General information for g5285.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative N-acylneuraminate cytidylyltransferase A.
Parent gene
- The parent gene g5285 is located on chr_2: 8389567..8391579 (+ strand)
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 | g5285 | g5285.t1 | isoform | g5285.t1 | 8389567 | 8390330 |
| chr_2 | g5285 | g5285.t1 | exon | g5285.t1.exon1 | 8389567 | 8389699 |
| chr_2 | g5285 | g5285.t1 | cds | g5285.t1.CDS1 | 8389567 | 8389699 |
| chr_2 | g5285 | g5285.t1 | exon | g5285.t1.exon2 | 8389770 | 8390157 |
| chr_2 | g5285 | g5285.t1 | cds | g5285.t1.CDS2 | 8389770 | 8390157 |
| chr_2 | g5285 | g5285.t1 | exon | g5285.t1.exon3 | 8390228 | 8390330 |
| chr_2 | g5285 | g5285.t1 | cds | g5285.t1.CDS3 | 8390228 | 8390330 |
| chr_2 | g5285 | g5285.t1 | TSS | g5285.t1 | NA | NA |
| chr_2 | g5285 | g5285.t1 | TTS | g5285.t1 | NA | NA |
Sequences
>g5285.t1 Gene=g5285 Length=624
ATGAAAAATATTCAAGAAATAGATGGAGTTTCTTTGTTGGGAATTTCACTAAAAGAAATT
TATAAGGCGGAAGTATTTTCAAGCATTTACGTCTCGACTGATAATGAAGAAATTGCAAAA
GAAGCAGAAAAATACAATGCAACGGTACATAAAAGAGATGCTTATTATGCAAGAGACGAG
TCAACATCAATTGAAGCAGTGCAAGAGTTTTTGAAGCATCATCCTAATGTTGAGAATTTA
GCTTTAATTCAGTGCACGTCGCCCTTCATTAGCCATCATTATTTACGTGATGCATTTCGG
AAATTCACAATTCAACGTGATTGCGTTTTTTCTGTGGTAAAAAGTTTCAAATTGAGATGG
AAACATTCTAATAGCGAAGGAAAAGAAAAATTCATTCCGGCAAATTTTGATAATAAGAAG
CGACCACGTCGACAAGATTGGAATGGCGAGTACATTGAAACGGGGATGTTTTATTTTGCG
AAGCGTAAACTTCTCGATGATGGACTTTTTCAGAATAATAATTGTGACGTAGTTGAGATA
AGAAGCAAGGATTCTTTAGAAATCGATACACCATATGATTTGGAGCTTGCGAGAATATTG
AAAAAGCACTTTAAAGCTCAATGA
>g5285.t1 Gene=g5285 Length=207
MKNIQEIDGVSLLGISLKEIYKAEVFSSIYVSTDNEEIAKEAEKYNATVHKRDAYYARDE
STSIEAVQEFLKHHPNVENLALIQCTSPFISHHYLRDAFRKFTIQRDCVFSVVKSFKLRW
KHSNSEGKEKFIPANFDNKKRPRRQDWNGEYIETGMFYFAKRKLLDDGLFQNNNCDVVEI
RSKDSLEIDTPYDLELARILKKHFKAQ
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g5285.t1 | CDD | cd02513 | CMP-NeuAc_Synthase | 2 | 200 | 0 |
| 5 | g5285.t1 | Gene3D | G3DSA:3.90.550.10 | Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A | 1 | 206 | 0 |
| 2 | g5285.t1 | PANTHER | PTHR21485:SF3 | N-ACYLNEURAMINATE CYTIDYLYLTRANSFERASE | 1 | 202 | 0 |
| 3 | g5285.t1 | PANTHER | PTHR21485 | HAD SUPERFAMILY MEMBERS CMAS AND KDSC | 1 | 202 | 0 |
| 1 | g5285.t1 | Pfam | PF02348 | Cytidylyltransferase | 2 | 198 | 0 |
| 4 | g5285.t1 | SUPERFAMILY | SSF53448 | Nucleotide-diphospho-sugar transferases | 2 | 201 | 0 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5285/g5285.t1; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5285.t1.fa.iupred3.txt does not exist
GO terms from InterProScan
There are no GO annotations for this transcript.
KEGG
Orthology
- This transcript has been annotated with K21749 (N-acylneuraminate/3-deoxy-D-glycero-D-galacto-nononate cytidylyltransferase)
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. There were no conditions that were differentially expressed