Gene loci information

Transcript annotation

  • This transcript has been annotated as cGMP-dependent protein kinase, isozyme 2 forms cD5/T2.

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 g5564 g5564.t1 TSS g5564.t1 10277530 10277530
chr_2 g5564 g5564.t1 isoform g5564.t1 10278034 10283840
chr_2 g5564 g5564.t1 exon g5564.t1.exon1 10278034 10279480
chr_2 g5564 g5564.t1 cds g5564.t1.CDS1 10278034 10279480
chr_2 g5564 g5564.t1 exon g5564.t1.exon2 10280747 10280966
chr_2 g5564 g5564.t1 cds g5564.t1.CDS2 10280747 10280966
chr_2 g5564 g5564.t1 exon g5564.t1.exon3 10281045 10281281
chr_2 g5564 g5564.t1 cds g5564.t1.CDS3 10281045 10281281
chr_2 g5564 g5564.t1 exon g5564.t1.exon4 10281351 10281500
chr_2 g5564 g5564.t1 cds g5564.t1.CDS4 10281351 10281500
chr_2 g5564 g5564.t1 exon g5564.t1.exon5 10281693 10282048
chr_2 g5564 g5564.t1 cds g5564.t1.CDS5 10281693 10282048
chr_2 g5564 g5564.t1 exon g5564.t1.exon6 10282145 10282321
chr_2 g5564 g5564.t1 cds g5564.t1.CDS6 10282145 10282321
chr_2 g5564 g5564.t1 exon g5564.t1.exon7 10282376 10282468
chr_2 g5564 g5564.t1 cds g5564.t1.CDS7 10282376 10282468
chr_2 g5564 g5564.t1 exon g5564.t1.exon8 10282524 10282713
chr_2 g5564 g5564.t1 cds g5564.t1.CDS8 10282524 10282713
chr_2 g5564 g5564.t1 exon g5564.t1.exon9 10282783 10282808
chr_2 g5564 g5564.t1 cds g5564.t1.CDS9 10282783 10282808
chr_2 g5564 g5564.t1 exon g5564.t1.exon10 10283809 10283840
chr_2 g5564 g5564.t1 cds g5564.t1.CDS10 10283809 10283840
chr_2 g5564 g5564.t1 TTS g5564.t1 NA NA

