Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative N-acetylneuraminate lyase.

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 g17204 g17204.t2 isoform g17204.t2 12812145 12813783
chr_4 g17204 g17204.t2 exon g17204.t2.exon1 12812145 12812390
chr_4 g17204 g17204.t2 TSS g17204.t2 12812177 12812177
chr_4 g17204 g17204.t2 exon g17204.t2.exon2 12812818 12813783
chr_4 g17204 g17204.t2 cds g17204.t2.CDS1 12812932 12813783
chr_4 g17204 g17204.t2 TTS g17204.t2 12813824 12813824

Sequences

>g17204.t2 Gene=g17204 Length=1212
TAAGCAGCTGATCAAGTGAAACTTTTTTCTTTGTATTGGTGATTTGTTTATAAACAAAAT
GAAAAAAAGTTTTGAAAAAGTTTCAGAAGTTGAATTTTTTTTCAAATTTATTTACCTGGT
TCTATAAAACCCTTAAAAAATAAACTTAAAAAATTAATTTTTTGTAAAAAAATATTCAAA
CAATTTTTGTTAATTAAAGAATTTGTTAATCGCTGCAAATTTTTTTTGATAAAATAATTT
CTTCTGATAAGCTCAAATCCACTCAAAACAAATAAAAAACTCTTTAAATAATTTTGCTTT
GTAATAGCACAGTAACATTATTAAAGTTGTTGAACGACAGTCAAGATTAAAAAATTCACA
ATGTCATCATTAAAATTGGTCAAGTTTGAAGGTTTAATGGCTCCAACATTTACGCCTTTT
GATGAGAATAATCAAGTAAATTACGACATTATTGAACCATATGCAAAATTTTTAAAATCA
AATGGAATTGAAGCAATTTTAATCAATGGCACAACAGGTGAAGGAATGTTAATGACAGTT
GAAGAACGTAAGAAAGTCACTGAAAAATGGCAAGAAGTTTGTAAAAAGTTAGAAATTCTC
ATGATGGTCCAGATTGCTGGCTGCTCTTTTGCTGATGTTATTGAACTTGCAAAACATGCT
GAAAAAATTGAAGTCGATGGAGTTTTGTGTCTACCTGAACTTTATTTTAAACCTAAAACA
ATTGAAAAACTTGTTGGATATTTAAAGGAAATTTCAAAATTTTGTCCAACTCGTCCACTT
TATTATTATCATATTCCGATGTTTGTAAGTGTTGATGTTCCAATGGCTGCTTTTATGGAA
CTTGCAAAGAAAGAAATTTCAACATTTAAAGGCATCAAATTTACATCTGGTGATTTAGAA
AAAGGATTTCCATGTTTAAAACATGGACAAGTTTATTTGGGAAGCGATACGATCTTATGT
GGTGCACTTGCATTGGGTTTCACTTCTGCAATTATGACATCACTCAATATTGTGCCTCAT
TTGGCTATAAAAATTGTTGAATACATGAAAAAAGGAGAAGTTGAAAAGGCAAGAGAACAA
CAAATGCTTTTGACTGAATTTGTTGAAAAAATTTTAAAAAAAGGAGGAGGCGACTGGGTG
CCATCAATGAAAAAAGCTTTTAATGAAAATTTTAAAGATATGAATTTAGGATGTGTTAGA
AAACCTTTGTAA

>g17204.t2 Gene=g17204 Length=283
MSSLKLVKFEGLMAPTFTPFDENNQVNYDIIEPYAKFLKSNGIEAILINGTTGEGMLMTV
EERKKVTEKWQEVCKKLEILMMVQIAGCSFADVIELAKHAEKIEVDGVLCLPELYFKPKT
IEKLVGYLKEISKFCPTRPLYYYHIPMFVSVDVPMAAFMELAKKEISTFKGIKFTSGDLE
KGFPCLKHGQVYLGSDTILCGALALGFTSAIMTSLNIVPHLAIKIVEYMKKGEVEKAREQ
QMLLTEFVEKILKKGGGDWVPSMKKAFNENFKDMNLGCVRKPL

Protein features from InterProScan

Transcript Database ID Name Start End E.value
7 g17204.t2 Gene3D G3DSA:3.20.20.70 Aldolase class I 6 283 2.8E-72
2 g17204.t2 PANTHER PTHR12128:SF21 N-ACETYLNEURAMINATE LYASE 5 283 4.0E-84
3 g17204.t2 PANTHER PTHR12128 DIHYDRODIPICOLINATE SYNTHASE 5 283 4.0E-84
8 g17204.t2 PIRSF PIRSF001365 DHDPS 4 270 3.4E-49
4 g17204.t2 PRINTS PR00146 Dihydrodipicolinate synthase signature 42 63 3.4E-7
5 g17204.t2 PRINTS PR00146 Dihydrodipicolinate synthase signature 138 155 3.4E-7
1 g17204.t2 Pfam PF00701 Dihydrodipicolinate synthetase family 8 254 2.9E-35
9 g17204.t2 ProSitePatterns PS00665 Dihydrodipicolinate synthase signature 1. 45 62 -
10 g17204.t2 SMART SM01130 DHDPS_2 8 283 1.1E-40
6 g17204.t2 SUPERFAMILY SSF51569 Aldolase 8 283 4.08E-61

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:0016829 lyase activity MF
GO:0003824 catalytic activity MF

KEGG

Orthology

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.

Raw TPM values