Gene loci information

Transcript annotation

  • This transcript has been annotated as cGMP-dependent 3’,5’-cyclic phosphodiesterase.

Parent gene

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 g6634 g6634.t2 isoform g6634.t2 17888213 17890103
chr_2 g6634 g6634.t2 exon g6634.t2.exon1 17888213 17888362
chr_2 g6634 g6634.t2 exon g6634.t2.exon2 17888426 17889432
chr_2 g6634 g6634.t2 cds g6634.t2.CDS1 17888565 17889432
chr_2 g6634 g6634.t2 exon g6634.t2.exon3 17889490 17890103
chr_2 g6634 g6634.t2 cds g6634.t2.CDS2 17889490 17890103
chr_2 g6634 g6634.t2 TTS g6634.t2 17890406 17890406
chr_2 g6634 g6634.t2 TSS g6634.t2 NA NA

Sequences

>g6634.t2 Gene=g6634 Length=1771
GGTCGTAGGCAAAGAACATAAAACATTGTTTTTTGATATCAAAAACTCTACCTCTCATAA
ATATAAGCAATATAATGCACTTTTTGTCTGCATAGCTGGTGACGATACGCATAAAAAATT
ATATGAATTTTACATTCGTCATACTTTTCGTTATGTACTTGGATACTTGCTAACTGCAAT
TGAACTGTATGAAGAAAAAAGAGTACGACTCCAATGTCAAAATTTACTTCAAGTTGCTCG
TCGTTTATTAAGTAAAATTGGTGATTTAGGTCAGCTTCTTCGTGGTGTTATGGCAGAAGC
ACGAGAACTAGCAAAAGCTGAAAGATGCTCACTTTTTCTAATTGATAAAGATACTGGAGA
ATTGGTATCGAAAATTTTTGATGGAAATGCAATAACACAACAAACAAAGCAATCAAAAGA
GATAAGGATAAGTGGCAATAAAGGCATTGCTGGGCATGTTGCACTTACTGGGAAATTGTT
AAATATTCATAACGCATATCAACATCCACTTTTTTACAAAGGAATTGATGAACAAACAGG
TTTTAAAACTAGAAACATTCTTTGTTTTCCCATATGTGATGAGGAATCAAAAGTTATCGG
TGTCGCTCAATTATGTAATAAACTTGATGGATTTCATTTTGATAAATGTGATGAAGAAAC
AAGTCGAGCATTTTCGGTTTATTGCGGAATTACCATCATGCATAGTCTTGTTCATAAACG
TGTGCAAAAAGCTGAAGCACGATATAAGTTATCACAAGAGCTTTTACTTTACCATATGAA
AGTTCCAGAACCTGATGTTATCAATTGCCTTAATCATGAACATTTAGACTCTGTTATTGA
AAAGTATCCAGAATTTTCAAGCTTTAGTTTTTGCCCACGTGACGTCGACGATCATACTTC
TATGCTTCTTAGTCTACATATGTTTATTGATTTGAATTTTATAAAGGAATTCAAAATACC
TGAAGATAAACTAGCTCGTTTCCTAATGCTTGTACAAAAAGGTTATCGAATGGTTCCATA
TCATAATTGGCACCATGCATTCAGTGTTACACATTTTGCCTATGCATGTATAAAAAATCT
AAAACTAATAGATCGCGGAATTATAACAAAACTTCAAGGACTTTCCTTTCTTATAGCTTG
CCTTTGTCATGATTTAGATCATCGTGGATTTAATAATTCGTATATGACACAAACAACAAG
TTTATTAGCAAGGCTTTATAGTTCAGAAGGGTCTATCAATGAGCGTCATCATTTGTCTCA
AGCAATTTGTATTCTTAACGATTCAGGTAGCAAAATTTTAGATTCATTAAATACAGAACA
ATTCATGGAATCAATCGATTATTTGAGAGAACTAATTCTTGCAACTGATCTTGCTAATCA
TTTCCGAATTTTCAAAGATTTAAAAAATCTGACAACTGACAACATAAAAGATACACCAAG
ATTATTGTTGTCACTGTTGATTACTTGCTCGGATCTAAATGATCAAATCAAAACTTGGTC
TACAGTTTATCGTGTTGCTGAATTAGTATATACAGAATTTTTCACACAAGGAGATTTGGA
AAAACAAATGGGCATGTCGCCAAATTTAATGTTTGACAGGAAAAAAGCAAACGTGCCATC
ACTTCAAATTGATTTTTTGGATACCGTTGTAAAGCCAACCTTTGAGATTTTCGTACAAAT
ATTTCCTGAAACATTGCAATTTCTTGATACAATTAATGAAAATCGACAACATTGGATTGA
AATTAAGGAAAATGAGAATAAAAATTTGTAA

