Gene loci information

Transcript annotation

  • This transcript has been annotated as Serine–pyruvate aminotransferase.

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.t11 TSS g17483.t11 13659535 13659535
chr_4 g17483 g17483.t11 isoform g17483.t11 13659588 13661029
chr_4 g17483 g17483.t11 exon g17483.t11.exon1 13659588 13659651
chr_4 g17483 g17483.t11 exon g17483.t11.exon2 13659877 13659991
chr_4 g17483 g17483.t11 cds g17483.t11.CDS1 13659970 13659991
chr_4 g17483 g17483.t11 exon g17483.t11.exon3 13660046 13660095
chr_4 g17483 g17483.t11 cds g17483.t11.CDS2 13660046 13660095
chr_4 g17483 g17483.t11 exon g17483.t11.exon4 13660208 13660591
chr_4 g17483 g17483.t11 cds g17483.t11.CDS3 13660208 13660591
chr_4 g17483 g17483.t11 exon g17483.t11.exon5 13660656 13660708
chr_4 g17483 g17483.t11 cds g17483.t11.CDS4 13660656 13660708
chr_4 g17483 g17483.t11 exon g17483.t11.exon6 13660794 13661029
chr_4 g17483 g17483.t11 cds g17483.t11.CDS5 13660794 13661028
chr_4 g17483 g17483.t11 TTS g17483.t11 13661511 13661511

Sequences

>g17483.t11 Gene=g17483 Length=902
ATGGATGTGCCAATTCCGGAAATTTTACAGACACCAATGGAAGTTGATGAAATGATAATG
ACAGGTGCTGGACCTTCAAATTATCATCCAAGGATAAGACATGCAATGTCATTACCTGTT
CTTGGTCATCTTCATCCTAAAACATTTAAAATCATGGATGACATTAAAATTGGTGTCAAT
TATCTACTTCAGACAAATAATTCTTACACATTTTGTATCTCTGGACCAGTTTTTAGCTAT
CGAATGTGCTTTTGTAAATTTGGTTGAAGACAACGATATAGTTGTTATTGGAAGTAGTGG
CTATTGGGGAATAAGAGCAGAAGATATTGCAAAACGATTAAATGCTGATGTAAAAGTCAT
CAATAAAGAATTAGGAGAGCAAATTGAATTAGAAGAAACACGAATATTTTTTGAGCAATA
TCATCCAAAAGTTTTCTTTTTGACTCATGGTGAATCAAGCACAGGAATGTTGCAACAAAA
TTTGGAACAATTTGGAAATTTATGTCAGGAATTTAATTGTCTTTTTGTGGTTGATTGCGT
TATAACAGTTGGATGCACTCCAGTTTATGTTGATAAATGGAATATTGATGTTGCTTTTAT
GGGAACACAAAAGGTTCTTAATGCACCACCAGGAATTTCTCCGATTACATTCAGTGCACG
AGCTTTGGATAAAATTGCAAAGAGAAAGACACCAGTAAAAAGCTATAATCTTGATGCAGT
AAACCTTGGTGAATATTGGAATTCTGGAAACCGTCCAAGAATTTATCATCATACAGTTTG
TTCAACATTACTCTACGGTTTGCGAGAGGCAATTGCAATTTTCATTGAGAATGGTGGTTT
AGAAGCTTCTTGGAAAAATCATGAAAATGTTGCCAAACATTTTTATACTCTGTTGGAAAA
GA

>g17483.t11 Gene=g17483 Length=248
MTLKLVSIIYFRQIILTHFVSLDQFLAIECAFVNLVEDNDIVVIGSSGYWGIRAEDIAKR
LNADVKVINKELGEQIELEETRIFFEQYHPKVFFLTHGESSTGMLQQNLEQFGNLCQEFN
CLFVVDCVITVGCTPVYVDKWNIDVAFMGTQKVLNAPPGISPITFSARALDKIAKRKTPV
KSYNLDAVNLGEYWNSGNRPRIYHHTVCSTLLYGLREAIAIFIENGGLEASWKNHENVAK
HFYTLLEK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
7 g17483.t11 Gene3D G3DSA:3.40.640.10 - 27 225 1.2E-79
6 g17483.t11 Gene3D G3DSA:3.90.1150.10 Aspartate Aminotransferase 227 247 1.2E-79
2 g17483.t11 PANTHER PTHR21152 AMINOTRANSFERASE CLASS V 15 248 5.4E-65
3 g17483.t11 PANTHER PTHR21152:SF22 SERINE–PYRUVATE AMINOTRANSFERASE 15 248 5.4E-65
1 g17483.t11 Pfam PF00266 Aminotransferase class-V 27 247 8.3E-31
5 g17483.t11 ProSitePatterns PS00595 Aminotransferases class-V pyridoxal-phosphate attachment site. 143 163 -
4 g17483.t11 SUPERFAMILY SSF53383 PLP-dependent transferases 26 247 2.48E-51

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