General information for g5990.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Calcium/calmodulin-dependent 3’,5’-cyclic nucleotide phosphodiesterase 1.
Parent gene
- The parent gene g5990 is located on chr_2: 13187683..13206986 (- 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 | g5990 | g5990.t1 | isoform | g5990.t1 | 13187683 | 13206986 |
| chr_2 | g5990 | g5990.t1 | exon | g5990.t1.exon1 | 13187683 | 13187780 |
| chr_2 | g5990 | g5990.t1 | cds | g5990.t1.CDS1 | 13187683 | 13187780 |
| chr_2 | g5990 | g5990.t1 | exon | g5990.t1.exon2 | 13187844 | 13188803 |
| chr_2 | g5990 | g5990.t1 | cds | g5990.t1.CDS2 | 13187844 | 13188803 |
| chr_2 | g5990 | g5990.t1 | exon | g5990.t1.exon3 | 13189466 | 13189628 |
| chr_2 | g5990 | g5990.t1 | cds | g5990.t1.CDS3 | 13189466 | 13189628 |
| chr_2 | g5990 | g5990.t1 | exon | g5990.t1.exon4 | 13190659 | 13190908 |
| chr_2 | g5990 | g5990.t1 | cds | g5990.t1.CDS4 | 13190659 | 13190908 |
| chr_2 | g5990 | g5990.t1 | exon | g5990.t1.exon5 | 13201742 | 13201960 |
| chr_2 | g5990 | g5990.t1 | cds | g5990.t1.CDS5 | 13201742 | 13201960 |
| chr_2 | g5990 | g5990.t1 | exon | g5990.t1.exon6 | 13203504 | 13203617 |
| chr_2 | g5990 | g5990.t1 | cds | g5990.t1.CDS6 | 13203504 | 13203617 |
| chr_2 | g5990 | g5990.t1 | exon | g5990.t1.exon7 | 13206265 | 13206544 |
| chr_2 | g5990 | g5990.t1 | cds | g5990.t1.CDS7 | 13206265 | 13206544 |
| chr_2 | g5990 | g5990.t1 | exon | g5990.t1.exon8 | 13206661 | 13206786 |
| chr_2 | g5990 | g5990.t1 | cds | g5990.t1.CDS8 | 13206661 | 13206786 |
| chr_2 | g5990 | g5990.t1 | exon | g5990.t1.exon9 | 13206980 | 13206986 |
| chr_2 | g5990 | g5990.t1 | cds | g5990.t1.CDS9 | 13206980 | 13206986 |
| chr_2 | g5990 | g5990.t1 | TSS | g5990.t1 | NA | NA |
| chr_2 | g5990 | g5990.t1 | TTS | g5990.t1 | NA | NA |
Sequences
>g5990.t1 Gene=g5990 Length=2217
ATGTTCTTTGCAAGCACACCAGAAAACATATTAAGTAAGACAGATACAATAGCATTAAGG
GATTTAAAAAGCACTGAGACTACATCCAGCAACATTCAGACTGAAGCACAATCACGAAAC
GGTCAAATTGCAACTGACGCTGGGCTAACGATAGTTCGTCGATTAAGCGGTAAAAAATCG
CAACAGCAACAGTCTGAATTGATGACAACAGCGGATAGCCAACAATTAGAGCAATACATT
TTTTCTTCTGATAGCCAACAAACAAACGTTACTAGCGGTTATAGTTCGTTCCTAGAAAAT
CGATTAAAAATGCAACCAACCTCTAATCTAGATGATTTAGATAATTTAGATTTGACGACG
GAAAATTTACCAGCTGTCGATACGCCAGATGCTTGTGATAAAGCTGCCTTAAGACTACGA
TGTCTCTTGAGGCAGCTTCAACGTGGAGAAATTTCTGCCGAGCTTTTACAGAAAAATCTC
CATTATGCAGCTCGAGTTCTCGAAGCTGTATTTATAGATGAGACCAATCAAGATGGTGGT
GGTGGCACTGAAAGGGAGAGTCACAATAAGCTCAAAAAGAGCAACAGTATAGCTGTTACG
GAGCATGGACGACATAGCGCATCAACAATGCCGCCAACACATGACAGTGCGTCATCAAAT
TCAGCGATTACAGGCAAAAGCAGTTTCATACAGCGAAGACGTTTGCGGCAGCCTTGTTGG
