetase)
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.
