General information for g5604.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as cGMP-dependent protein kinase, isozyme 1.
Parent gene
- The parent gene g5604 is located on chr_2: 10571523..10579375 (+ 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 | g5604 | g5604.t1 | isoform | g5604.t1 | 10571523 | 10579375 |
| chr_2 | g5604 | g5604.t1 | exon | g5604.t1.exon1 | 10571523 | 10572497 |
| chr_2 | g5604 | g5604.t1 | cds | g5604.t1.CDS1 | 10571523 | 10572497 |
| chr_2 | g5604 | g5604.t1 | exon | g5604.t1.exon2 | 10572844 | 10572963 |
| chr_2 | g5604 | g5604.t1 | cds | g5604.t1.CDS2 | 10572844 | 10572963 |
| chr_2 | g5604 | g5604.t1 | exon | g5604.t1.exon3 | 10573240 | 10573446 |
| chr_2 | g5604 | g5604.t1 | cds | g5604.t1.CDS3 | 10573240 | 10573446 |
| chr_2 | g5604 | g5604.t1 | exon | g5604.t1.exon4 | 10576007 | 10576347 |
| chr_2 | g5604 | g5604.t1 | cds | g5604.t1.CDS4 | 10576007 | 10576347 |
| chr_2 | g5604 | g5604.t1 | exon | g5604.t1.exon5 | 10576411 | 10576691 |
| chr_2 | g5604 | g5604.t1 | cds | g5604.t1.CDS5 | 10576411 | 10576691 |
| chr_2 | g5604 | g5604.t1 | exon | g5604.t1.exon6 | 10576796 | 10576968 |
| chr_2 | g5604 | g5604.t1 | cds | g5604.t1.CDS6 | 10576796 | 10576968 |
| chr_2 | g5604 | g5604.t1 | exon | g5604.t1.exon7 | 10577449 | 10577551 |
| chr_2 | g5604 | g5604.t1 | cds | g5604.t1.CDS7 | 10577449 | 10577551 |
| chr_2 | g5604 | g5604.t1 | exon | g5604.t1.exon8 | 10577674 | 10577946 |
| chr_2 | g5604 | g5604.t1 | cds | g5604.t1.CDS8 | 10577674 | 10577946 |
| chr_2 | g5604 | g5604.t1 | exon | g5604.t1.exon9 | 10578203 | 10578409 |
| chr_2 | g5604 | g5604.t1 | cds | g5604.t1.CDS9 | 10578203 | 10578409 |
| chr_2 | g5604 | g5604.t1 | exon | g5604.t1.exon10 | 10578463 | 10578786 |
| chr_2 | g5604 | g5604.t1 | cds | g5604.t1.CDS10 | 10578463 | 10578786 |
| chr_2 | g5604 | g5604.t1 | exon | g5604.t1.exon11 | 10578838 | 10579120 |
| chr_2 | g5604 | g5604.t1 | cds | g5604.t1.CDS11 | 10578838 | 10579120 |
| chr_2 | g5604 | g5604.t1 | exon | g5604.t1.exon12 | 10579213 | 10579375 |
| chr_2 | g5604 | g5604.t1 | cds | g5604.t1.CDS12 | 10579213 | 10579375 |
| chr_2 | g5604 | g5604.t1 | TTS | g5604.t1 | 10579705 | 10579705 |
| chr_2 | g5604 | g5604.t1 | TSS | g5604.t1 | NA | NA |
