General information for g5167.t1
Yuki Yoshida
6/2/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Short-chain dehydrogenase/reductase family 16C member 6.
Parent gene
- The parent gene g5167 is located on chr_2: 7411505..7416724 (- 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 | g5167 | g5167.t1 | TTS | g5167.t1 | 7406629 | 7406629 |
| chr_2 | g5167 | g5167.t1 | isoform | g5167.t1 | 7406910 | 7416317 |
| chr_2 | g5167 | g5167.t1 | exon | g5167.t1.exon1 | 7406910 | 7407261 |
| chr_2 | g5167 | g5167.t1 | cds | g5167.t1.CDS1 | 7406910 | 7407261 |
| chr_2 | g5167 | g5167.t1 | exon | g5167.t1.exon2 | 7407356 | 7407671 |
| chr_2 | g5167 | g5167.t1 | cds | g5167.t1.CDS2 | 7407356 | 7407671 |
| chr_2 | g5167 | g5167.t1 | exon | g5167.t1.exon3 | 7407737 | 7407779 |
| chr_2 | g5167 | g5167.t1 | cds | g5167.t1.CDS3 | 7407737 | 7407779 |
| chr_2 | g5167 | g5167.t1 | exon | g5167.t1.exon4 | 7409729 | 7409853 |
| chr_2 | g5167 | g5167.t1 | cds | g5167.t1.CDS4 | 7409729 | 7409853 |
| chr_2 | g5167 | g5167.t1 | exon | g5167.t1.exon5 | 7411505 | 7411658 |
| chr_2 | g5167 | g5167.t1 | cds | g5167.t1.CDS5 | 7411505 | 7411658 |
| chr_2 | g5167 | g5167.t1 | exon | g5167.t1.exon6 | 7416186 | 7416317 |
| chr_2 | g5167 | g5167.t1 | cds | g5167.t1.CDS6 | 7416186 | 7416317 |
| chr_2 | g5167 | g5167.t1 | TSS | g5167.t1 | 7416724 | 7416724 |
Sequences
>g5167.t1 Gene=g5167 Length=1122
ATGGCTACAGGAAAATGGTCATTGTTTGCTGACAGATTTGAAGCTCGAAAACCAGCATCA
GAAATGACTAAACTCGATGCTATTTTAGACTTCTTTGCCTTCATCACAATATCAATTGGC
TATATTATTCAGTCAATATTCTACACAATCTTCGGATGGCCAGAAAAAGATCTCAATGGA
GAGTTATGCGTAATTACTGGAGGCGGTGGTGGATTAGGAAGATTATTAGCCATGCGTTTA
GTTAGATTAGGAGTTAAGGTTATTCTATGGGATATTAGTCAACAAGGTCTAGATGAGTCT
AAAAAAATAGTCGATTCAATGGGTGGCTGGTGTCGTTCACAAATAGTTGACATATCAAAA
CGACAAGAAGTATACAAAGCAGCAGAAGACATCAAGAATCAATATGGCAATGTTACATTG
CTTATAAATAACGCAGGAGTATTAAGTGGTCGAGCACTGCTTGATACACCTGATCATTTA
ATAGAGAGATCTTTCAATGTCAATGTAATTGCACATTTTTGGACAGTAAAAGCATTCCTT
CCAACAATGATTGAGAAGGATCATGGACATATAGTGACAATAGCAAGTATGGCGGGCCAT
GTTGGCATTGCTAAACTTATCGACTATTGCAGTACAAAATTTGCTGCCGTTGGCTTCGAT
GAGGCACTTCGACTTGAGCTTGAAGTAATGGGCATTAAAAACATTCACACATCTGTAATT
TGTCCGTATTTTATACAAGCCACTGGAATGTTTGATGATGTTAACTCAAGATGGGTTAAC
ACATTAAGTTCAAATGATGTAGCAGATCGTATTATAGAAGCAGTGAGAAAGAATGAAAAA
ATGGCACTTATACCTTGGTATTTCAACATCATGCTCATTCTAAAAACTATCTTCCCTTGG
GGCTGCACATCAGGATTTCTTCGGCGACTTGTCCCTGATGCTACACCTCAGCATCTTCTT
ACAACACCCGTATCAACGCCATCAATTACAAAGCAGGAGGAAATGCAATTTATGAACAAC
AACAATCATCATGTCTTAAACAATAATAATAACAATAATGATAAAGAAACAACTCTGATA
AAACGAATGGCTGCGACTATTGAGGGTGAACGAGTGTTGTGA
>g5167.t1 Gene=g5167 Length=373
MATGKWSLFADRFEARKPASEMTKLDAILDFFAFITISIGYIIQSIFYTIFGWPEKDLNG
