Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative Serine–pyruvate aminotransferase, 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_4 g17483 g17483.t78 TSS g17483.t78 13659535 13659535
chr_4 g17483 g17483.t78 isoform g17483.t78 13660417 13661275
chr_4 g17483 g17483.t78 exon g17483.t78.exon1 13660417 13660580
chr_4 g17483 g17483.t78 cds g17483.t78.CDS1 13660545 13660580
chr_4 g17483 g17483.t78 exon g17483.t78.exon2 13660656 13660708
chr_4 g17483 g17483.t78 cds g17483.t78.CDS2 13660656 13660708
chr_4 g17483 g17483.t78 exon g17483.t78.exon3 13660794 13661195
chr_4 g17483 g17483.t78 cds g17483.t78.CDS3 13660794 13661195
chr_4 g17483 g17483.t78 exon g17483.t78.exon4 13661253 13661275
chr_4 g17483 g17483.t78 cds g17483.t78.CDS4 13661253 13661274
chr_4 g17483 g17483.t78 TTS g17483.t78 13661511 13661511

Sequences

>g17483.t78 Gene=g17483 Length=642
TTTGACTCATGGTGAATCAAGCACAGGAATGTTGCAACAAAATTTGGAACAATTTGGAAA
TTTATGTCAGGAATTTAATTGTCTTTTTGTGGTTGATTGCGTTATAACAGTTGGATGCAC
TCCAGTTTATGTTGATAAATGGAATATTGATGTTGCTTTTATGGGTTCTTAATGCACCAC
CAGGAATTTCTCCGATTACATTCAGTGCACGAGCTTTGGATAAAATTGCAAAGAGAAAGA
CACCAGTAAAAAGCTATAATCTTGATGCAGTAAACCTTGGTGAATATTGGAATTCTGGAA
ACCGTCCAAGAATTTATCATCATACAGTTTGTTCAACATTACTCTACGGTTTGCGAGAGG
CAATTGCAATTTTCATTGAGAATGGTGGTTTAGAAGCTTCTTGGAAAAATCATGAAAATG
TTGCCAAACATTTTTATACTCTGTTGGAAAAGAATGGTTTGGAATTATTCATTACTGATC
CTAAAAATCGTGTTCCATCAGTTACAGCTATAAAAGTACCTGAGAATATCGATGCAAATG
AAATTATAAAACATTCAATGAATGAATACAATGTTGAAATTAGTGGTGGTATAGGACCAA
TGTTGGGGGTAGTTTTGAGAGTTGGACTAATGGGAATAAACT

>g17483.t78 Gene=g17483 Length=171
MLINGILMLLLWVLNAPPGISPITFSARALDKIAKRKTPVKSYNLDAVNLGEYWNSGNRP
RIYHHTVCSTLLYGLREAIAIFIENGGLEASWKNHENVAKHFYTLLEKNGLELFITDPKN
RVPSVTAIKVPENIDANEIIKHSMNEYNVEISGGIGPMLGVVLRVGLMGIN

Protein features from InterProScan

Transcript Database ID Name Start End E.value
7 g17483.t78 Gene3D G3DSA:3.40.640.10 - 13 85 2.6E-52
6 g17483.t78 Gene3D G3DSA:3.90.1150.10 Aspartate Aminotransferase 87 171 2.6E-52
2 g17483.t78 PANTHER PTHR21152 AMINOTRANSFERASE CLASS V 13 171 4.3E-48
3 g17483.t78 PANTHER PTHR21152:SF22 SERINE–PYRUVATE AMINOTRANSFERASE 13 171 4.3E-48
1 g17483.t78 Pfam PF00266 Aminotransferase class-V 15 154 3.7E-12
9 g17483.t78 Phobius SIGNAL_PEPTIDE Signal peptide region 1 26 -
10 g17483.t78 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide. 1 5 -
11 g17483.t78 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide. 6 14 -
12 g17483.t78 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide. 15 26 -
8 g17483.t78 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 27 171 -
4 g17483.t78 SUPERFAMILY SSF53383 PLP-dependent transferases 14 170 6.58E-31
5 g17483.t78 SignalP_EUK SignalP-noTM SignalP-noTM 1 22 -

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:0003824 catalytic 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