Sequences
>g5604.t1 Gene=g5604 Length=3450
ATGGAAAAGATATCAACAACCCCCTTGGCACACAGCAATAACAATAATTTTGCTGGAATT
AGCTCAACCAATACAACGACAGTCGCGTCAAATAAAATTCTCAATCTGCAATTCGATGGT
TTGTCAACGACAGCAAATAGAAACGAAAACTCAGTACGCGCAGTGCCGTTGAGGGCAAAC
TTCAAGAAATCTAATACTTGCGGGAGCCTTTTTGCCAAATGTCACTGTAGTAATCATGTG
CATCATCATTCAACTGTAATTCCATTAATAACTGAAATTGATTGTGATAAAGAACGTTCA
AAGTTGGAACGCAACAGTCGAAAAACACAATCCTTCTCACATCCTGATACACCAGTAATT
TTTACCGAAGAGAATCGGTATCCAGGTAATTGTGATGTTTTATCGCGTTTACGAACATCA
CAAGAGACAATAATTACAACAGACAAGGAGAAAATTGAAATCAAACATTCCTCAAAAAGA
GCTTCATCCCCAAATTTATATGTCAATGGAAATGGCATCGATATTCATCCGGAATTTCAA
GTGCAAGTGAAACCAAAAAGTCCTGTGCCTACAACACCGCCACTTGATTCGGATATCAAT
TCATTATCATCACCACACTCTATTCGACGACCATTTCTAAAGAAAGCATCGAAAAGCTTT
CCACAACAGCGTTCATCGTCCTTCCGCTCATTTGATTCAATTGGCGAGAGAACACGTTCA
TCGTCTTCATATAGCGTCGATGAGACGAGCGAGGAAATTGAATTAAGTGGCAAACTTCAA
TCGAATTTGCTTGTTAGTGAAACGAAAAATTCTTCATCGAAAACTACAACAGTCGCCGAC
ATTCATTGCAGTGAGAACCATCAAATAAATAACAACGACAGTAAATTTGAGAAAGTAGAA
AAGTTACCTAATAGTCCAGTGAATATACAGTCCCAGCCCCATGATAAATCCATTACGGAT
GAAAAATTTTTACAGGCATCCAAAGAGTTTTTAATGCAATCTGGCATCCTCGGACCGATG
GGTAACGTTTCAAGTATTTTAAAGAAATCTTCACGAATTAAGCCAATACTTAGTGATCCA
AACACAAAAGAGCAGATTCGTAAAACATCACTTGTACTTCTTGGACATCGTTATGACATG
AAAAAGAAACGCTCTATTTCAGAGAGTTATGCACAACATCCATTAACGCAAGAAGACTTG
AATTCTATTTCATTACACGAAGAAATTCGACAATTGAAAGAAACCATACAAAATCGTGAT
GAAGAGATTGGCAAGCTTCGACGTGAGATTCACAAATTAAAGAGTGTCTTGCATCAGCAA
GCAAAAAGAAATCTAAAATGTGAATGTCATTTGTCAAGTCCGCAAGCTGCGAATTTTGGA
ATAGTTGGGACGATAACTCAGCAAACATCACCATATGACAGCAAGAATCAAATTGAGAGC
AATGAAAATGCCGCAATGTCTTCCATCACATCAATTGCATCGATGCCACTTCCATCCGAG
CACAATAATCATAATCATCACTTTCATCATCAACATCATCCAAATAATATTAAGAAACAA
GGAGTGAGTGGAGAGAGCTGTGAAAGCAGTTTTATTGGACGTTCGAGTGACATTTTGATA
AGGAAATATGAAAAGGATTTCAAATCGAAACAGCAAATAAAGGATGCAATTTCAGACAAT
GACTTCTTGAAACATCTCGATTGTGTACAAGTACGAGAACTCGTTGAATCAATGTATAGT
CGCGATATTAACGAAGGAGAATACGTCATTCGAGAGAATGAAGCAGGCAATCATCTCTAT
GTGTCGGCAGAGGGCGAATTTGAGATTGAAGTAAATGGAAAAGCTTTGGGAATTTTATCA
TCTGGAAAGGCCTTTGGCGAATTAGCAATTTTATATAATTGCCGACGAACAGCTTCAATT
AGAGCAATAAAGCCAAATTCTCGCGTGTGGGTTCTCGATCGACGTGCCTTTCAGCAAATT
ATGATGCGTACGGGCTTACAACGTATCGAAGAGAACGTCAATTTCCTAAAATCGGTGCCG
TTACTAAAGAACTTGAACGAGGAGGTGCTTAGTAAAATTGCTGACGTACTTGAATTGGAA
TTTTATCCATCTGATGCTTACATCATTCGACAAGGAGCTCGAGGCGACACTTTCTTTTTA
