General information for g5125.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Probable 3’,5’-cyclic phosphodiesterase pde-5.
Parent gene
- The parent gene g5125 is located on chr_2: 7179768..7181006 (- 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 | g5125 | g5125.t1 | isoform | g5125.t1 | 7175042 | 7180269 |
| chr_2 | g5125 | g5125.t1 | exon | g5125.t1.exon1 | 7175042 | 7175200 |
| chr_2 | g5125 | g5125.t1 | cds | g5125.t1.CDS1 | 7175042 | 7175200 |
| chr_2 | g5125 | g5125.t1 | exon | g5125.t1.exon2 | 7175266 | 7175562 |
| chr_2 | g5125 | g5125.t1 | cds | g5125.t1.CDS2 | 7175266 | 7175562 |
| chr_2 | g5125 | g5125.t1 | exon | g5125.t1.exon3 | 7175665 | 7176775 |
| chr_2 | g5125 | g5125.t1 | cds | g5125.t1.CDS3 | 7175665 | 7176775 |
| chr_2 | g5125 | g5125.t1 | exon | g5125.t1.exon4 | 7177253 | 7177985 |
| chr_2 | g5125 | g5125.t1 | cds | g5125.t1.CDS4 | 7177253 | 7177985 |
| chr_2 | g5125 | g5125.t1 | exon | g5125.t1.exon5 | 7178185 | 7178232 |
| chr_2 | g5125 | g5125.t1 | cds | g5125.t1.CDS5 | 7178185 | 7178232 |
| chr_2 | g5125 | g5125.t1 | exon | g5125.t1.exon6 | 7180221 | 7180269 |
| chr_2 | g5125 | g5125.t1 | cds | g5125.t1.CDS6 | 7180221 | 7180269 |
| chr_2 | g5125 | g5125.t1 | TSS | g5125.t1 | 7181006 | 7181006 |
| chr_2 | g5125 | g5125.t1 | TTS | g5125.t1 | NA | NA |
Sequences
>g5125.t1 Gene=g5125 Length=2397
ATGGATCGAGCTGCAGGATTTTGGAGAAATCGTCGTTTCTTTAAATTCCGTAGCAACAGT
AATGGAAATACAGCACAGCGCATCTCTGATCATAAAGATATGAATGAGCAAGAAATTCAA
GTATATTTACGAAATCATCCTGAAATACTAGAGCATTTTGTGATGGATGAAGTGGAACTT
GAGCAACTCGAACGATGGATGATACGAAGAACACAAAAAGCAAAGAAAATGAATTATGCA
AATAGAAAAACTAGTTTGAGTCGTTGGCGTTTCTGTGTGCATGCGGATAAAAGACAAATG
CTTGAGCAATTGACACAACAGCTTCAAAATAAACCAACCAAAGCACACGTTCTATTTGAG
TTAGCATCGTGTATATCAAATGCTGTAAATGCTGATGGATTTCGTCTCTATCTCGTTGAG
GATGCATCAGAAACTCTCACATTTGTTTTAGACTCGGAAACATTTGATGAAAATGGCGAC
CCAAAGATACAAAAAATTCGTGATAATCCCGTCATTGCTCGATATGTTGCGTCCACGCGT
GATCAAGTACGGTATTCTCGTGGAGATATCGATCCACGTTTTTCTAATGCCGGCATATGT
GACCGAGAGACACAACATGTGTTATGTCAAGCTATTGTCTATCCTGAAGGAAGCCTTGTT
GCTGTAATTGAGCTGTGGAGAGGTGAAAGCAGCTCAAGATTTCATGAAGAAGATGAGGAA
ATAGGAAATTCTTATCTCGTTTGGGGCGGTATAGCATTACACTATATGTCCATTTACATC
AACTTGAATAAGCAAAAAAAACTCAATGATTTTCTCCTGGCTGTCGTTAAATCAATTTTT
CAAGATATGGTATCAATGGATATGCTTGTCATAAAAATCATGAATTATGCACAACGTTTA
GTCAACGCAGATCGTGCATCGCTTTTTCTTATCGATTCAAAGACACAAGAACTTTATGCG
ACAATATTCGATATTGGCTTTGAGGATGATATACAAGAGAAAATGAATTCACCGCGTGGT
GCAAAGGAAGCAACGGAGAAAATGAAGAGTGAAGAAATACGATTTCCTATGGGAACAGGC
ATTGCTGGTCAATGTGCATTACGTGGCGAAGTTTTCAATATTGTTGATGCATATAGCGAT
GAAAGATTTAACCGTAATATAGATCAATTGACTGGCTACAAAACTGATACGATACTTTGT
