Gene loci information

Transcript annotation

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

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 g5883 g5883.t6 isoform g5883.t6 12576087 12578032
chr_2 g5883 g5883.t6 exon g5883.t6.exon1 12576087 12578032
chr_2 g5883 g5883.t6 cds g5883.t6.CDS1 12576245 12578032
chr_2 g5883 g5883.t6 TTS g5883.t6 12578134 12578134
chr_2 g5883 g5883.t6 TSS g5883.t6 NA NA

Sequences

>g5883.t6 Gene=g5883 Length=1946
GTCGTGGATATGTTTTGCGTAGAATTTTAAGACGTGCTGTTCGCTATGCAACTGAAAAAT
TAAATGCTAAGCCGGGATTCTTTGCTACCCTCGTAACTACAGTAGTTGAATTGCTTGGCG
ATACTTTCCCTGAATTAAGAAAAGATCCACTGCACACAATGAATATTATCAATGAAGAGG
AACAACAATTTTTGAAGACACTTTCAAGAGGCAGAAATTTACTAAATCGAACAATTGCTA
AGCTGAAGGATAACGTCTTACCAGGTGATGTTGCCTGGCGCTTATATGATACATATGGTT
TCCCTATTGATTTAACGCATTTGATGGTAGAAGAAAGAAATTTATCAATTGATATGGTCG
CTTATGAAGAAGCTAAACACAAAAGTTACATTGCATCACAAGGAAAAACAGCAAGTACTT
TAGATACTGTCAATCTTGATGTCCATGCTATTTCAGAGTTACAAGAGAAAGGTGTTCCAA
CTACAAATGATTCATTCAAATATCGCTATCGTGCCGAATCAATTGATTCAAAGGCAGAGT
ACATTTTTGAAGGATGTAAAGGAAAAATTTTAGCAATTCGTTTCAATAATCAATTTGTCG
ATGAAGTCACAAGCGGACAAGAATGTGGCTTGATTTTGGATCAAACCAATTTTTATGCTG
AATCAGGTGGACAAATTTACGATCAAGGGTTCTTTGTCAAATTAACGGATGAAGCAACAG
AATTTTCAGTAAGAACAGTTTACAATAAAGGCGGTTATATCTTACATATTGGTGTCGTTG
AGGGAACATTGAAAGTTGGCGATGAACTTGAATTACATTTAGACACTGTTCGTCGCTCAT
TAACAATGAAAAATCATTCTGCCACACATGCTTTGAATCACTCACTGCTCAAAGTTCTTG
GTAATGATACAGAACAACGTGGCTCATTAGTTATTCCTGAAAAATTGCGATTTGATTTTA
CCAGCAAAAATGCAATGACAGTGCAACAAGTTTCTGATACTGAAAAGCGCACTCAAGATG
TTGTTCAAAAGAATATGCAGATTTATGCAAAGGAATCGAATTTAAAAGTTGCAAAATCAA
TCAATGGATTAAGATCTGTCTTTGACGAAGTTTATCCCGATCCTGTAAGAGTTATTTCAT
TTGGCGTTCCCGTTGAAACACTAGAAAAGAATCCAGAAGGAGAGGAAGGTGTTGAAACAT
CTGTTGAATTTTGTGGAGGAACACATTTACATCAATCTGGTCATATTGTTGATTTTATAA
TCACAAATGAAGAAGCAATTGCAAAAGGCATTCGAAGAATTGTAGCTCTTACTGGACCTG
AAGCCGAAAAAGCACGTCAAAAGACAGCTCTTTTAGAAAATGATTTGAACAAACTTAAAT
CAAAAATCGATGCTGCCGGTGATAATGTGAATATTAAAGAAGTAACAAGAGAAATTGTTG
CTCTTACTGAAGACGTTTCGCAAGCTACAATTTCATATGTTAAAAAGGATGAAATGCGTA
ATATTTTGAATGGTCTCAAGAAGGCTCTTGGTGATAAGGAGCGTGCAATGAAAGCAGCTG
TTGTAAATGTCGTTTCTGAGCAAGCAAAACAACTTGTTGAACAAAATAAGGATGCTAAAT
TTTTAGTTCATCGCTTTGAAGCATACAATAATACAAAAGCACTCGATGCAGCTTTGAAAC
AGGTACAAAAAGTTAGCCCTGATGCTTCAGCTCTATTTGTTACAGTTGATGAAGATTCGA
AAAAGATTTTCTGTTTGGCTAATGCATCAAAGTCTGCTATTGAAAAAGGACTCAAAGCTA
ATGAATGGGTACAACAAGTTCAATCATTGATGAATGGAAAAGGAGGTGGTAAACCAGAAT
CCGCACAAGCTTCAGGCAGCAATTATGAAAAGGTTGATGAAATAATTGCTTTAGCGAAAT
CATTTGCTAACTCTAAATTGGAGTAA

