General information for g2875.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Cyclin-dependent kinase 2.
Parent gene
- The parent gene g2875 is located on chr_3: 20835156..20835654 (+ 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_3 | g2875 | g2875.t1 | isoform | g2875.t1 | 20834302 | 20835654 |
| chr_3 | g2875 | g2875.t1 | exon | g2875.t1.exon1 | 20834302 | 20834346 |
| chr_3 | g2875 | g2875.t1 | cds | g2875.t1.CDS1 | 20834302 | 20834346 |
| chr_3 | g2875 | g2875.t1 | exon | g2875.t1.exon2 | 20834454 | 20834542 |
| chr_3 | g2875 | g2875.t1 | cds | g2875.t1.CDS2 | 20834454 | 20834542 |
| chr_3 | g2875 | g2875.t1 | exon | g2875.t1.exon3 | 20834774 | 20835087 |
| chr_3 | g2875 | g2875.t1 | cds | g2875.t1.CDS3 | 20834774 | 20835087 |
| chr_3 | g2875 | g2875.t1 | exon | g2875.t1.exon4 | 20835152 | 20835654 |
| chr_3 | g2875 | g2875.t1 | cds | g2875.t1.CDS4 | 20835152 | 20835654 |
| chr_3 | g2875 | g2875.t1 | TSS | g2875.t1 | NA | NA |
| chr_3 | g2875 | g2875.t1 | TTS | g2875.t1 | NA | NA |
Sequences
>g2875.t1 Gene=g2875 Length=951
ATGAATGATCTTAATCATCTTCCGTCGTTCCAGAAAATTGAAAAAATTGGAGAAGGGACT
TATGGAATCGTTTATCGCGCAAAACACAAACACAATGGCATTGATGTAGCATTGAAAAAG
ATTCGATTAGAAAGTGAAACTGAAGGCATACCTTCTACAGCAATGCGAGAAATATCTTTA
CTGAAAAATATAAAGCATCACTCTATCGTACAATTGTTTGATGTAATTGTAGCCGGTGGT
TGTATATATATGGTATTTGAATATCTTGACATGGATTTAAAGAAGTTGTTAGATCGTAAA
AAGAGCATGCTGACGCCAAAACTCGTTAAGAGCTACATGCATCAATTACTCGAAGCCATA
GATTATTGTCACATGAATAGAATTTTACATAGAGATTTAAAACCACAAAATTTGTTACTC
GATTGCGCTGGTCACATCAAATTAGCTGATTTCGGTTTAGCCCGCACTTTCAATATTCCT
CTTCGAGCATATACACATGAAGTTGTAACACTATGGTATCGAGCTCCTGAAATTTTACTT
GGATGTAAATTATATTCAACAGGCGTTGATTTATGGAGTCTTGGATGCATATTTGCTGAA
ATGATGATGCTAAGACCAATGTTTCAAGGTGATAGCGAGATTGATCAATTATATAGAATA
TTTAGACAATTTGGAACGCCTGATGAAACTACTTGGAAAAATATACGCCATTTGCCTGAT
TACAAGCCATCATTTCCAAAGTGGGAAAGACAAGTGTTACCTCATCGCTTTTATTCAGAC
AACAATGCTGTAGAGTTGTTTCTAGCAATGACAAAATACGATCCTGATCAGAGAATATCA
GCTAAAGATGCATTAGCACATAAATATTTTGATAATGTAGCCTTAATACCAGTAGAACTT
CCTTTACCACCCGGCACACAGAAATCAAATACTTCTTCATATCTTTTGTGA
>g2875.t1 Gene=g2875 Length=316
MNDLNHLPSFQKIEKIGEGTYGIVYRAKHKHNGIDVALKKIRLESETEGIPSTAMREISL
LKNIKHHSIVQLFDVIVAGGCIYMVFEYLDMDLKKLLDRKKSMLTPKLVKSYMHQLLEAI
DYCHMNRILHRDLKPQNLLLDCAGHIKLADFGLARTFNIPLRAYTHEVVTLWYRAPEILL
GCKLYSTGVDLWSLGCIFAEMMMLRPMFQGDSEIDQLYRIFRQFGTPDETTWKNIRHLPD
YKPSFPKWERQVLPHRFYSDNNAVELFLAMTKYDPDQRISAKDALAHKYFDNVALIPVEL
PLPPGTQKSNTSSYLL
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 5 | g2875.t1 | Gene3D | G3DSA:3.30.200.20 | Phosphorylase Kinase; domain 1 | 3 | 89 | 7.1E-31 |
| 6 | g2875.t1 | Gene3D | G3DSA:1.10.510.10 | Transferase(Phosphotransferase) domain 1 | 93 | 295 | 1.9E-67 |
| 2 | g2875.t1 | PANTHER | PTHR24056:SF371 | CYCLIN-DEPENDENT KINASE A-2 | 9 | 295 | 5.9E-112 |
| 3 | g2875.t1 | PANTHER | PTHR24056 | CELL DIVISION PROTEIN KINASE | 9 | 295 | 5.9E-112 |
| 1 | g2875.t1 | Pfam | PF00069 | Protein kinase domain | 10 | 290 | 7.4E-74 |
| 8 | g2875.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 1 | 68 | - |
| 9 | g2875.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 69 | 89 | - |
| 7 | g2875.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 90 | 316 | - |
| 11 | g2875.t1 | ProSitePatterns | PS00107 | Protein kinases ATP-binding region signature. | 16 | 39 | - |
| 10 | g2875.t1 | ProSitePatterns | PS00108 | Serine/Threonine protein kinases active-site signature. | 128 | 140 | - |
| 13 | g2875.t1 | ProSiteProfiles | PS50011 | Protein kinase domain profile. | 10 | 290 | 47.665 |
| 12 | g2875.t1 | SMART | SM00220 | serkin_6 | 10 | 290 | 6.9E-97 |
| 4 | g2875.t1 | SUPERFAMILY | SSF56112 | Protein kinase-like (PK-like) | 5 | 294 | 4.59E-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:0005524 | ATP binding | MF |
| GO:0004672 | protein kinase activity | MF |
| GO:0006468 | protein phosphorylation | BP |
KEGG
Orthology
- This transcript has been annotated with K02206 (cyclin-dependent kinase 2)
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.
