General information for g4230.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Dual 3’,5’-cyclic-AMP and -GMP phosphodiesterase 11.
Parent gene
- The parent gene g4230 is located on chr_2: 410319..454234 (+ 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 | g4230 | g4230.t1 | isoform | g4230.t1 | 410319 | 454234 |
| chr_2 | g4230 | g4230.t1 | exon | g4230.t1.exon1 | 410319 | 410367 |
| chr_2 | g4230 | g4230.t1 | cds | g4230.t1.CDS1 | 410319 | 410367 |
| chr_2 | g4230 | g4230.t1 | exon | g4230.t1.exon2 | 410518 | 410899 |
| chr_2 | g4230 | g4230.t1 | cds | g4230.t1.CDS2 | 410518 | 410899 |
| chr_2 | g4230 | g4230.t1 | exon | g4230.t1.exon3 | 411072 | 411294 |
| chr_2 | g4230 | g4230.t1 | cds | g4230.t1.CDS3 | 411072 | 411294 |
| chr_2 | g4230 | g4230.t1 | exon | g4230.t1.exon4 | 411357 | 411493 |
| chr_2 | g4230 | g4230.t1 | cds | g4230.t1.CDS4 | 411357 | 411493 |
| chr_2 | g4230 | g4230.t1 | exon | g4230.t1.exon5 | 418454 | 418604 |
| chr_2 | g4230 | g4230.t1 | cds | g4230.t1.CDS5 | 418454 | 418604 |
| chr_2 | g4230 | g4230.t1 | exon | g4230.t1.exon6 | 438807 | 438965 |
| chr_2 | g4230 | g4230.t1 | cds | g4230.t1.CDS6 | 438807 | 438965 |
| chr_2 | g4230 | g4230.t1 | exon | g4230.t1.exon7 | 450949 | 451149 |
| chr_2 | g4230 | g4230.t1 | cds | g4230.t1.CDS7 | 450949 | 451149 |
| chr_2 | g4230 | g4230.t1 | exon | g4230.t1.exon8 | 451215 | 451523 |
| chr_2 | g4230 | g4230.t1 | cds | g4230.t1.CDS8 | 451215 | 451523 |
| chr_2 | g4230 | g4230.t1 | exon | g4230.t1.exon9 | 451587 | 451763 |
| chr_2 | g4230 | g4230.t1 | cds | g4230.t1.CDS9 | 451587 | 451763 |
| chr_2 | g4230 | g4230.t1 | exon | g4230.t1.exon10 | 451832 | 452196 |
| chr_2 | g4230 | g4230.t1 | cds | g4230.t1.CDS10 | 451832 | 452196 |
| chr_2 | g4230 | g4230.t1 | exon | g4230.t1.exon11 | 452268 | 452456 |
| chr_2 | g4230 | g4230.t1 | cds | g4230.t1.CDS11 | 452268 | 452456 |
| chr_2 | g4230 | g4230.t1 | exon | g4230.t1.exon12 | 453369 | 453678 |
| chr_2 | g4230 | g4230.t1 | cds | g4230.t1.CDS12 | 453369 | 453678 |
| chr_2 | g4230 | g4230.t1 | exon | g4230.t1.exon13 | 453752 | 454234 |
| chr_2 | g4230 | g4230.t1 | cds | g4230.t1.CDS13 | 453752 | 454234 |
| chr_2 | g4230 | g4230.t1 | TSS | g4230.t1 | NA | NA |
| chr_2 | g4230 | g4230.t1 | TTS | g4230.t1 | NA | NA |