ELCVITGGGGGLGRLLAMRLVRLGVKVILWDISQQGLDESKKIVDSMGGWCRSQIVDISK
RQEVYKAAEDIKNQYGNVTLLINNAGVLSGRALLDTPDHLIERSFNVNVIAHFWTVKAFL
PTMIEKDHGHIVTIASMAGHVGIAKLIDYCSTKFAAVGFDEALRLELEVMGIKNIHTSVI
CPYFIQATGMFDDVNSRWVNTLSSNDVADRIIEAVRKNEKMALIPWYFNIMLILKTIFPW
GCTSGFLRRLVPDATPQHLLTTPVSTPSITKQEEMQFMNNNNHHVLNNNNNNNDKETTLI
KRMAATIEGERVL
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 19 | g5167.t1 | CDD | cd05339 | 17beta-HSDXI-like_SDR_c | 77 | 302 | 2.33355E-100 |
| 13 | g5167.t1 | Gene3D | G3DSA:3.40.50.720 | - | 52 | 308 | 4.6E-60 |
| 2 | g5167.t1 | PANTHER | PTHR24322:SF634 | FI23927P1-RELATED | 31 | 336 | 6.0E-101 |
| 3 | g5167.t1 | PANTHER | PTHR24322 | PKSB | 31 | 336 | 6.0E-101 |
| 9 | g5167.t1 | PRINTS | PR00081 | Glucose/ribitol dehydrogenase family signature | 62 | 79 | 3.5E-19 |
| 5 | g5167.t1 | PRINTS | PR00080 | Short-chain dehydrogenase/reductase (SDR) superfamily signature | 136 | 147 | 3.5E-8 |
| 8 | g5167.t1 | PRINTS | PR00081 | Glucose/ribitol dehydrogenase family signature | 136 | 147 | 3.5E-19 |
| 7 | g5167.t1 | PRINTS | PR00081 | Glucose/ribitol dehydrogenase family signature | 183 | 199 | 3.5E-19 |
| 4 | g5167.t1 | PRINTS | PR00080 | Short-chain dehydrogenase/reductase (SDR) superfamily signature | 189 | 197 | 3.5E-8 |
| 6 | g5167.t1 | PRINTS | PR00080 | Short-chain dehydrogenase/reductase (SDR) superfamily signature | 209 | 228 | 3.5E-8 |
| 10 | g5167.t1 | PRINTS | PR00081 | Glucose/ribitol dehydrogenase family signature | 209 | 228 | 3.5E-19 |
| 11 | g5167.t1 | PRINTS | PR00081 | Glucose/ribitol dehydrogenase family signature | 233 | 250 | 3.5E-19 |
| 1 | g5167.t1 | Pfam | PF00106 | short chain dehydrogenase | 63 | 256 | 2.5E-43 |
| 15 | g5167.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 1 | 30 | - |
| 17 | g5167.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 31 | 51 | - |
| 14 | g5167.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 52 | 285 | - |
| 18 | g5167.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 286 | 307 | - |
| 16 | g5167.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 308 | 373 | - |
| 12 | g5167.t1 | SUPERFAMILY | SSF51735 | NAD(P)-binding Rossmann-fold domains | 56 | 308 | 2.39E-59 |
| 20 | g5167.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 31 | 53 | - |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5167/g5167.t1; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5167.t1.fa.iupred3.txt does not exist
GO terms from InterProScan
## [1] "No matching GO terms"KEGG
Orthology
- This transcript has been annotated with K15734 (all-trans-retinol dehydrogenase (NAD+))
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.