Sequences

>g5564.t1 Gene=g5564 Length=2928
ATGAAATTAAAATCTTACCCTGGTCACGTCGTTGATGCAAATTTTTCGGTTGGAAAATGC
AAGTCAATGGCCGTGCTATATGAGGCAAATTGGAATGGTGCTGGCAATGAAGATGATGAT
GGCAACAAAAGACTTCAATTTCCTCAATCAGAGAGTACCAATAATATATCGACATTGGGC
CATTACCAATATCGCGTCGATCATATAAGATCATATGGAGAGAAGCAAGATAGGGGCAAA
TATTTGACAATGGCACGACCACAAATAGTATTAAGAAGAAGCAGACTGGACGAAAATACT
GAATGGGACTGTGATAATATTAATGTTGAAAAGAAAAATACTCAAATGATTAATCCCTTG
TATAATCATACTCAAAACAACTGGCATTCGTCAGACTACTTAACTGACTTAGATGATAAG
CATCCAGATTCAAAAAAGATGCAAATTAAAAGATCTCAAACAGTGATTGTGAAGCAGCCA
ACATCGACCGTAAAAAAAGACTCAAATTATGGTACAATCAACTTTAAGCAGTACTTTAAG
AGAGGCGGTCGACCGCAATTGAATGAGATGCTTCCAAACGGATTTAACGATAGAAATAAA
CAAAACTGTGATAACTTTGATGAAGTGAGCTCACTGAAGGAAGACGTAAAGAAGCTCAGC
ATGAATAGTGCGCATGCAAATGCTGAAAAGTCTATGCCGAGTCGTATGCATAGTTATAAA
ACAATAGATTTTCATGCTTCGAATGAAGGCTATGGAAACTTACAAAATCGAAATTTCACA
AACGGCACTATGCCATCAAAATGCTTGCTCAATCCGCTAGCTCGAAATAAAAGTATAAAA
ATAAATCATTTTGATATGATTAATATGGCAAACAGTGATGAACAGAAGATTGAAAACAAT
GATGATGATAATGGCAAATTTTACAATGAGAACGAAAACTCACCTAAAAAAGAAAAAAAA
TTAAGTTTTGGCAGACGATTTTATAATACTATTTCGGCGGGTTCGAAGCTACCAAAAGTA
TTTTTAGGACGATCAAAAAGCCAAAGAACAAAATTAGACATTGTCGAATTTAATGAGCAA
TTTGATAAATTAAATGGCAACAGTTCAGAGGCACCAATGAAGTCAACTTCTTCATCATCA
AATTCTTCAACTCTATCCACAGCATCGCCTTCATCAATTGTTTCCGACTTGCCCAAGACT
ACGATCCCAATGATAAATAATAGTGCTACTGCTGCTATTGCTTCTGCTTCTAGGAAGAGA
TTTTTCCCATCAACAAAAAACAGCAAGACAACAACACAAAAAGACTCACATTCTGACTCA
TTCTTCATTCCTCGTCCACATTTAATTGTTCCCGTGCATTCGTATGCGCGAAAGCGAAGA
ACTGGTAACTTGACTAAAGATCATTCAATGACTAATGCGAAAACTCAACCCATTTTAAAT
GGCAAAGAGGGACGTGTTGAGGTTTCTCGCGAGGGAAAATATCTATCGTCATTGTCAGGT
GCTAAAGTGTTGGGTGAACTCGCAATTTTATATAATTGTCAACGAACTGCAACAATCACT
GCGGTAACTGACTGCAAATTATGGGCAATCGAACGACAATGCTTTCAAACAATAATGATG
AGAACGGGTCTCATCAAACAAACTGAATATACTGATTTCCTCAAAAGTGTTCCAATATTC
AAAGATCTTCCGGAAGACACTCTTATTAAAATTTCTGATGTGCTAGAAGAATGTTATTAT
CGTAAAGGCGATTATATAATCCGCCAAGGTGCTAGAGGTGACACATTCTTCATCATCTCT
AAAGGACAAGTAAAAGTCACAATTAGACCAGAAGATTCCTTTGAGGAAACTTTCATACGA
ACTCTTGGAAAGGGTGACTTTTTCGGTGAAAAGGCGCTTCAAGGAGATGATTTGAGAACG
GCAAATATTATTTGCGATTCACCAGAAGGCGTTACCTGCTTGGTTATTGATCGTGAAACA
TTTATTCAATTGATATCGAATCTAGACGAAGTAAAGAATCGCTATACTGATGAGAGTACA
ATTGAAAGAAGAAGAATTAATGAAGAGTTCCGTGAAGTTCAGTTAACTGATTTGCGAATC
ATCACTACGCTTGGCGTTGGCGGATTTGGCAGAGTTGAATTGGTGCAAATAAAAGATGAC
GCGACGCGGTCTTATGCACTTAAGCAAATGAAAAAATCACAAATTGTTGAAACAAGGCAA
CAACAACACATTATGTCAGAGAAAGAAATAATGGCTGAAGCAAATAGTGATTTCATCGTT
AAGCTCTTTAAAACATTTAAAGATCGCAAATATTTGTACATGCTTATGGAAAGTTGTTTA
GGTGGCGAATTATGGACAATTTTGCGTGATCGTGGCCATTTCGATGATTCGACGACTCGT
TTTTATACAGCATGCGTGGTTGAAGCATTTGATTACTTACACTCGAGAAACATAATCTAT
AGAGATTTAAAACCCGAAAATTTATTACTCGATGTCACTGGCTATGTGAAGCTGGTCGAC
TTCGGTTTTGCCAAAAAGTTGCAGAGTGGTCGACATTTCAAAACATGGACTTTTTGTGGT
ACTCCAGAATATGTTGCACCTGAGGTTATTTTAAATCGTGGTCATGATATAAGTGCTGAT
TATTGGTCTTTGGGTGTTTTAATGTTTGAATTACTGACAGGAACACCACCATTTACTGGC
CCTGATCCAATGAGAACTTATAATATAATTTTGAAAGGAATAGATGCCATTGAGTTTCCA
AGAAACATCACACGAAATGCAACAGCATTAATTAAAAAACTCTGTCGCGATAACCCATCT
GAACGTTTAGGATATCAACGTGGTGGCATTCAAGAGATTCAAAAGCATAAATGGTTTGAT
GGATTTTATTGGGAAGATCAATTCTTTGAAGCTTCCGCAACGGAATAA

>g5564.t1 Gene=g5564 Length=975
MKLKSYPGHVVDANFSVGKCKSMAVLYEANWNGAGNEDDDGNKRLQFPQSESTNNISTLG
HYQYRVDHIRSYGEKQDRGKYLTMARPQIVLRRSRLDENTEWDCDNINVEKKNTQMINPL
YNHTQNNWHSSDYLTDLDDKHPDSKKMQIKRSQTVIVKQPTSTVKKDSNYGTINFKQYFK
RGGRPQLNEMLPNGFNDRNKQNCDNFDEVSSLKEDVKKLSMNSAHANAEKSMPSRMHSYK
TIDFHASNEGYGNLQNRNFTNGTMPSKCLLNPLARNKSIKINHFDMINMANSDEQKIENN
DDDNGKFYNENENSPKKEKKLSFGRRFYNTISAGSKLPKVFLGRSKSQRTKLDIVEFNEQ
FDKLNGNSSEAPMKSTSSSSNSSTLSTASPSSIVSDLPKTTIPMINNSATAAIASASRKR
FFPSTKNSKTTTQKDSHSDSFFIPRPHLIVPVHSYARKRRTGNLTKDHSMTNAKTQPILN
GKEGRVEVSREGKYLSSLSGAKVLGELAILYNCQRTATITAVTDCKLWAIERQCFQTIMM
RTGLIKQTEYTDFLKSVPIFKDLPEDTLIKISDVLEECYYRKGDYIIRQGARGDTFFIIS
KGQVKVTIRPEDSFEETFIRTLGKGDFFGEKALQGDDLRTANIICDSPEGVTCLVIDRET
FIQLISNLDEVKNRYTDESTIERRRINEEFREVQLTDLRIITTLGVGGFGRVELVQIKDD
ATRSYALKQMKKSQIVETRQQQHIMSEKEIMAEANSDFIVKLFKTFKDRKYLYMLMESCL
GGELWTILRDRGHFDDSTTRFYTACVVEAFDYLHSRNIIYRDLKPENLLLDVTGYVKLVD
FGFAKKLQSGRHFKTWTFCGTPEYVAPEVILNRGHDISADYWSLGVLMFELLTGTPPFTG
PDPMRTYNIILKGIDAIEFPRNITRNATALIKKLCRDNPSERLGYQRGGIQEIQKHKWFD
GFYWEDQFFEASATE