Sequences
>g4230.t1 Gene=g4230 Length=3135
ATGTGTTACTTCAGCACATCTTGTCGTTATAAGAAGAATAAAAAACCAGTTTCTTTTCTA
CCAGGACTGCACTTACGAAGCATAGAAGAGCCCCAAAACAGAATGCCCACTCTTGAGGGG
CATCATACAAATTTGGGGCTCGAAAACAATAACATAAACAACAACAGTAGTAGCGGTGGT
GCCCGAACAAGCAATCATTATGATGCGGAATATGCTCGCATGGAAGCATGGTTAGACGAG
CATCAGGAATTTGCACAAGAATATTTTATTCGAAAAGCAACTCGAAATGTCGTTGATGCT
TGGCTTGTGGCGCACGCTTCTCCAGGTGCTTTTGCTGCAACGGACATGATGATGCTCGTC
TCATCGCCAACACACGTAAATTCACAACAATGTTCATCACGAAGTGGCAGTGGTGCCACA
ACTCCTGTTAGAAAAATCTCAGCTCATGAATTCGAACGTGGCGGGCTATTGAAACCAATT
GTTAATACAATAGACGGCACACCAACATTTCTCAGCATCAATTCACAAAATGATTCTACA
ATGAGTTCAATACAAAATCAAAATGGCACAATGCATAGTATTATAAACAGAACGCAGAGG
CTGTCACGAAATGAACTAAAACATATGGACGAGAAAGAACTGATATTTCAGTTGGTCAAG
GATATTTGCAATGAACTTGATGTGACATCATTGTGTCATAAAATCCTTCAAAATGTGTCA
ATTCTATTAAATGCAGATCGTGGTTCACTGTTTCTTGTGCAGGGCAAAATGAGTTCTGAT
GGACCAAAAAAATGCTTAGTTTCAAAGCTATTCGATGTGTGTCCTCGAAGTACGATGGAA
GAAATGGAAACGCAAGATGAAGTAAGAGTGCCATGGGGTACTGGTATTGCTGGTCACGTC
GCTGAAAGTGGCGAGCCAGTGAATATCCCAGATGCTTATGAGGATCAACGATTTAATCGT
GATGTCGACTTAGTGACTGGTTATAGAACAAAAGCGCTACTTTGCATGCCGATTAAGGAC
GCAAGCGGCGATGTGATTGGTGTGGCACAAGTGATAAATAAGCTGGGCGGCGAACAATGC
TTTACTGCAAATGATGAAAAGGTGTTTGCATCATATCTACAATTCTGTGGAATTGGTTTA
CGTAATGCACAGCTTTATGAGAAATCTCAGTTAGAAGTGAAGCGAAATCAAGTGCTATTA
GATTTAGCACGAATGATATTCGAGGAACAAAGTACAATAGAACACATGGTATTTAGAATT
TTAACCCATATGCAAAGTCTTATTCAGTGCCAAAGAGTACAGATACTGCTAGTACATGAA
GCATCCAAAGGAAGTTTTTCACGTGTTTTTGATTTTGAAGCTAATGATGATCTCAATGAA
AGAACTAGTCCGTTTGAATCACGTTTTCCAATTAATATTGGTATCACCGGACATGTTGCA
GCAACTGGTGAAACTGTAAATATACCACATGCATATGAAGATTCAAGATTTGATCCTAGT
GTTGATGAAAACACATTTTTCAAACATAAGTCAATTTTATGTATGGCAATTAAAAATTCG
CTCGGACAGATTGTTGGCGTGATTCAATTGATCAATAAATTTGACGATTTAATTTTCACC
AAAAACGATGAAAATTTTGTTGAGGCTTTTGCAATATTTTGCGGTATGGGCATTCATAAT
ACACATATGTATGAAAAGGCGATAGTAGCAATGGCAAAGCAGAGTGTTACACTTGAAGTG
CTTAGCTATCATGCATCGGCATCAACTGATGATGCTCTTCGACTAATGCGTTTGAAAGTT
CCATCGTCAGCATACTTTCAACTACACGATTTTGCATTCGATGATTTGCACTTGGACGAT
GATGATACGCTTAAAGCATGCTTGCGAATGTTTCTTGATTTGGATCTCGTTGAAAGATTT
CATATCGATTACGAGATGTTATGTCGATGGCTGCTGAGCGTAAAAAAGAACTATCGAAAT
GTCACTTATCATAATTGGCGTCATGCATTTAATGTTTGCCAGATGATGTTTGCTATTCTC
ACATCAACACAATGGTGGAAAGTTTTTGGTGAAATTGAGTGCCTTGCATTGATGATTGGA
TGTTTAGGACACGACTTAGATCATCGTGGTGTCAACAATGCTTTCCAAATTAAAGCATCA