>g5883.t6 Gene=g5883 Length=595
MNIINEEEQQFLKTLSRGRNLLNRTIAKLKDNVLPGDVAWRLYDTYGFPIDLTHLMVEER
NLSIDMVAYEEAKHKSYIASQGKTASTLDTVNLDVHAISELQEKGVPTTNDSFKYRYRAE
SIDSKAEYIFEGCKGKILAIRFNNQFVDEVTSGQECGLILDQTNFYAESGGQIYDQGFFV
KLTDEATEFSVRTVYNKGGYILHIGVVEGTLKVGDELELHLDTVRRSLTMKNHSATHALN
HSLLKVLGNDTEQRGSLVIPEKLRFDFTSKNAMTVQQVSDTEKRTQDVVQKNMQIYAKES
NLKVAKSINGLRSVFDEVYPDPVRVISFGVPVETLEKNPEGEEGVETSVEFCGGTHLHQS
GHIVDFIITNEEAIAKGIRRIVALTGPEAEKARQKTALLENDLNKLKSKIDAAGDNVNIK
EVTREIVALTEDVSQATISYVKKDEMRNILNGLKKALGDKERAMKAAVVNVVSEQAKQLV
EQNKDAKFLVHRFEAYNNTKALDAALKQVQKVSPDASALFVTVDEDSKKIFCLANASKSA
IEKGLKANEWVQQVQSLMNGKGGGKPESAQASGSNYEKVDEIIALAKSFANSKLE

Protein features from InterProScan

Transcript Database ID Name Start End E.value
14 g5883.t6 Coils Coil Coil 12 32 -
15 g5883.t6 Coils Coil Coil 389 416 -
12 g5883.t6 Gene3D G3DSA:2.40.30.130 - 135 220 2.3E-10
11 g5883.t6 Gene3D G3DSA:3.30.980.10 - 225 381 4.7E-41
13 g5883.t6 Gene3D G3DSA:3.30.54.20 - 293 363 4.7E-41
10 g5883.t6 Gene3D G3DSA:3.10.310.40 - 479 591 4.8E-16
4 g5883.t6 PANTHER PTHR11777:SF34 ALANINE–TRNA LIGASE, CYTOPLASMIC 2 594 4.4E-170
5 g5883.t6 PANTHER PTHR11777 ALANYL-TRNA SYNTHETASE 2 594 4.4E-170
2 g5883.t6 Pfam PF01411 tRNA synthetases class II (A) 2 223 3.1E-55
3 g5883.t6 Pfam PF07973 Threonyl and Alanyl tRNA synthetase second additional domain 323 382 9.9E-15
1 g5883.t6 Pfam PF02272 DHHA1 domain 445 589 1.4E-17
16 g5883.t6 ProSiteProfiles PS50860 Alanyl-transfer RNA synthetases family profile. 1 395 46.815
9 g5883.t6 SMART SM00863 tRNA_SAD_4 323 382 5.7E-16
7 g5883.t6 SUPERFAMILY SSF101353 Putative anticodon-binding domain of alanyl-tRNA synthetase (AlaRS) 1 100 7.06E-21
8 g5883.t6 SUPERFAMILY SSF50447 Translation proteins 145 219 1.3E-15
6 g5883.t6 SUPERFAMILY SSF55186 ThrRS/AlaRS common domain 225 389 3.53E-35

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

Data is missing for g5883/g5883.t6; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5883.t6.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 gene did not have any KEGG ortholog annotations (KAAS, GHOSTZ).

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