>g6634.t2 Gene=g6634 Length=493
MAEARELAKAERCSLFLIDKDTGELVSKIFDGNAITQQTKQSKEIRISGNKGIAGHVALT
GKLLNIHNAYQHPLFYKGIDEQTGFKTRNILCFPICDEESKVIGVAQLCNKLDGFHFDKC
DEETSRAFSVYCGITIMHSLVHKRVQKAEARYKLSQELLLYHMKVPEPDVINCLNHEHLD
SVIEKYPEFSSFSFCPRDVDDHTSMLLSLHMFIDLNFIKEFKIPEDKLARFLMLVQKGYR
MVPYHNWHHAFSVTHFAYACIKNLKLIDRGIITKLQGLSFLIACLCHDLDHRGFNNSYMT
QTTSLLARLYSSEGSINERHHLSQAICILNDSGSKILDSLNTEQFMESIDYLRELILATD
LANHFRIFKDLKNLTTDNIKDTPRLLLSLLITCSDLNDQIKTWSTVYRVAELVYTEFFTQ
GDLEKQMGMSPNLMFDRKKANVPSLQIDFLDTVVKPTFEIFVQIFPETLQFLDTINENRQ
HWIEIKENENKNL

Protein features from InterProScan

Transcript Database ID Name Start End E.value
14 g6634.t2 CDD cd00077 HDc 244 418 1.05293E-10
13 g6634.t2 Gene3D G3DSA:3.30.450.40 - 1 152 9.9E-47
12 g6634.t2 Gene3D G3DSA:1.10.1300.10 Catalytic domain of cyclic nucleotide phosphodiesterase 4b2b 167 493 1.3E-102
3 g6634.t2 PANTHER PTHR11347:SF102 PHOSPHODIESTERASE 1 485 6.4E-151
4 g6634.t2 PANTHER PTHR11347 CYCLIC NUCLEOTIDE PHOSPHODIESTERASE 1 485 6.4E-151
7 g6634.t2 PRINTS PR00387 3’5’-cyclic nucleotide phosphodiesterase signature 240 253 5.6E-22
9 g6634.t2 PRINTS PR00387 3’5’-cyclic nucleotide phosphodiesterase signature 287 302 5.6E-22
8 g6634.t2 PRINTS PR00387 3’5’-cyclic nucleotide phosphodiesterase signature 315 331 5.6E-22
6 g6634.t2 PRINTS PR00387 3’5’-cyclic nucleotide phosphodiesterase signature 391 404 5.6E-22
5 g6634.t2 PRINTS PR00387 3’5’-cyclic nucleotide phosphodiesterase signature 408 424 5.6E-22
1 g6634.t2 Pfam PF01590 GAF domain 1 135 3.5E-11
2 g6634.t2 Pfam PF00233 3’5’-cyclic nucleotide phosphodiesterase 244 475 1.6E-66
15 g6634.t2 ProSitePatterns PS00126 3’5’-cyclic nucleotide phosphodiesterase domain signature. 287 298 -
18 g6634.t2 ProSiteProfiles PS51845 3’5’-cyclic nucleotide phosphodiesterase domain profile. 163 489 101.003
16 g6634.t2 SMART SM00065 gaf_1 1 146 7.9E-18
17 g6634.t2 SMART SM00471 hd_13 242 409 2.2E-7
11 g6634.t2 SUPERFAMILY SSF55781 GAF domain-like 2 163 1.08E-40
10 g6634.t2 SUPERFAMILY SSF109604 HD-domain/PDEase-like 180 491 1.61E-97

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

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.

Raw TPM values