TCACCACTTGCGCAACTTTATTCGACATCTACTATGGAACATCATCATTTTGATCAATGT
GTTATGATTCTCAACAGTCCTGGAAATCAAATCCTATCAAATTTGTCCTCAGAGGATTAT
AGTCGTGTGATTAAAGTACTTGAAGATGCAATTCTTTCAACTGATTTGGCTGTTTACTTC
AGAAAACGTGGTCCTTTTTTGAATTTGATAAAAAATCAAACAATAATACATGAGCAATTC
ACAAATGAGGAAAACCGTTCTTTACTTCGAGCCATGAGTATGACTGTGTGTGATTTATCG
GCAATAACAAAACCATGGGAGATTGAGAAGCGCGTTGCCGATCTTGTAAGCTCAGAGTTT
TTCGAGCAAGGTGATATGGAGAGACAAGAATTAAATATTACACCTATTGACATCATGAAT
CGTGAAAAAGAAGATCAATTACCAATGATGCAAGTTGGTTTTATCGATTCAATTTGCTTA
CCAATTTATGAGGCTTTTGCTGATTTATCAAAGGAACTGAAACCATTAGTAGAAGGTGTT
AAAGATAATAAAAAACACTGGCTTGAACTCGCTCAAACAGCTCAGGAAACGATAAAAAAT
CGAAAAAATAGTTTAAAATCTTTATCAAACGGGAGCATTAATAATAACTACTACACAAAT
GTGAATAATAGCATAGAGAATACAAAAAATAATAACAACAATACAAGTCTTAATAACAAC
AACAATAATAATAATAATAACAGCAGTGGAGATGAATTAAATAATACTAGCAACAGCAAT
GACAGCTTGAAAATGTCGAAAATTGTGGGAAAATTTCCTTTGGATATTACCGGTATCACA
TCAGTTAATTCAATATTTGCACCAACCTATATCAAACCATCACAAAATGGATATATCAAT
TCTTATAAAGCATCTTCCATAGTGCGTTATGATAGTTGGATGAAAAAAGATGAGGAAGAA
GTTATGGACCAATGA
>g4230.t1 Gene=g4230 Length=1044
MCYFSTSCRYKKNKKPVSFLPGLHLRSIEEPQNRMPTLEGHHTNLGLENNNINNNSSSGG
ARTSNHYDAEYARMEAWLDEHQEFAQEYFIRKATRNVVDAWLVAHASPGAFAATDMMMLV
SSPTHVNSQQCSSRSGSGATTPVRKISAHEFERGGLLKPIVNTIDGTPTFLSINSQNDST
MSSIQNQNGTMHSIINRTQRLSRNELKHMDEKELIFQLVKDICNELDVTSLCHKILQNVS
ILLNADRGSLFLVQGKMSSDGPKKCLVSKLFDVCPRSTMEEMETQDEVRVPWGTGIAGHV
AESGEPVNIPDAYEDQRFNRDVDLVTGYRTKALLCMPIKDASGDVIGVAQVINKLGGEQC
FTANDEKVFASYLQFCGIGLRNAQLYEKSQLEVKRNQVLLDLARMIFEEQSTIEHMVFRI
LTHMQSLIQCQRVQILLVHEASKGSFSRVFDFEANDDLNERTSPFESRFPINIGITGHVA
ATGETVNIPHAYEDSRFDPSVDENTFFKHKSILCMAIKNSLGQIVGVIQLINKFDDLIFT
KNDENFVEAFAIFCGMGIHNTHMYEKAIVAMAKQSVTLEVLSYHASASTDDALRLMRLKV
PSSAYFQLHDFAFDDLHLDDDDTLKACLRMFLDLDLVERFHIDYEMLCRWLLSVKKNYRN
VTYHNWRHAFNVCQMMFAILTSTQWWKVFGEIECLALMIGCLGHDLDHRGVNNAFQIKAS
SPLAQLYSTSTMEHHHFDQCVMILNSPGNQILSNLSSEDYSRVIKVLEDAILSTDLAVYF
RKRGPFLNLIKNQTIIHEQFTNEENRSLLRAMSMTVCDLSAITKPWEIEKRVADLVSSEF
FEQGDMERQELNITPIDIMNREKEDQLPMMQVGFIDSICLPIYEAFADLSKELKPLVEGV
KDNKKHWLELAQTAQETIKNRKNSLKSLSNGSINNNYYTNVNNSIENTKNNNNNTSLNNN
NNNNNNNSSGDELNNTSNSNDSLKMSKIVGKFPLDITGITSVNSIFAPTYIKPSQNGYIN
SYKASSIVRYDSWMKKDEEEVMDQ
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 18 | g4230.t1 | CDD | cd00077 | HDc | 663 | 841 | 5.0841E-11 |
| 17 | g4230.t1 | Gene3D | G3DSA:3.30.450.40 | - | 195 | 406 | 1.1E-63 |
