General information for g1338.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Prolyl 4-hydroxylase subunit alpha-2.
Parent gene
- The parent gene g1338 is located on chr_3: 9902805..9904018 (- 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 | g1338 | g1338.t1 | TTS | g1338.t1 | 9900501 | 9900501 |
| chr_3 | g1338 | g1338.t1 | isoform | g1338.t1 | 9900857 | 9903230 |
| chr_3 | g1338 | g1338.t1 | exon | g1338.t1.exon1 | 9900857 | 9900969 |
| chr_3 | g1338 | g1338.t1 | cds | g1338.t1.CDS1 | 9900857 | 9900969 |
| chr_3 | g1338 | g1338.t1 | exon | g1338.t1.exon2 | 9901289 | 9901424 |
| chr_3 | g1338 | g1338.t1 | cds | g1338.t1.CDS2 | 9901289 | 9901424 |
| chr_3 | g1338 | g1338.t1 | exon | g1338.t1.exon3 | 9901508 | 9901585 |
| chr_3 | g1338 | g1338.t1 | cds | g1338.t1.CDS3 | 9901508 | 9901585 |
| chr_3 | g1338 | g1338.t1 | exon | g1338.t1.exon4 | 9901649 | 9902890 |
| chr_3 | g1338 | g1338.t1 | cds | g1338.t1.CDS4 | 9901649 | 9902890 |
| chr_3 | g1338 | g1338.t1 | exon | g1338.t1.exon5 | 9903153 | 9903230 |
| chr_3 | g1338 | g1338.t1 | cds | g1338.t1.CDS5 | 9903153 | 9903230 |
| chr_3 | g1338 | g1338.t1 | TSS | g1338.t1 | 9903983 | 9903983 |
Sequences
>g1338.t1 Gene=g1338 Length=1647
ATGATCTGCAAGCAGTGGAAAATACTCTCTTTAGCTGTAATAATAATTTTAACGACAACA
TCGAATGTTGGTTGTGAAGTTTTCACAGCTCTTTCTGATATGGAGGGGCTTTTAGAGACT
GAAAGTGTATTGATAAATAATTTAGAAGGCTATATTAGTGCACAAGAGGATAGATTAGAG
TATTTAAGGAAAAAAATGTCTGAATACCAAAGAGAACATGAAACAGCAGGAAAAGATGTT
TCATCATATCTACTTAATCCTATTAATGCATATTTACTAACAAAAAGATTAACAACGGAT
TGGAAAGAGGTTGAACAGATCATGACAGATGATGTTGGTTATCAATTTACACAGAATGTT
TCCAATTTCCGAAATATATTAAAATTCCCTACAGATGAGGATTTAGCGGGAGCCGCAAAT
GCATTAATCCGTTTGCAAGATACATATGGAATGAAAACTGAAGATGTAGCTCGTGGAAAA
TTGCATGGTGTTCAATTTCCTATAGAAATGTCAAGTGAAGATTGTTTTGAAATTGGAAGG
CAGACTTATATTAATCATGATTTCCGTCATACAATCCAATGGATGAATGAAGCATTAAAA
CGTTTAGAAAATGATTCAATCATTCAACGTTCAGATGTGCTAGAATATCTTGCATTCTCA
ACATTCAAAGAGGGTAATGTGCATGAAGCTCTCGATATGACAAACGAGTTGCTTGAACTT
GCACCAAATCATCAACGTGCAAGAGGTAATAAATATTATTATGAACGTGAGCTGCAGAAA
TATAATCAAAAGTCACAATTGCGAGGTGATGATGGAAGTGATGATGTGATAATCGATGAT
AGTCTTGAATTTCATCACATTTCAAATCCCAATAACTATGACTTGCCTGAAAGAAAACTT
TATGAACTTGCATGTCGCGGTGAACTACGTCCTGCAGAGAATGTATTAGCTCAATTAAAT
TGTCGCTATACGGATAATAATGTGCCATTCTTAAAAATTGCGCCACTTAAAATAGAACAA
ATTTATTTAGATCCTTATATTGTTATTTATCACGATGTCATGTCTGACTCGGAAATTGAA
ACGATAAAAAGTTTAGCACGCCCAAAAATGAGAAGAGCAACCGTGCAGAATCACAAAACA
GGTGAGCTTGAAACAGCTCAATATCGAATTAGCAAATCAGCATGGCTGAAAGAAGAAGAT
CATGATGTTGTAAAAACTGTGGTGCAGCGAATTAAAGACATGACTGGTTTATCAATGGAA
ACAGCTGAAGAGCTTCAAATTGCAAATTACGGCATTGGAGGACATTATGAACCTCATTAT
GATTTTGCACGTAAAGAAGAGACAAATGCATTTAAAAATCATGAAGGAGGCAATCGTATT
GCCACAGTTTTATTCTATATGACCGATGTTGAGTTGGGTGGTGCAACTGTTTTCCCAGCA
TTAAGAACAGCTTTATGGCCGAAAAAAGGTGCTGCTGCATTTTGGTTCAATTTACGAAGG
TCAGGGCAAGGCGATTATAAAACAAGACATGCCGCATGTCCAGTAATAGTAGGAAACAAA
TGGGTTTCAAATAAATGGATTCACGAACGTGGTCAGGAATTTATTAGACCTTGTGCACTC
GAGCCTGATCATGATATGGAATTTTAA
>g1338.t1 Gene=g1338 Length=548