ATTAGTCAAGGTTCAGTTAAAGTCACTCAACGTATACCAGGAAGCTCAAAAGAAGAAGAA
ATAAGAACTCTTGGTCGCGGTGATTACTTTGGTGAACAAGCATTAATAAAAGAAGACAAA
CGAACAGCAAATATTATTGCTTTAAGTCCAGGAGTGGAATGTTTAACTTTAGATCGTGAT
AGCTTCAATCAACATATTGGCGATTTAATTGAACTACATCAAAGAGACTATGGTGACAAG
GATCGAATTTATGCAATTAAAAATCTTAAGAACAAACAAATTCCTATTAACGATCGCAGT
GAATTCCTTAAAGAATATGAGAATATGGAGCTCAAAGATCTGGTTACACTTGCGACTATT
GGAATTGGGGGATTTGGAAGAGTTCTTTTAGTGAAACATTATAATTTTGCAAAAGACTCG
TCAATAAATATTTTTGCTTTGAAACAAATGAAGAAAGCTCATATTGTAGAAACAAAACAG
GAAGAACATGTATTTAATGAGAGAAAAATCATGCTTGCGTGTGCCGATTGTCCTTTCATT
TGTCGTCTCTATCGAACGTTCCGTGATTCAAAATTTATATATCTTTTACTAGAGCCTTGT
TTGGGTGGTGAAGTATGGACAATATTAAGAAATCAAGGACGATTCGATGAGACAACAACA
CAATTTATCATTGGTTGCGTGCTCGAAGCATTCGAATTTCTGCACTCACGTGGAATTATT
TATAGAGATTTAAAGCCTGAAAATTTAATGTTGACCGCCAATGGTTATGTAAAGTTGGTC
GATTTTGGTTTTGCTAAAAGAATTGGTTATTCAAATAAAACTTTTACATTTTGTGGAACT
CCTGAGTATGTTGCACCCGAGATAATTTTGAACAAAGGACATGACAGAGCTGTCGATTGT
TGGGCACTTGGAGTTTTGATATTTGAGCTCATCACAGGAACCCCACCTTTCACATCAAAT
GATCCACTTAAAACTTACAACCTCATTCTTAAAGGCATCGATGCTATCGAATTTCCACGA
CATGTTTCAAGATCTGCTATAAGTTTAATCAAAAAATTATGTAGAGATGTTCCAACAGAG
CGGTTAGGATATCAAAGACATGGCATTTGCGACATACGAAAACAAAAATGGTTTCAAGGA
TTCGATTTTGAGAGCTTATCAAATTTAACATTTAAACCACCACAAATTTCATGCGTAAAT
GGGCCACTAGATCTATCAAATTTTGACACTTTTGTCACCGAATATGAAATGCCACCAGAC
GAGACATCAGGCTGGGATGAATCGTTCTAG
>g5604.t1 Gene=g5604 Length=1149
MEKISTTPLAHSNNNNFAGISSTNTTTVASNKILNLQFDGLSTTANRNENSVRAVPLRAN
FKKSNTCGSLFAKCHCSNHVHHHSTVIPLITEIDCDKERSKLERNSRKTQSFSHPDTPVI
FTEENRYPGNCDVLSRLRTSQETIITTDKEKIEIKHSSKRASSPNLYVNGNGIDIHPEFQ
VQVKPKSPVPTTPPLDSDINSLSSPHSIRRPFLKKASKSFPQQRSSSFRSFDSIGERTRS
SSSYSVDETSEEIELSGKLQSNLLVSETKNSSSKTTTVADIHCSENHQINNNDSKFEKVE
KLPNSPVNIQSQPHDKSITDEKFLQASKEFLMQSGILGPMGNVSSILKKSSRIKPILSDP
NTKEQIRKTSLVLLGHRYDMKKKRSISESYAQHPLTQEDLNSISLHEEIRQLKETIQNRD
EEIGKLRREIHKLKSVLHQQAKRNLKCECHLSSPQAANFGIVGTITQQTSPYDSKNQIES
NENAAMSSITSIASMPLPSEHNNHNHHFHHQHHPNNIKKQGVSGESCESSFIGRSSDILI
RKYEKDFKSKQQIKDAISDNDFLKHLDCVQVRELVESMYSRDINEGEYVIRENEAGNHLY
VSAEGEFEIEVNGKALGILSSGKAFGELAILYNCRRTASIRAIKPNSRVWVLDRRAFQQI
MMRTGLQRIEENVNFLKSVPLLKNLNEEVLSKIADVLELEFYPSDAYIIRQGARGDTFFL
ISQGSVKVTQRIPGSSKEEEIRTLGRGDYFGEQALIKEDKRTANIIALSPGVECLTLDRD
SFNQHIGDLIELHQRDYGDKDRIYAIKNLKNKQIPINDRSEFLKEYENMELKDLVTLATI