GCACGCACAACAATGACACAGAAAAAACGCTTGGCAGATGAGGATGATGAGCTATCAGAA
GTGCAACCAGACGCAGTGCCGCCAGAAGTCCGTGAATGGCTGGCATCAACATTCACACGA
CAACTCGCCACAACCCGCAAGAAAAGTGATGAAAAACCTAAATTTCGATCTGTCGCACAC
GCCATTCGTGCTGGTATTTTTGTGGATCGCATATATCGACGTGTGTCAAGTACAGCTCTC
ATGCAATTTCCACCAGAAGTTGTAAAAGTTCTAAAGCATCTCGACGAGTGGTCGTTTGAT
GTGTTTGCTTTGGCAGAATCAGGAAACTGTCAACCGGTTAAATACGTCGGATATGATCTT
CTTAATCGCTATGGAATGATTCACAAATTTAAAGTTCCATCTGCAACGTTAGAAACTTTT
CTAACGAGAATTGAGGAAGGATATTGTCGTTTTCGTAATCCCTATCACAATAACTTACAT
GCAGCAGATGTTGCTCAAACGGTCCATCATGTTCTTTGTCAAACGGGCTTGATGCATTGG
TTGTCAGATTTAGAAATATTTGCAACACTAGTAGCAGCACTCATTCATGATTACGAGCAT
ACGGGTACGACAAATAATTTCCATGTCATGTCTGGTAGTGATACAGCAATGCTCTATAAT
GATCGAGCTGTACTTGAAAATCATCATATAAGTGCGGCCTTTCGCGTCCTCAAAGACGAT
GACTGTAATATACTACAAAATTTATCGCGTGATGAGTATAGGGAACTGAGAACACTCATA
ATCGATATGGTGCTCGCGACAGACATGTCGTTTCACTTTCAGCAACTGAAAAATATGAGA
AATTTGCTGACACTTGCTGAGCCAAGCGTGGATAAGTCAAAAGCAATGTCACTGGTGCTG
CATTGCTGCGATATTTCACATCCAGCTAAAAAATGGGATCTTCATCATAAATGGACCATG
TTACTACTGGAAGAATTTTTCAGACAAGGTGATTTAGAGCGAGAACTTGGTCTACCTTTT
AGTCCACTCTGCGATCGAAATAATACATTAGTAGCAGAATCACAAATTGGTTTTATTGAG
TTTATTGTTGAACCAAGTATGGCCGTATGCTCTGATATGCTCGAAACTATTTTGGCACCA
ATTGCACCAATCACTAATAACAATAATAATAATAATAGTTTAAGTAATAAAGCGATAGCG
TCAGTAAGTGAAGACAATGCAACAAATACTCTGAATGTGCCGGGTGAAAGTGGTAGCTCG
TGCAGTGAAGCAATAGTTAAGACTAAAAATGAAGAGGCTAAAAATGAATGTGAGAAGCCC
ACACGATTCAAAATTAAAAAGCCATGGACCACGTGTCTTGCTGAAAATAAGAAAATTTGG
AAAGACCAAGCAGTGAAAGATGCTGAAGCACGAGCAGCAGCAGCAGCGGCAGCAGCAGAG
CAAGAGAAGGAAGAAAAACGTCTCGAATTAGAAAGTGCAGCGCAAGCAGAAGAATAA
>g5990.t1 Gene=g5990 Length=738
MFFASTPENILSKTDTIALRDLKSTETTSSNIQTEAQSRNGQIATDAGLTIVRRLSGKKS
QQQQSELMTTADSQQLEQYIFSSDSQQTNVTSGYSSFLENRLKMQPTSNLDDLDNLDLTT
ENLPAVDTPDACDKAALRLRCLLRQLQRGEISAELLQKNLHYAARVLEAVFIDETNQDGG
GGTERESHNKLKKSNSIAVTEHGRHSASTMPPTHDSASSNSAITGKSSFIQRRRLRQPCW
ARTTMTQKKRLADEDDELSEVQPDAVPPEVREWLASTFTRQLATTRKKSDEKPKFRSVAH
AIRAGIFVDRIYRRVSSTALMQFPPEVVKVLKHLDEWSFDVFALAESGNCQPVKYVGYDL
LNRYGMIHKFKVPSATLETFLTRIEEGYCRFRNPYHNNLHAADVAQTVHHVLCQTGLMHW
LSDLEIFATLVAALIHDYEHTGTTNNFHVMSGSDTAMLYNDRAVLENHHISAAFRVLKDD
DCNILQNLSRDEYRELRTLIIDMVLATDMSFHFQQLKNMRNLLTLAEPSVDKSKAMSLVL
HCCDISHPAKKWDLHHKWTMLLLEEFFRQGDLERELGLPFSPLCDRNNTLVAESQIGFIE
FIVEPSMAVCSDMLETILAPIAPITNNNNNNNSLSNKAIASVSEDNATNTLNVPGESGSS
CSEAIVKTKNEEAKNECEKPTRFKIKKPWTTCLAENKKIWKDQAVKDAEARAAAAAAAAE
QEKEEKRLELESAAQAEE
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 16 | g5990.t1 | CDD | cd00077 | HDc | 400 | 567 | 2.67722E-15 |
| 15 | g5990.t1 | Coils | Coil | Coil | 705 | 738 | - |
| 14 | g5990.t1 | Gene3D | G3DSA:1.10.1300.10 | Catalytic domain of cyclic nucleotide phosphodiesterase 4b2b | 316 | 710 | 9.1E-142 |
