Gene loci information

Transcript annotation

  • This transcript has been annotated as Sialic acid synthase.

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 g8005 g8005.t1 isoform g8005.t1 27806141 27807460
chr_2 g8005 g8005.t1 exon g8005.t1.exon1 27806141 27806947
chr_2 g8005 g8005.t1 cds g8005.t1.CDS1 27806141 27806947
chr_2 g8005 g8005.t1 exon g8005.t1.exon2 27807060 27807293
chr_2 g8005 g8005.t1 cds g8005.t1.CDS2 27807060 27807293
chr_2 g8005 g8005.t1 exon g8005.t1.exon3 27807377 27807460
chr_2 g8005 g8005.t1 cds g8005.t1.CDS3 27807377 27807460
chr_2 g8005 g8005.t1 TSS g8005.t1 NA NA
chr_2 g8005 g8005.t1 TTS g8005.t1 NA NA

Sequences

>g8005.t1 Gene=g8005 Length=1125
ATGGATTTGAGAAATTTAAAATCAGTTTTTATCATCGCAGAAATTGGACAGAATCACCAG
GGTGACATTGGCAAGGCGAAAGAAATGATTCTAGAGGCATCGCGAGCTGGCGTCGATTGT
GTCAAATTTCAAAAGTCTTGTTTAGAAGCTAAATTTACAAAAAGTGCTCTTGAACGACCC
TACAATTCGGTAAATGCTTTTGGCGCAACATACGGTAAACATAAGAGCTTTTTAGAATTT
ACGATTGAACAGTTTAAAGAATTGAAAGATTATGCTGAGTCATGTGGATTAGTTTTTAGT
GCTTCAGCTATGGACCAAGTTTCATTTGATGAGCTGAAGCAATTGGGTCTACAATTTATC
AAAATAGGTTCAGGCGATACGAATAATATTCCGATGATTCGTTATATATCAAAGCAGAAC
GTTTCTCTAATTGTGTCCACTGGAATGCAAACAGATGCTACAATCAAGAAAGTTCATGAC
ATTCTTAAAGATTCCAATGCCAATTTTGCTCTCTTGCATTGTATCTCGTCTTATCCAACA
AGTACAGAGGATACTAAATTAAACTATATCATATACTTTCAAAAGCATTTTCCCAACATT
CCAATCGGTTACAGTGGTCATGAGAAAGGCATTGAATGTTCGTGCTTGGCAGTATTGATG
GGAGCAAGAATTCTAGAGCGACATTTCACACTCGATAAAAATCAAAAGGGCTCAGATCAT
TGTTCTTCACTGGACGCAAGTGAACTTCATGCACTCGTCAAGAAAGTTCGCTTGATTGAA
AAGAATGTGAATGGCGTAATACCGAATGATTTACTTTGCTCTACTGTAACAGACTTGAAT
CTTTTTGAATGCCCAAGGGGATTTGTCGAGAAGGCATGCCAACCCGTTGAAGACACACCG
AAATCAATTTTTCCATGTGAGTTGGCGTGCAAGCAGAAGTTGGGCAAGAGTTTGGTTTTT
GCAAGAGACATGAAAAAGGGACAATGTCTCATTGCGGACGATATTGGTGTGAAAGTAAGC
GAACCAAATGGAATCCCCGCGGAATTTTATGATGATGTTGTTGGAAAGGTACTGATGCGT
GATGTGTTTCATGACGAAGCTGTAATGGAGTGTGACGTCAATTGA

>g8005.t1 Gene=g8005 Length=374
MDLRNLKSVFIIAEIGQNHQGDIGKAKEMILEASRAGVDCVKFQKSCLEAKFTKSALERP
YNSVNAFGATYGKHKSFLEFTIEQFKELKDYAESCGLVFSASAMDQVSFDELKQLGLQFI
KIGSGDTNNIPMIRYISKQNVSLIVSTGMQTDATIKKVHDILKDSNANFALLHCISSYPT
STEDTKLNYIIYFQKHFPNIPIGYSGHEKGIECSCLAVLMGARILERHFTLDKNQKGSDH
CSSLDASELHALVKKVRLIEKNVNGVIPNDLLCSTVTDLNLFECPRGFVEKACQPVEDTP
KSIFPCELACKQKLGKSLVFARDMKKGQCLIADDIGVKVSEPNGIPAEFYDDVVGKVLMR
DVFHDEAVMECDVN

Protein features from InterProScan

Transcript Database ID Name Start End E.value
11 g8005.t1 CDD cd11615 SAF_NeuB_like 315 373 0.000000
8 g8005.t1 Gene3D G3DSA:3.20.20.70 Aldolase class I 2 276 0.000000
9 g8005.t1 Gene3D G3DSA:3.90.1210.10 - 313 374 0.000000
3 g8005.t1 PANTHER PTHR42966 N-ACETYLNEURAMINATE SYNTHASE 6 373 0.000000
4 g8005.t1 PANTHER PTHR42966:SF1 SIALIC ACID SYNTHASE 6 373 0.000000
2 g8005.t1 Pfam PF03102 NeuB family 29 263 0.000000
1 g8005.t1 Pfam PF08666 SAF domain 317 370 0.000022
10 g8005.t1 ProSiteProfiles PS50844 Antifreeze protein-like domain profile. 317 374 16.440000
7 g8005.t1 SMART SM00858 SAF_3 315 374 0.004600
5 g8005.t1 SUPERFAMILY SSF51569 Aldolase 7 267 0.000000
6 g8005.t1 SUPERFAMILY SSF51269 AFP III-like domain 315 373 0.000000

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:0016051 carbohydrate biosynthetic process BP
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