GIGGFGRVLLVKHYNFAKDSSINIFALKQMKKAHIVETKQEEHVFNERKIMLACADCPFI
CRLYRTFRDSKFIYLLLEPCLGGEVWTILRNQGRFDETTTQFIIGCVLEAFEFLHSRGII
YRDLKPENLMLTANGYVKLVDFGFAKRIGYSNKTFTFCGTPEYVAPEIILNKGHDRAVDC
WALGVLIFELITGTPPFTSNDPLKTYNLILKGIDAIEFPRHVSRSAISLIKKLCRDVPTE
RLGYQRHGICDIRKQKWFQGFDFESLSNLTFKPPQISCVNGPLDLSNFDTFVTEYEMPPD
ETSGWDESF
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 21 | g5604.t1 | CDD | cd00038 | CAP_ED | 562 | 663 | 2.63072E-24 |
| 20 | g5604.t1 | CDD | cd00038 | CAP_ED | 681 | 784 | 1.71197E-28 |
| 22 | g5604.t1 | CDD | cd05572 | STKc_cGK | 840 | 1104 | 1.20643E-151 |
| 19 | g5604.t1 | Coils | Coil | Coil | 409 | 436 | - |
| 18 | g5604.t1 | Gene3D | G3DSA:2.60.120.10 | Jelly Rolls | 539 | 679 | 2.6E-40 |
| 17 | g5604.t1 | Gene3D | G3DSA:2.60.120.10 | Jelly Rolls | 680 | 814 | 1.2E-39 |
| 15 | g5604.t1 | Gene3D | G3DSA:3.30.200.20 | Phosphorylase Kinase; domain 1 | 832 | 1129 | 6.8E-99 |
| 16 | g5604.t1 | Gene3D | G3DSA:1.10.510.10 | Transferase(Phosphotransferase) domain 1 | 924 | 1118 | 6.8E-99 |
| 32 | g5604.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 184 | 248 | - |
| 31 | g5604.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 193 | 207 | - |
| 33 | g5604.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 218 | 248 | - |
| 4 | g5604.t1 | PANTHER | PTHR24353:SF111 | PROTEIN KINASE CGMP-DEPENDENT 1 | 378 | 1149 | 4.2E-286 |
| 5 | g5604.t1 | PANTHER | PTHR24353 | CYCLIC NUCLEOTIDE-DEPENDENT PROTEIN KINASE | 378 | 1149 | 4.2E-286 |
| 11 | g5604.t1 | PRINTS | PR00104 | cGMP-dependent protein kinase signature | 687 | 701 | 1.3E-17 |
| 9 | g5604.t1 | PRINTS | PR00104 | cGMP-dependent protein kinase signature | 722 | 731 | 1.3E-17 |
| 6 | g5604.t1 | PRINTS | PR00104 | cGMP-dependent protein kinase signature | 740 | 747 | 1.3E-17 |
| 8 | g5604.t1 | PRINTS | PR00104 | cGMP-dependent protein kinase signature | 758 | 767 | 1.3E-17 |
| 7 | g5604.t1 | PRINTS | PR00104 | cGMP-dependent protein kinase signature | 772 | 781 | 1.3E-17 |
| 10 | g5604.t1 | PRINTS | PR00104 | cGMP-dependent protein kinase signature | 782 | 796 | 1.3E-17 |
| 2 | g5604.t1 | Pfam | PF00027 | Cyclic nucleotide-binding domain | 582 | 663 | 1.1E-15 |
