General information for g7540.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Thymidylate kinase.
Parent gene
- The parent gene g7540 is located on chr_2: 24388843..24389532 (- 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 | g7540 | g7540.t1 | TTS | g7540.t1 | 24388749 | 24388749 |
| chr_2 | g7540 | g7540.t1 | isoform | g7540.t1 | 24388843 | 24389532 |
| chr_2 | g7540 | g7540.t1 | exon | g7540.t1.exon1 | 24388843 | 24389201 |
| chr_2 | g7540 | g7540.t1 | cds | g7540.t1.CDS1 | 24388843 | 24389201 |
| chr_2 | g7540 | g7540.t1 | exon | g7540.t1.exon2 | 24389265 | 24389532 |
| chr_2 | g7540 | g7540.t1 | cds | g7540.t1.CDS2 | 24389265 | 24389532 |
| chr_2 | g7540 | g7540.t1 | TSS | g7540.t1 | 24389586 | 24389586 |
Sequences
>g7540.t1 Gene=g7540 Length=627
ATGTACATAAAGAGAGGAGCATTGATAGTTTTTGAAGGTGTTGATCGTGCAGGAAAAACA
ACACAATGCAAAAAGCTTGTCGAACGGCTACTAAGTCAGAATATAAAAGCAAAATTCATG
AATTTTCCGAACAGAACAACAAAAACTGGTCAAATTATTGACGAATATTTAAGAAATAAA
ACGGATCTGACAGATGAAGGCATTCATCTACTCTTTACAGTAAATCGATGGGAAGCTCGA
AATGAAATGGAGAAAGAATTAAATGCTGGTACAACTATAATTGTTGACCGTTATTCATAC
TCTGGTGTCGCATTCACAGCTGCAAAAGGACTTGATTTTGAGTGGTGCAAGATGCCTGAA
AAAGGTTTGATAAGACCAGATATGGTTGTTTATTTAACTTTAAATCAAGAGGCAATGGCA
AGAAGAGGAGGTTTTGGTGGTGAAAGATATGAAACTAATGATTTTCAGAAAAATGTGAGG
AAGATTTATGAAAGACTCATTGAGCGTCCTTTATGGCAAATCATTGATGCAGATAAAACT
GAAGATGAGCTTAGTGATGAATTGGAGCAATTAATTAGGAGGAAAATTGAAGAGACCGGT
GATCAACCATTACAATTATTGTGGTAG
>g7540.t1 Gene=g7540 Length=208
MYIKRGALIVFEGVDRAGKTTQCKKLVERLLSQNIKAKFMNFPNRTTKTGQIIDEYLRNK
TDLTDEGIHLLFTVNRWEARNEMEKELNAGTTIIVDRYSYSGVAFTAAKGLDFEWCKMPE
KGLIRPDMVVYLTLNQEAMARRGGFGGERYETNDFQKNVRKIYERLIERPLWQIIDADKT
EDELSDELEQLIRRKIEETGDQPLQLLW
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g7540.t1 | CDD | cd01672 | TMPK | 8 | 193 | 2.54404E-28 |
| 7 | g7540.t1 | Coils | Coil | Coil | 174 | 194 | - |
| 6 | g7540.t1 | Gene3D | G3DSA:3.40.50.300 | - | 1 | 208 | 1.4E-66 |
| 4 | g7540.t1 | Hamap | MF_00165 | Thymidylate kinase [tmk]. | 7 | 196 | 15.267337 |
| 2 | g7540.t1 | PANTHER | PTHR10344 | THYMIDYLATE KINASE | 3 | 202 | 2.2E-78 |
| 3 | g7540.t1 | PANTHER | PTHR10344:SF1 | THYMIDYLATE KINASE | 3 | 202 | 2.2E-78 |
| 1 | g7540.t1 | Pfam | PF02223 | Thymidylate kinase | 11 | 187 | 5.4E-43 |
| 9 | g7540.t1 | ProSitePatterns | PS01331 | Thymidylate kinase signature. | 94 | 106 | - |
| 5 | g7540.t1 | SUPERFAMILY | SSF52540 | P-loop containing nucleoside triphosphate hydrolases | 1 | 198 | 8.42E-43 |
| 10 | g7540.t1 | TIGRFAM | TIGR00041 | DTMP_kinase: dTMP kinase | 3 | 186 | 6.9E-37 |
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:0004798 | thymidylate kinase activity | MF |
| GO:0005524 | ATP binding | MF |
| GO:0006233 | dTDP biosynthetic process | BP |
KEGG
Orthology
- This transcript has been annotated with K00943 (dTMP kinase)
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.