| 16 | g4230.t1 | Gene3D | G3DSA:3.30.450.40 | - | 407 | 564 | 2.7E-49 |
| 15 | g4230.t1 | Gene3D | G3DSA:1.10.1300.10 | Catalytic domain of cyclic nucleotide phosphodiesterase 4b2b | 588 | 914 | 1.7E-110 |
| 4 | g4230.t1 | PANTHER | PTHR11347 | CYCLIC NUCLEOTIDE PHOSPHODIESTERASE | 74 | 922 | 3.6E-271 |
| 5 | g4230.t1 | PANTHER | PTHR11347:SF20 | PHOSPHODIESTERASE | 74 | 922 | 3.6E-271 |
| 6 | g4230.t1 | PRINTS | PR00387 | 3’5’-cyclic nucleotide phosphodiesterase signature | 659 | 672 | 1.0E-27 |
| 10 | g4230.t1 | PRINTS | PR00387 | 3’5’-cyclic nucleotide phosphodiesterase signature | 690 | 703 | 1.0E-27 |
| 8 | g4230.t1 | PRINTS | PR00387 | 3’5’-cyclic nucleotide phosphodiesterase signature | 704 | 719 | 1.0E-27 |
| 9 | g4230.t1 | PRINTS | PR00387 | 3’5’-cyclic nucleotide phosphodiesterase signature | 730 | 746 | 1.0E-27 |
| 11 | g4230.t1 | PRINTS | PR00387 | 3’5’-cyclic nucleotide phosphodiesterase signature | 814 | 827 | 1.0E-27 |
| 7 | g4230.t1 | PRINTS | PR00387 | 3’5’-cyclic nucleotide phosphodiesterase signature | 831 | 847 | 1.0E-27 |
| 1 | g4230.t1 | Pfam | PF01590 | GAF domain | 227 | 371 | 3.8E-17 |
| 2 | g4230.t1 | Pfam | PF01590 | GAF domain | 415 | 557 | 1.7E-11 |
| 3 | g4230.t1 | Pfam | PF00233 | 3’5’-cyclic nucleotide phosphodiesterase | 663 | 900 | 2.8E-77 |
| 19 | g4230.t1 | ProSitePatterns | PS00126 | 3’5’-cyclic nucleotide phosphodiesterase domain signature. | 704 | 715 | - |
| 23 | g4230.t1 | ProSiteProfiles | PS51845 | 3’5’-cyclic nucleotide phosphodiesterase domain profile. | 588 | 914 | 130.757 |
| 21 | g4230.t1 | SMART | SM00065 | gaf_1 | 227 | 390 | 8.2E-32 |
| 20 | g4230.t1 | SMART | SM00065 | gaf_1 | 412 | 568 | 2.2E-21 |
| 22 | g4230.t1 | SMART | SM00471 | hd_13 | 661 | 832 | 1.1E-6 |
| 13 | g4230.t1 | SUPERFAMILY | SSF55781 | GAF domain-like | 209 | 408 | 3.27E-45 |
| 14 | g4230.t1 | SUPERFAMILY | SSF55781 | GAF domain-like | 393 | 586 | 1.16E-40 |
| 12 | g4230.t1 | SUPERFAMILY | SSF109604 | HD-domain/PDEase-like | 602 | 953 | 1.68E-111 |
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: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 K13298 (dual 3’,5’-cyclic-AMP and -GMP phosphodiesterase 11)
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.