| 3 | g5604.t1 | Pfam | PF00027 | Cyclic nucleotide-binding domain | 701 | 784 | 3.8E-18 |
| 1 | g5604.t1 | Pfam | PF00069 | Protein kinase domain | 837 | 1098 | 4.2E-64 |
| 27 | g5604.t1 | ProSitePatterns | PS00889 | Cyclic nucleotide-binding domain signature 2. | 625 | 642 | - |
| 29 | g5604.t1 | ProSitePatterns | PS00888 | Cyclic nucleotide-binding domain signature 1. | 708 | 724 | - |
| 28 | g5604.t1 | ProSitePatterns | PS00889 | Cyclic nucleotide-binding domain signature 2. | 750 | 767 | - |
| 30 | g5604.t1 | ProSitePatterns | PS00107 | Protein kinases ATP-binding region signature. | 840 | 868 | - |
| 26 | g5604.t1 | ProSitePatterns | PS00108 | Serine/Threonine protein kinases active-site signature. | 959 | 971 | - |
| 35 | g5604.t1 | ProSiteProfiles | PS50042 | cAMP/cGMP binding motif profile. | 562 | 678 | 31.768 |
| 36 | g5604.t1 | ProSiteProfiles | PS50042 | cAMP/cGMP binding motif profile. | 681 | 803 | 33.068 |
| 37 | g5604.t1 | ProSiteProfiles | PS50011 | Protein kinase domain profile. | 834 | 1098 | 43.057 |
| 34 | g5604.t1 | ProSiteProfiles | PS51285 | AGC-kinase C-terminal domain profile. | 1099 | 1149 | 8.365 |
| 23 | g5604.t1 | SMART | SM00100 | cnmp_10 | 562 | 676 | 1.3E-17 |
| 24 | g5604.t1 | SMART | SM00100 | cnmp_10 | 681 | 804 | 6.4E-28 |
| 25 | g5604.t1 | SMART | SM00220 | serkin_6 | 834 | 1098 | 5.8E-81 |
| 12 | g5604.t1 | SUPERFAMILY | SSF51206 | cAMP-binding domain-like | 549 | 663 | 2.36E-26 |
| 13 | g5604.t1 | SUPERFAMILY | SSF51206 | cAMP-binding domain-like | 670 | 792 | 5.37E-31 |
| 14 | g5604.t1 | SUPERFAMILY | SSF56112 | Protein kinase-like (PK-like) | 818 | 1140 | 6.54E-80 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5604/g5604.t1; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5604.t1.fa.iupred3.txt does not exist
GO terms from InterProScan
| GOID | TERM | ONTOLOGY |
|---|---|---|
| GO:0005524 | ATP binding | MF |
| GO:0004674 | protein serine/threonine kinase activity | MF |
| GO:0004672 | protein kinase activity | MF |
| GO:0006468 | protein phosphorylation | BP |
| GO:0004692 | cGMP-dependent protein kinase activity | MF |
KEGG
Orthology
- This transcript has been annotated with K07376 (cGMP-dependent protein kinase 1)
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.