MICKQWKILSLAVIIILTTTSNVGCEVFTALSDMEGLLETESVLINNLEGYISAQEDRLE
YLRKKMSEYQREHETAGKDVSSYLLNPINAYLLTKRLTTDWKEVEQIMTDDVGYQFTQNV
SNFRNILKFPTDEDLAGAANALIRLQDTYGMKTEDVARGKLHGVQFPIEMSSEDCFEIGR
QTYINHDFRHTIQWMNEALKRLENDSIIQRSDVLEYLAFSTFKEGNVHEALDMTNELLEL
APNHQRARGNKYYYERELQKYNQKSQLRGDDGSDDVIIDDSLEFHHISNPNNYDLPERKL
YELACRGELRPAENVLAQLNCRYTDNNVPFLKIAPLKIEQIYLDPYIVIYHDVMSDSEIE
TIKSLARPKMRRATVQNHKTGELETAQYRISKSAWLKEEDHDVVKTVVQRIKDMTGLSME
TAEELQIANYGIGGHYEPHYDFARKEETNAFKNHEGGNRIATVLFYMTDVELGGATVFPA
LRTALWPKKGAAAFWFNLRRSGQGDYKTRHAACPVIVGNKWVSNKWIHERGQEFIRPCAL
EPDHDMEF
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 9 | g1338.t1 | Coils | Coil | Coil | 52 | 72 | - |
| 7 | g1338.t1 | Gene3D | G3DSA:1.25.40.10 | - | 132 | 259 | 2.7E-43 |
| 8 | g1338.t1 | Gene3D | G3DSA:2.60.120.620 | q2cbj1_9rhob like domain | 337 | 528 | 2.4E-64 |
| 3 | g1338.t1 | PANTHER | PTHR10869:SF151 | FI16820P1-RELATED | 46 | 541 | 1.8E-169 |
| 4 | g1338.t1 | PANTHER | PTHR10869 | PROLYL 4-HYDROXYLASE ALPHA SUBUNIT | 46 | 541 | 1.8E-169 |
| 1 | g1338.t1 | Pfam | PF08336 | Prolyl 4-Hydroxylase alpha-subunit, N-terminal region | 30 | 163 | 2.1E-39 |
| 2 | g1338.t1 | Pfam | PF13640 | 2OG-Fe(II) oxygenase superfamily | 425 | 528 | 8.1E-15 |
| 11 | g1338.t1 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 25 | - |
| 12 | g1338.t1 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 7 | - |
| 13 | g1338.t1 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 8 | 19 | - |
| 14 | g1338.t1 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 20 | 25 | - |
| 10 | g1338.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 26 | 548 | - |
| 18 | g1338.t1 | ProSiteProfiles | PS50005 | TPR repeat profile. | 211 | 244 | 8.496 |
| 20 | g1338.t1 | ProSiteProfiles | PS50293 | TPR repeat region circular profile. | 211 | 244 | 9.193 |
| 19 | g1338.t1 | ProSiteProfiles | PS51471 | Fe(2+) 2-oxoglutarate dioxygenase domain profile. | 421 | 529 | 11.045 |
| 17 | g1338.t1 | SMART | SM00702 | p4hc | 345 | 528 | 1.2E-75 |
| 5 | g1338.t1 | SUPERFAMILY | SSF48452 | TPR-like | 174 | 263 | 8.44E-9 |
| 6 | g1338.t1 | SignalP_EUK | SignalP-noTM | SignalP-noTM | 1 | 25 | - |
| 15 | g1338.t1 | SignalP_GRAM_NEGATIVE | SignalP-noTM | SignalP-noTM | 1 | 24 | - |
| 16 | g1338.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 9 | 31 | - |
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:0016702 | oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen | MF |
| GO:0005783 | endoplasmic reticulum | CC |
| GO:0005506 | iron ion binding | MF |
| GO:0055114 | NA | NA |
| GO:0031418 | L-ascorbic acid binding | MF |
| GO:0016705 | oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen | MF |
| GO:0005515 | protein binding | MF |
| GO:0004656 | procollagen-proline 4-dioxygenase activity | MF |
| GO:0016491 | oxidoreductase activity | MF |
KEGG
Orthology
- This transcript has been annotated with K00472 (prolyl 4-hydroxylase)
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.
