General information for g15493.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as GDP-mannose 4,6 dehydratase.
Parent gene
- The parent gene g15493 is located on chr_4: 5627966..5629257 (+ 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_4 | g15493 | g15493.t1 | TSS | g15493.t1 | 5627869 | 5627869 |
| chr_4 | g15493 | g15493.t1 | isoform | g15493.t1 | 5627966 | 5629257 |
| chr_4 | g15493 | g15493.t1 | exon | g15493.t1.exon1 | 5627966 | 5628025 |
| chr_4 | g15493 | g15493.t1 | cds | g15493.t1.CDS1 | 5627966 | 5628025 |
| chr_4 | g15493 | g15493.t1 | exon | g15493.t1.exon2 | 5628238 | 5629257 |
| chr_4 | g15493 | g15493.t1 | cds | g15493.t1.CDS2 | 5628238 | 5629257 |
| chr_4 | g15493 | g15493.t1 | TTS | g15493.t1 | 5629415 | 5629415 |
Sequences
>g15493.t1 Gene=g15493 Length=1080
ATGTCATCAGCAAGTGAAAGTAATAGAAAAGTTGCATTAATTACAGGAATTACTGGACAG
GATGGTTCCTACTTAGCTGAATTCCTTCTTCAAAAAGGCTATCAAGTCCATGGCATAATT
CGTCGTTCTTCCAGTTTCAATACGCACAGAATCGAACATCTTTATCAAAATCCATTTTCC
CATCAAGAAGGTTCCTTTTTTAAACTTCATTATGGTGACATGACTGACAGCAGTTGTCTC
GTAAAAATAATTATGCAAGTTCGACCAACTGAAATTTACAATCTCGCTGCACAATCACAT
GTGAAAATTTCATTTGATCTCTCTGAATATACAGCAGAAGTTGATGGTGTTGGAACTTTG
AGACTTCTCGATGCAATTCGAACTTGTGGACTTGAAAAGCAAGTGAAATTTTATCAAGCA
TCAACATCAGAATTGTATGGAAAAGTTCTTGAAACACCACAAAATGAGAAAACTCCTTTT
TATCCACGCAGTCCATATGCAGCTGCAAAACTTTATGCATACTGGATTGTTGTGAATTAT
CGTGAAGCTTATGACATGTATGCATGCAATGGAATTCTTTTCAATCATGAATCACCAAGA
CGTGGTGAAAATTTTGTAACACGTAAAATTACAAGGTCAGTCGCAAAAATTTCTCTAAAA
CAACAAGAAGTCCTTGAACTCGGAAATTTAGATTCAAAACGTGATTGGGGTCATGCAAGA
GATTATGTCGAGGCAATGTGGATGATGTTGCAATTGGACAAAGCTGAAGATTTTGTTATT
GCAACAGGTGAAACGCACAGTGTAAGAGAATTTGTGATAGCAGCATTTCAGTATATTGGA
AAAGAAATTGAATGGCGAGGGTCTGGAGTTAATGAAGTTGGTGTTGAAAAAGGCACAGAA
ATTGTTCGTGTAAAAATCAATCCAAAATATTTTCGTCCAACTGAAGTTGATTTGTTGCTT
GGTGATGCAAGTAAGGCTAAAAATATGTTAAAATGGGAACCAAAATGCAGATTTGATGAA
TTGGTTAAAGAAATGATGGCAGCAGATATTGAATTAATGAAGAAAAATCCACTCGCTTAA
>g15493.t1 Gene=g15493 Length=359
MSSASESNRKVALITGITGQDGSYLAEFLLQKGYQVHGIIRRSSSFNTHRIEHLYQNPFS
HQEGSFFKLHYGDMTDSSCLVKIIMQVRPTEIYNLAAQSHVKISFDLSEYTAEVDGVGTL
RLLDAIRTCGLEKQVKFYQASTSELYGKVLETPQNEKTPFYPRSPYAAAKLYAYWIVVNY
REAYDMYACNGILFNHESPRRGENFVTRKITRSVAKISLKQQEVLELGNLDSKRDWGHAR
DYVEAMWMMLQLDKAEDFVIATGETHSVREFVIAAFQYIGKEIEWRGSGVNEVGVEKGTE
IVRVKINPKYFRPTEVDLLLGDASKAKNMLKWEPKCRFDELVKEMMAADIELMKKNPLA
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 9 | g15493.t1 | CDD | cd05260 | GDP_MD_SDR_e | 11 | 351 | 0.00000 |
| 6 | g15493.t1 | Gene3D | G3DSA:3.40.50.720 | - | 12 | 336 | 0.00000 |
| 7 | g15493.t1 | Gene3D | G3DSA:3.90.25.10 | - | 202 | 350 | 0.00000 |
| 4 | g15493.t1 | Hamap | MF_00955 | GDP-mannose 4,6-dehydratase [gmd]. | 10 | 355 | 56.50869 |
| 2 | g15493.t1 | PANTHER | PTHR43715 | GDP-MANNOSE 4,6-DEHYDRATASE | 4 | 357 | 0.00000 |
| 3 | g15493.t1 | PANTHER | PTHR43715:SF1 | GDP-MANNOSE 4,6 DEHYDRATASE | 4 | 357 | 0.00000 |
| 1 | g15493.t1 | Pfam | PF16363 | GDP-mannose 4,6 dehydratase | 13 | 345 | 0.00000 |
| 5 | g15493.t1 | SUPERFAMILY | SSF51735 | NAD(P)-binding Rossmann-fold domains | 10 | 350 | 0.00000 |
| 8 | g15493.t1 | TIGRFAM | TIGR01472 | gmd: GDP-mannose 4,6-dehydratase | 10 | 352 | 0.00000 |
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:0019673 | GDP-mannose metabolic process | BP |
| GO:0008446 | GDP-mannose 4,6-dehydratase activity | MF |
KEGG
Orthology
- This transcript has been annotated with K01711 (GDPmannose 4,6-dehydratase)
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.
