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_3 g3833 g3833.t11 isoform g3833.t11 28290022 28291097
chr_3 g3833 g3833.t11 exon g3833.t11.exon1 28290022 28291097
chr_3 g3833 g3833.t11 cds g3833.t11.CDS1 28290303 28291097
chr_3 g3833 g3833.t11 TTS g3833.t11 28291200 28291200
chr_3 g3833 g3833.t11 TSS g3833.t11 NA NA

Sequences

>g3833.t11 Gene=g3833 Length=1076
ATCCACAACCATTCATAAGAACTCGTGAATTTTTATGGCAAGAAGGTCACACTGCATTTG
CAACATCAAAAGAGGCTCAGGAAGAAGTTTACGAAATTCTGGAATTATACAAACAAATTT
ATACTGATTTGTTAGCAATTCCAGTTGTAAAAGGACGTAAGACCGAGAAAGAAAAGTTTC
CTGGTGGTGATTTTACAACAACAGTTGAAGCTTTTATTTCTGCAAGTGGTCGCGGAATTC
AAGGTGCAACCAGTCACTTTCTTGGTCAAAACTTTTCAAAAATGTTTGACATTATTTTCG
AGAATCCAGAAACTCAAGAAAAGGAATATGTTTATCAGAATTCATGGGGAATTAGCACTA
GAACTATTGGTGTAATGGTAATGGTGCATGCTGATAATCAAGGAATTGTTTTGCCACCTC
GAGTGGCTTATACACAAGTTATTATAGTTCCTTGCGGTATCACTGCCACAACATCGAATA
CTGATCGTAAAACTCTTATTGATAGTTGCAAAGAATTGGAAAAGCAATTGCAAGCATGCA
ATATTCGTATAGATGGAGATTATCGTGACAATTACTCTCCTGGTTGGAAATATAATCATT
GGGAATTAAAAGGTGTCCCAATTCGCATCGAATTGGGACCAAAAGATTTGAAGGCTCAAC
AATTTGTTGCAGTACGACGTGATAATTTTGAAAAGTTGACCATCAGTAGAAGTAAAGCTT
CAACAGATATTCCAGAATTACTTGAAAAGATTCATCAAAATATGTTAACAAAAGCAACAA
AAGATTTAACCGATCACTTAAAAACAACAAAAAATTGGAAAGAATTTACATCATTTTTGG
ATTCAAAATATATTATTATGGCTCCATTCTGTGGAGACATTCTTTGTGAAGAAAAGATCA
AGACAGATAGTGCACGTGAAGAGACCGATGAAGCTGTTCAAGGACCTGCAATGGGAGCAA
AATCCTTGTGTATTCCATTTGAACAGCCAGCTGAAATTCAAGAAAGCGACAAATGCATTC
ATCCAGAGTGCAACAACAAACCGAAGTTCTACACACTTTTCGGAAGAAGCTACTAA

>g3833.t11 Gene=g3833 Length=264
MFDIIFENPETQEKEYVYQNSWGISTRTIGVMVMVHADNQGIVLPPRVAYTQVIIVPCGI
TATTSNTDRKTLIDSCKELEKQLQACNIRIDGDYRDNYSPGWKYNHWELKGVPIRIELGP
KDLKAQQFVAVRRDNFEKLTISRSKASTDIPELLEKIHQNMLTKATKDLTDHLKTTKNWK
EFTSFLDSKYIIMAPFCGDILCEEKIKTDSAREETDEAVQGPAMGAKSLCIPFEQPAEIQ
ESDKCIHPECNNKPKFYTLFGRSY

Protein features from InterProScan

Transcript Database ID Name Start End E.value
13 g3833.t11 CDD cd00862 ProRS_anticodon_zinc 41 264 2.14712E-86
12 g3833.t11 Coils Coil Coil 69 89 -
11 g3833.t11 Gene3D G3DSA:3.30.930.10 Bira Bifunctional Protein; Domain 2 1 45 4.0E-11
10 g3833.t11 Gene3D G3DSA:3.40.50.800 - 46 171 2.7E-43
9 g3833.t11 Gene3D G3DSA:3.30.110.30 - 173 263 2.9E-33
3 g3833.t11 PANTHER PTHR43382 PROLYL-TRNA SYNTHETASE 1 264 1.7E-120
4 g3833.t11 PANTHER PTHR43382:SF2 BIFUNCTIONAL GLUTAMATE/PROLINE–TRNA LIGASE 1 264 1.7E-120
2 g3833.t11 Pfam PF03129 Anticodon binding domain 52 150 2.7E-18
1 g3833.t11 Pfam PF09180 Prolyl-tRNA synthetase, C-terminal 179 264 4.0E-22
8 g3833.t11 SMART SM00946 ProRS_C_1_2 179 264 3.0E-29
5 g3833.t11 SUPERFAMILY SSF55681 Class II aaRS and biotin synthetases 2 58 1.37E-7
7 g3833.t11 SUPERFAMILY SSF52954 Class II aaRS ABD-related 41 171 3.11E-30
6 g3833.t11 SUPERFAMILY SSF64586 C-terminal domain of ProRS 175 264 3.34E-17

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:0000166 nucleotide binding MF
GO:0005737 cytoplasm CC
GO:0004827 proline-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