| 22 | g5990.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 177 | 221 | - |
| 23 | g5990.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 179 | 199 | - |
| 20 | g5990.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 200 | 221 | - |
| 19 | g5990.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 716 | 738 | - |
| 21 | g5990.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 718 | 738 | - |
| 4 | g5990.t1 | PANTHER | PTHR11347:SF32 | CALCIUM/CALMODULIN-DEPENDENT 3’,5’-CYCLIC NUCLEOTIDE PHOSPHODIESTERASE 1C | 105 | 177 | 1.9E-205 |
| 6 | g5990.t1 | PANTHER | PTHR11347 | CYCLIC NUCLEOTIDE PHOSPHODIESTERASE | 105 | 177 | 1.9E-205 |
| 3 | g5990.t1 | PANTHER | PTHR11347:SF32 | CALCIUM/CALMODULIN-DEPENDENT 3’,5’-CYCLIC NUCLEOTIDE PHOSPHODIESTERASE 1C | 248 | 715 | 1.9E-205 |
| 5 | g5990.t1 | PANTHER | PTHR11347 | CYCLIC NUCLEOTIDE PHOSPHODIESTERASE | 248 | 715 | 1.9E-205 |
| 8 | g5990.t1 | PRINTS | PR00387 | 3’5’-cyclic nucleotide phosphodiesterase signature | 391 | 404 | 1.7E-32 |
| 10 | g5990.t1 | PRINTS | PR00387 | 3’5’-cyclic nucleotide phosphodiesterase signature | 422 | 435 | 1.7E-32 |
| 9 | g5990.t1 | PRINTS | PR00387 | 3’5’-cyclic nucleotide phosphodiesterase signature | 436 | 451 | 1.7E-32 |
| 12 | g5990.t1 | PRINTS | PR00387 | 3’5’-cyclic nucleotide phosphodiesterase signature | 463 | 479 | 1.7E-32 |
| 11 | g5990.t1 | PRINTS | PR00387 | 3’5’-cyclic nucleotide phosphodiesterase signature | 540 | 553 | 1.7E-32 |
| 7 | g5990.t1 | PRINTS | PR00387 | 3’5’-cyclic nucleotide phosphodiesterase signature | 557 | 573 | 1.7E-32 |
| 1 | g5990.t1 | Pfam | PF08499 | 3’5’-cyclic nucleotide phosphodiesterase N-terminal | 250 | 310 | 1.6E-31 |
| 2 | g5990.t1 | Pfam | PF00233 | 3’5’-cyclic nucleotide phosphodiesterase | 395 | 616 | 4.7E-83 |
| 18 | g5990.t1 | ProSitePatterns | PS00126 | 3’5’-cyclic nucleotide phosphodiesterase domain signature. | 436 | 447 | - |
| 24 | g5990.t1 | ProSiteProfiles | PS51845 | 3’5’-cyclic nucleotide phosphodiesterase domain profile. | 319 | 707 | 121.524 |
| 17 | g5990.t1 | SMART | SM00471 | hd_13 | 393 | 558 | 3.2E-4 |
| 13 | g5990.t1 | SUPERFAMILY | SSF109604 | HD-domain/PDEase-like | 323 | 638 | 5.61E-111 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5990/g5990.t1; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5990.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:0004114 | 3’,5’-cyclic-nucleotide phosphodiesterase activity | MF |
KEGG
Orthology
- This transcript has been annotated with K13755 (calcium/calmodulin-dependent 3’,5’-cyclic nucleotide phosphodiesterase)
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