General information for g4620.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Hydroxysteroid dehydrogenase-like protein 1.
Parent gene
- The parent gene g4620 is located on chr_2: 3655830..3656955 (- 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 | g4620 | g4620.t1 | TTS | g4620.t1 | 3655793 | 3655793 |
| chr_2 | g4620 | g4620.t1 | isoform | g4620.t1 | 3655830 | 3656955 |
| chr_2 | g4620 | g4620.t1 | exon | g4620.t1.exon1 | 3655830 | 3656146 |
| chr_2 | g4620 | g4620.t1 | cds | g4620.t1.CDS1 | 3655830 | 3656146 |
| chr_2 | g4620 | g4620.t1 | exon | g4620.t1.exon2 | 3656200 | 3656556 |
| chr_2 | g4620 | g4620.t1 | cds | g4620.t1.CDS2 | 3656200 | 3656556 |
| chr_2 | g4620 | g4620.t1 | exon | g4620.t1.exon3 | 3656612 | 3656734 |
| chr_2 | g4620 | g4620.t1 | cds | g4620.t1.CDS3 | 3656612 | 3656734 |
| chr_2 | g4620 | g4620.t1 | exon | g4620.t1.exon4 | 3656802 | 3656955 |
| chr_2 | g4620 | g4620.t1 | cds | g4620.t1.CDS4 | 3656802 | 3656955 |
| chr_2 | g4620 | g4620.t1 | TSS | g4620.t1 | 3656977 | 3656977 |
Sequences
>g4620.t1 Gene=g4620 Length=951
ATGCTGCTTGAATTTTTCTTTTTAGTTGGTCTTTATAGCACACTTTGCTATTTGCATGAA
AATTTAACTTCATTATTTCAAATTATTTCAAGTCTTTTATATGAATTTTTTGTAAAGAAA
AGAAATTTACAAGAAAAATATGGTGAATGGGCAATTGTTACTGGATCATCAGATGGAATA
GGCAAAGAATATGCTAAAGAACTAGCAAAACATGGCATGAATATCGTTCTTATCTCAAGA
ACTGAGTCAAAATTGATTGAAGTCGCTAAAGACATTGAGTCAATGTACTCGGTAAAGACA
AAGTATGTGGCTGTTGACTTTGGCAATGGCAAAAAAATCTATGAAAAAGTAAAAGAAGAA
TTAAAGTCAATGGACATTGGAATATTGGTTAATAATGTTGCTAACATGTATGATTTTCCT
GATGAATTCGATAAGAAGTCTGAGGAAATGATATTAAAAATGCTTAATGTTAATATTGGT
GCTGCAACAATGATGTCAAGAATGATAATTCCACAAATGAAAGCAAATAAAAGAGGAATG
ATTGTCAATTTATCGTCAACTGTTCAAGATCAACCAATTCCATTAGCTAACGTTTATGCA
TCAACTAAAGCTTATATAAAATTTTTTACAATTGGAATTCAAAAAGAGCTCAAAAAATTC
AATGTTGAAGTTCAATTGTTAACTCCATCATTTGTTAAAACAAAAGCAAATTGTTTCACA
AGATTTTATATGCATGATGCTTTTTTCATTACACCAATTGAATCTTATGTGAAATCAGCT
GTTTTTACTTTAGGCAGAAGTGATGAATCAACAGGTTATTGGGCACATGCTCTTCAATTT
GCATTATTAAAATGGATTCCTCGTAATATCAGAATGATTTTCATGCATAAAATTGCAAAG
TTTTATAGAAGAAAACATTATGAAAATTTTGAATCAGATAAAATAAAATAA
>g4620.t1 Gene=g4620 Length=316
MLLEFFFLVGLYSTLCYLHENLTSLFQIISSLLYEFFVKKRNLQEKYGEWAIVTGSSDGI
GKEYAKELAKHGMNIVLISRTESKLIEVAKDIESMYSVKTKYVAVDFGNGKKIYEKVKEE
LKSMDIGILVNNVANMYDFPDEFDKKSEEMILKMLNVNIGAATMMSRMIIPQMKANKRGM
IVNLSSTVQDQPIPLANVYASTKAYIKFFTIGIQKELKKFNVEVQLLTPSFVKTKANCFT
RFYMHDAFFITPIESYVKSAVFTLGRSDESTGYWAHALQFALLKWIPRNIRMIFMHKIAK
FYRRKHYENFESDKIK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 18 | g4620.t1 | CDD | cd05356 | 17beta-HSD1_like_SDR_c | 48 | 290 | 4.22397E-103 |
| 11 | g4620.t1 | Gene3D | G3DSA:3.40.50.720 | - | 42 | 275 | 2.8E-45 |
| 2 | g4620.t1 | PANTHER | PTHR43899:SF9 | MIP25013P-RELATED | 3 | 309 | 2.3E-113 |
| 3 | g4620.t1 | PANTHER | PTHR43899 | RH59310P | 3 | 309 | 2.3E-113 |
| 17 | g4620.t1 | PIRSF | PIRSF000126 | 11-beta-HSD1 | 3 | 309 | 1.0E-94 |
| 5 | g4620.t1 | PRINTS | PR00081 | Glucose/ribitol dehydrogenase family signature | 50 | 67 | 2.4E-13 |
| 8 | g4620.t1 | PRINTS | PR00081 | Glucose/ribitol dehydrogenase family signature | 124 | 135 | 2.4E-13 |
| 7 | g4620.t1 | PRINTS | PR00081 | Glucose/ribitol dehydrogenase family signature | 173 | 189 | 2.4E-13 |
| 4 | g4620.t1 | PRINTS | PR00081 | Glucose/ribitol dehydrogenase family signature | 199 | 218 | 2.4E-13 |
| 6 | g4620.t1 | PRINTS | PR00081 | Glucose/ribitol dehydrogenase family signature | 220 | 237 | 2.4E-13 |
| 1 | g4620.t1 | Pfam | PF00106 | short chain dehydrogenase | 50 | 237 | 1.3E-38 |
| 13 | g4620.t1 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 18 | - |
| 14 | g4620.t1 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 1 | - |
| 15 | g4620.t1 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 2 | 13 | - |
| 16 | g4620.t1 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 14 | 18 | - |
| 12 | g4620.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 19 | 316 | - |
| 19 | g4620.t1 | ProSitePatterns | PS00061 | Short-chain dehydrogenases/reductases family signature. | 186 | 214 | - |
| 9 | g4620.t1 | SUPERFAMILY | SSF51735 | NAD(P)-binding Rossmann-fold domains | 47 | 306 | 2.25E-46 |
| 10 | g4620.t1 | SignalP_EUK | SignalP-noTM | SignalP-noTM | 1 | 16 | - |
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:0055114 | NA | NA |
| GO:0016491 | oxidoreductase activity | MF |
KEGG
Orthology
- This transcript has been annotated with K10251 (17beta-estradiol 17-dehydrogenase / very-long-chain 3-oxoacyl-CoA reductase)
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