General information for g2521.t1
Yuki Yoshida
6/2/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Farnesol dehydrogenase.
Parent gene
- The parent gene g2521 is located on chr_3: 18426939..18427842 (+ 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_3 | g2521 | g2521.t1 | TSS | g2521.t1 | 18426846 | 18426846 |
| chr_3 | g2521 | g2521.t1 | isoform | g2521.t1 | 18426939 | 18427842 |
| chr_3 | g2521 | g2521.t1 | exon | g2521.t1.exon1 | 18426939 | 18427066 |
| chr_3 | g2521 | g2521.t1 | cds | g2521.t1.CDS1 | 18426939 | 18427066 |
| chr_3 | g2521 | g2521.t1 | exon | g2521.t1.exon2 | 18427135 | 18427594 |
| chr_3 | g2521 | g2521.t1 | cds | g2521.t1.CDS2 | 18427135 | 18427594 |
| chr_3 | g2521 | g2521.t1 | exon | g2521.t1.exon3 | 18427660 | 18427842 |
| chr_3 | g2521 | g2521.t1 | cds | g2521.t1.CDS3 | 18427660 | 18427842 |
| chr_3 | g2521 | g2521.t1 | TTS | g2521.t1 | 18428018 | 18428018 |
Sequences
>g2521.t1 Gene=g2521 Length=771
ATGGAAGAAGGCATGAAAAGATGGGAAGGAAAGGTGGCAATTGTCACTGGAGCATCACAG
GGTATTGGCTCGGCAATAGCTGTTGCATTAGCTAAGAGTGGGATGATCGTTTGTGGACTT
GCAAAACGAAAAGATAAAATAGAAGCACTGAGAGTTGGATTGCTTAAAATAAAAGGACAG
TTGAACGCAGTCGAGTGCGATATAGGAAATGAGCAGAGTGTGCAAAGTGTTTTTGTTTGG
ATAGAAAAAACTTTCGGTGGAGTCGATCTGGTTGTAAATAACGCAGGAATTTTTACAAAA
GCACTCTTTCTTGACGACAATAATACTAAAGAACTTAAAAATGTTATTGATAATGAAATT
ATGGGAAATATTTACATAACTCGCCAGGCGATTAAATCTATGCAAGCACGTGATGTTAAT
GGACATATTATCAACATATGTAGTATTTTTGGACATAATGTCAATCAAGCTGTACCAGGA
AACAAGCCAATGAATTCACTCTATCCACCAGTGAAGCATGCAGTTAAAGCCATGACTGAG
TGCATTCGTCAAGAGCTTACTTATTTGGCGACACAAATTAAAATCACTTCAATCAGTCCA
GGTCTTTGTGAAGGTGATATTATTTCAACATGCACTGATAATGAACTCGTGTCATTGATG
CCAAAACTTAAACCAGAGGATGTTGCTAATGCAATTCTTTATTGCATCACACTTCCTGAT
GGATGCAATGTTCATGAGATGGTACTCAAACCAATGGGAGAATTTGTATAA
>g2521.t1 Gene=g2521 Length=256
MEEGMKRWEGKVAIVTGASQGIGSAIAVALAKSGMIVCGLAKRKDKIEALRVGLLKIKGQ
LNAVECDIGNEQSVQSVFVWIEKTFGGVDLVVNNAGIFTKALFLDDNNTKELKNVIDNEI
MGNIYITRQAIKSMQARDVNGHIINICSIFGHNVNQAVPGNKPMNSLYPPVKHAVKAMTE
CIRQELTYLATQIKITSISPGLCEGDIISTCTDNELVSLMPKLKPEDVANAILYCITLPD
GCNVHEMVLKPMGEFV
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 14 | g2521.t1 | Gene3D | G3DSA:3.40.50.720 | - | 2 | 252 | 3.4E-50 |
| 2 | g2521.t1 | PANTHER | PTHR43115 | DEHYDROGENASE/REDUCTASE SDR FAMILY MEMBER 11 | 4 | 254 | 3.1E-79 |
| 3 | g2521.t1 | PANTHER | PTHR43115:SF4 | DEHYDROGENASE/REDUCTASE SDR FAMILY MEMBER 11 | 4 | 254 | 3.1E-79 |
| 7 | g2521.t1 | PRINTS | PR00081 | Glucose/ribitol dehydrogenase family signature | 12 | 29 | 2.5E-25 |
| 5 | g2521.t1 | PRINTS | PR00080 | Short-chain dehydrogenase/reductase (SDR) superfamily signature | 86 | 97 | 4.7E-9 |
| 11 | g2521.t1 | PRINTS | PR00081 | Glucose/ribitol dehydrogenase family signature | 86 | 97 | 2.5E-25 |
| 12 | g2521.t1 | PRINTS | PR00081 | Glucose/ribitol dehydrogenase family signature | 135 | 151 | 2.5E-25 |
| 6 | g2521.t1 | PRINTS | PR00080 | Short-chain dehydrogenase/reductase (SDR) superfamily signature | 141 | 149 | 4.7E-9 |
| 4 | g2521.t1 | PRINTS | PR00080 | Short-chain dehydrogenase/reductase (SDR) superfamily signature | 168 | 187 | 4.7E-9 |
| 10 | g2521.t1 | PRINTS | PR00081 | Glucose/ribitol dehydrogenase family signature | 168 | 187 | 2.5E-25 |
| 9 | g2521.t1 | PRINTS | PR00081 | Glucose/ribitol dehydrogenase family signature | 191 | 208 | 2.5E-25 |
| 8 | g2521.t1 | PRINTS | PR00081 | Glucose/ribitol dehydrogenase family signature | 218 | 238 | 2.5E-25 |
| 1 | g2521.t1 | Pfam | PF00106 | short chain dehydrogenase | 11 | 209 | 3.3E-36 |
| 16 | g2521.t1 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 31 | - |
| 17 | g2521.t1 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 11 | - |
| 18 | g2521.t1 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 12 | 23 | - |
| 19 | g2521.t1 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 24 | 31 | - |
| 15 | g2521.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 32 | 256 | - |
| 13 | g2521.t1 | SUPERFAMILY | SSF51735 | NAD(P)-binding Rossmann-fold domains | 5 | 248 | 2.67E-50 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
GO terms from InterProScan
## [1] "No matching GO terms"KEGG
Orthology
- This transcript has been annotated with K15890 (NADP+-dependent farnesol dehydrogenase)
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.