Protein features from InterProScan

Transcript Database ID Name Start End E.value
19 g5564.t1 CDD cd00038 CAP_ED 483 550 3.19573E-13
20 g5564.t1 CDD cd00038 CAP_ED 559 675 1.14271E-29
21 g5564.t1 CDD cd05572 STKc_cGK 704 966 9.9752E-176
18 g5564.t1 Gene3D G3DSA:2.60.120.10 Jelly Rolls 481 545 1.5E-21
17 g5564.t1 Gene3D G3DSA:2.60.120.10 Jelly Rolls 546 675 7.4E-45
15 g5564.t1 Gene3D G3DSA:3.30.200.20 Phosphorylase Kinase; domain 1 696 782 9.6E-102
16 g5564.t1 Gene3D G3DSA:1.10.510.10 Transferase(Phosphotransferase) domain 1 783 966 9.6E-102
29 g5564.t1 MobiDBLite mobidb-lite consensus disorder prediction 298 321 -
30 g5564.t1 MobiDBLite mobidb-lite consensus disorder prediction 366 392 -
4 g5564.t1 PANTHER PTHR24353:SF130 AGAP008863-PA 463 965 0.0
5 g5564.t1 PANTHER PTHR24353 CYCLIC NUCLEOTIDE-DEPENDENT PROTEIN KINASE 463 965 0.0
8 g5564.t1 PRINTS PR00104 cGMP-dependent protein kinase signature 565 579 9.7E-27
11 g5564.t1 PRINTS PR00104 cGMP-dependent protein kinase signature 600 609 9.7E-27
10 g5564.t1 PRINTS PR00104 cGMP-dependent protein kinase signature 618 625 9.7E-27
6 g5564.t1 PRINTS PR00104 cGMP-dependent protein kinase signature 636 645 9.7E-27
9 g5564.t1 PRINTS PR00104 cGMP-dependent protein kinase signature 651 660 9.7E-27
7 g5564.t1 PRINTS PR00104 cGMP-dependent protein kinase signature 661 675 9.7E-27
2 g5564.t1 Pfam PF00027 Cyclic nucleotide-binding domain 483 541 9.0E-9
3 g5564.t1 Pfam PF00027 Cyclic nucleotide-binding domain 579 666 1.1E-18
1 g5564.t1 Pfam PF00069 Protein kinase domain 700 959 4.0E-69
25 g5564.t1 ProSitePatterns PS00889 Cyclic nucleotide-binding domain signature 2. 504 521 -
27 g5564.t1 ProSitePatterns PS00888 Cyclic nucleotide-binding domain signature 1. 586 602 -
26 g5564.t1 ProSitePatterns PS00889 Cyclic nucleotide-binding domain signature 2. 628 645 -
28 g5564.t1 ProSitePatterns PS00107 Protein kinases ATP-binding region signature. 704 728 -
24 g5564.t1 ProSitePatterns PS00108 Serine/Threonine protein kinases active-site signature. 818 830 -
32 g5564.t1 ProSiteProfiles PS50042 cAMP/cGMP binding motif profile. 483 556 23.465
31 g5564.t1 ProSiteProfiles PS50042 cAMP/cGMP binding motif profile. 559 682 33.301
33 g5564.t1 ProSiteProfiles PS50011 Protein kinase domain profile. 698 959 47.439
22 g5564.t1 SMART SM00100 cnmp_10 559 683 4.1E-26
23 g5564.t1 SMART SM00220 serkin_6 698 959 5.4E-85
13 g5564.t1 SUPERFAMILY SSF51206 cAMP-binding domain-like 483 541 7.2E-13
12 g5564.t1 SUPERFAMILY SSF51206 cAMP-binding domain-like 546 675 3.4E-32
14 g5564.t1 SUPERFAMILY SSF56112 Protein kinase-like (PK-like) 678 969 5.88E-84

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

Data is missing for g5564/g5564.t1; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5564.t1.fa.iupred3.txt does not exist

GO terms from InterProScan

GOID TERM ONTOLOGY
GO:0005524 ATP binding MF
GO:0004672 protein kinase activity MF
GO:0006468 protein phosphorylation BP
GO:0004692 cGMP-dependent protein kinase 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