ATGCCTATATTCATTCGAGGTTCAATCATTGGTGTAGTCGAAATGGTGAATAAACGAACT
GGATATTTTTCAAAAGAAGACGAAGAAGCATTTGAGACATTTGCCGTTTATTGTGGTTTG
GCATTACATCATGCAAAGCTTTATGACAAAATTAGACGTTCTGAGAAAAAATATCGTGTA
GCATTGGAAGTTTTAAGCTATCATAATACATGCAGTGAAGAGGAAATTGAGAGATGCGAA
AAAATGGGTATTCCCGCCAATATTCCAAATCTCAATGATTTTTACTTTAATCCATTTGAA
ATTGATGAATTTGTCAAAGTCAATTACGTAATTTATATGTTTAAGGATTTATTTGGATTC
AATCGTTTTGATAAGAAAGACTTGATGCGATTTACATTGACAGTGAAACGTAATTACAGA
AGAGTCCCATATCACAATTGGACTCATGGTTTTGCCGTCGCCAATTCAATGTATTCAATA
TTGAAAAATTCAAAAATGTCATTTCGACCTAACGAGTGTTTGGCCTTATTTATTGGCTCA
TTATGTCATGATCTCGACCATCGTGGAAAAAGTAATAAATTTATGTTAGAATCTGAATCA
CCTATCGCTGCTATTTATTCTACTTCTACAATGGAACATCATCATTTTAATCAAACTGTA
ACAATTTTACAACAAGATGGTCACAATATTCTAGCAAAATTAAGCTCAACGGAATACAAA
CAAATTCTCAGTTTAATTAAGCATTGTATACTTGCAACAGATCTCGCATTATTCTTTCCT
AACAAAGACAAATTAATGGCACTCGTCGACCAAGAAAAATTCTCATGGAGCATTTTAGAA
CATCGTATGATGGTGAATTGTATTGCAATGACTGCTGCTGACTTGTCAGCGAGCGCAAAG
CCATGGGAGATTCAATCCGAAACAGTGAAGGGAATATTTGAGGAATTTTATGAGCAAGGC
GACGCAGAGAGGCGTGCGGGAAGAGTGCCAATGGCAATGATGGATCGAAATCAAAAAGAT
CATCAAGCGAGTTCTCAATTGGGTTTTCTCAATGGCATTTGTATTCCTTGTTACTCTCTA
CTTTATCGTCTCATTCCTGAAACTCGACCGATGTTGAAGCAATGTCAGGACAATTTGACA
CGCTGGCAAGCTATTGATGATTTGAAGAAAAAGGAAGCTATTGAATTAAAAAAATAA
>g5125.t1 Gene=g5125 Length=798
MDRAAGFWRNRRFFKFRSNSNGNTAQRISDHKDMNEQEIQVYLRNHPEILEHFVMDEVEL
EQLERWMIRRTQKAKKMNYANRKTSLSRWRFCVHADKRQMLEQLTQQLQNKPTKAHVLFE
LASCISNAVNADGFRLYLVEDASETLTFVLDSETFDENGDPKIQKIRDNPVIARYVASTR
DQVRYSRGDIDPRFSNAGICDRETQHVLCQAIVYPEGSLVAVIELWRGESSSRFHEEDEE
IGNSYLVWGGIALHYMSIYINLNKQKKLNDFLLAVVKSIFQDMVSMDMLVIKIMNYAQRL
VNADRASLFLIDSKTQELYATIFDIGFEDDIQEKMNSPRGAKEATEKMKSEEIRFPMGTG
IAGQCALRGEVFNIVDAYSDERFNRNIDQLTGYKTDTILCMPIFIRGSIIGVVEMVNKRT
GYFSKEDEEAFETFAVYCGLALHHAKLYDKIRRSEKKYRVALEVLSYHNTCSEEEIERCE
KMGIPANIPNLNDFYFNPFEIDEFVKVNYVIYMFKDLFGFNRFDKKDLMRFTLTVKRNYR
RVPYHNWTHGFAVANSMYSILKNSKMSFRPNECLALFIGSLCHDLDHRGKSNKFMLESES
PIAAIYSTSTMEHHHFNQTVTILQQDGHNILAKLSSTEYKQILSLIKHCILATDLALFFP
NKDKLMALVDQEKFSWSILEHRMMVNCIAMTAADLSASAKPWEIQSETVKGIFEEFYEQG
DAERRAGRVPMAMMDRNQKDHQASSQLGFLNGICIPCYSLLYRLIPETRPMLKQCQDNLT
RWQAIDDLKKKEAIELKK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 20 | g5125.t1 | CDD | cd00077 | HDc | 544 | 717 | 1.79794E-9 |
| 15 | g5125.t1 | Gene3D | G3DSA:3.30.450.40 | - | 92 | 261 | 5.7E-15 |
| 16 | g5125.t1 | Gene3D | G3DSA:3.30.450.40 | - | 262 | 456 | 3.9E-57 |
| 14 | g5125.t1 | Gene3D | G3DSA:1.10.1300.10 | Catalytic domain of cyclic nucleotide phosphodiesterase 4b2b | 466 | 794 | 1.1E-104 |
| 3 | g5125.t1 | PANTHER | PTHR11347 | CYCLIC NUCLEOTIDE PHOSPHODIESTERASE | 88 | 785 | 1.9E-247 |
| 4 | g5125.t1 | PANTHER | PTHR11347:SF111 | CAMP AND CAMP-INHIBITED CGMP 3’,5’-CYCLIC PHOSPHODIESTERASE 10A | 88 | 785 | 1.9E-247 |
| 10 | g5125.t1 | PRINTS | PR00387 | 3’5’-cyclic nucleotide phosphodiesterase signature | 540 | 553 | 8.4E-24 |
| 7 | g5125.t1 | PRINTS | PR00387 | 3’5’-cyclic nucleotide phosphodiesterase signature | 569 | 582 | 8.4E-24 |
| 5 | g5125.t1 | PRINTS | PR00387 | 3’5’-cyclic nucleotide phosphodiesterase signature | 583 | 598 | 8.4E-24 |
| 9 | g5125.t1 | PRINTS | PR00387 | 3’5’-cyclic nucleotide phosphodiesterase signature | 609 | 625 | 8.4E-24 |
| 8 | g5125.t1 | PRINTS | PR00387 | 3’5’-cyclic nucleotide phosphodiesterase signature | 690 | 703 | 8.4E-24 |
| 6 | g5125.t1 | PRINTS | PR00387 | 3’5’-cyclic nucleotide phosphodiesterase signature | 707 | 723 | 8.4E-24 |
| 1 | g5125.t1 | Pfam | PF01590 | GAF domain | 287 | 442 | 1.2E-16 |
| 2 | g5125.t1 | Pfam | PF00233 | 3’5’-cyclic nucleotide phosphodiesterase | 544 | 776 | 6.1E-70 |
| 18 | g5125.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 1 | 746 | - |
| 19 | g5125.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 747 | 765 | - |
| 17 | g5125.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 766 | 798 | - |
| 24 | g5125.t1 | ProSitePatterns | PS00126 | 3’5’-cyclic nucleotide phosphodiesterase domain signature. | 583 | 594 | - |
| 25 | g5125.t1 | ProSiteProfiles | PS51845 | 3’5’-cyclic nucleotide phosphodiesterase domain profile. | 469 | 789 | 100.427 |
| 22 | g5125.t1 | SMART | SM00065 | gaf_1 | 96 | 263 | 0.26 |
| 21 | g5125.t1 | SMART | SM00065 | gaf_1 | 285 | 452 | 3.7E-26 |
| 23 | g5125.t1 | SMART | SM00471 | hd_13 | 542 | 708 | 3.1E-6 |
| 13 | g5125.t1 | SUPERFAMILY | SSF55781 | GAF domain-like | 95 | 274 | 7.06E-18 |
| 12 | g5125.t1 | SUPERFAMILY | SSF55781 | GAF domain-like | 267 | 469 | 9.81E-48 |
| 11 | g5125.t1 | SUPERFAMILY | SSF109604 | HD-domain/PDEase-like | 487 | 793 | 7.96E-96 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5125/g5125.t1; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5125.t1.fa.iupred3.txt does not exist
GO terms from InterProScan
| GOID | TERM | ONTOLOGY |
|---|---|---|
| GO:0008081 | phosphoric diester hydrolase activity | MF |
| GO:0007165 | signal transduction | BP |
| GO:0005515 | protein binding | MF |
| GO:0004114 | 3’,5’-cyclic-nucleotide phosphodiesterase activity | MF |
KEGG
Orthology
- This transcript has been annotated with K18438 (cAMP and cAMP-inhibited cGMP 3’,5’-cyclic phosphodiesterase 10)
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.
