Gene loci information

Transcript annotation

  • This transcript has been annotated as Nucleoside diphosphate kinase.

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 g8645 g8645.t12 TTS g8645.t12 32079417 32079417
chr_2 g8645 g8645.t12 isoform g8645.t12 32079537 32080578
chr_2 g8645 g8645.t12 exon g8645.t12.exon1 32079537 32079590
chr_2 g8645 g8645.t12 cds g8645.t12.CDS1 32079537 32079590
chr_2 g8645 g8645.t12 exon g8645.t12.exon2 32079672 32079865
chr_2 g8645 g8645.t12 cds g8645.t12.CDS2 32079672 32079865
chr_2 g8645 g8645.t12 exon g8645.t12.exon3 32079947 32080031
chr_2 g8645 g8645.t12 cds g8645.t12.CDS3 32079947 32080031
chr_2 g8645 g8645.t12 exon g8645.t12.exon4 32080110 32080358
chr_2 g8645 g8645.t12 cds g8645.t12.CDS4 32080110 32080235
chr_2 g8645 g8645.t12 exon g8645.t12.exon5 32080436 32080578
chr_2 g8645 g8645.t12 TSS g8645.t12 NA NA

Sequences

>g8645.t12 Gene=g8645 Length=725
ATGTCTAAATTGTTAGTTTCATTAACTAAAAATTATAATTCAATTCGGACGGCTCAAGTA
AAATTGTTTTGCAAGCGACGGCGACCTCTCGACGATTCAAGTAATTTTTTTTATTCTCAA
TTGAGTTATTCGCCGAAGAAGAGTTTGATTGCTTTTCTAATACTCGCAAGCTGTGTTCAC
ACATTTTTAGTATATTATTTATATTTCTCTGCTTCAGTCTAAATTTCACTTGCGATCTTG
AAAACGAAAAAAGCAGAAGTAACAACATGGCAAATAATGAAAGAACTTTTATCATGTGCA
AGCCTGATGCCGTTCAACGCGGAATTGTTGGAGAAATAATCAAACGCTTCGAAACAAAAG
GTTTCAAACTCGTTGGAATGAAATTTATGTGGGCATCCAAAGATCTTTTGGAGAAACATT
ATGCCGATTTAAGCTCACGTCCCTTCTTCCCAGGTCTTGTTAATTACATGTCATCAGGTC
CTGTTGTTCCAATGGTTTGGGAAGGATTAAATGCAGTCAAAACAGGCAGAGTTATGTTGG
GAGCAACTAATCCAGCTGATTCAGCACCTGGAACAATCAGAGGAGATTTGTGCGTTCAAG
TTGGTCGTAATATAATCCACGGCTCTGACTCTGTTGAGAGTGCAAAGAAAGAAATCGCAT
TGTGGTTCAATGAGAATGAGTTGGTCAACTGGACACCAGCAGCTGTTAATTGGGTTTATG
AATAA

>g8645.t12 Gene=g8645 Length=152
MANNERTFIMCKPDAVQRGIVGEIIKRFETKGFKLVGMKFMWASKDLLEKHYADLSSRPF
FPGLVNYMSSGPVVPMVWEGLNAVKTGRVMLGATNPADSAPGTIRGDLCVQVGRNIIHGS
DSVESAKKEIALWFNENELVNWTPAAVNWVYE

Protein features from InterProScan

Transcript Database ID Name Start End E.value
14 g8645.t12 CDD cd04413 NDPk_I 5 134 1.55695E-95
13 g8645.t12 Gene3D G3DSA:3.30.70.141 - 1 152 3.2E-67
6 g8645.t12 Hamap MF_00451 Nucleoside diphosphate kinase [ndk]. 4 139 33.824646
2 g8645.t12 PANTHER PTHR11349 NUCLEOSIDE DIPHOSPHATE KINASE 1 64 1.6E-82
4 g8645.t12 PANTHER PTHR11349:SF103 NUCLEOSIDE DIPHOSPHATE KINASE 1 64 1.6E-82
3 g8645.t12 PANTHER PTHR11349 NUCLEOSIDE DIPHOSPHATE KINASE 63 152 1.6E-82
5 g8645.t12 PANTHER PTHR11349:SF103 NUCLEOSIDE DIPHOSPHATE KINASE 63 152 1.6E-82
7 g8645.t12 PRINTS PR01243 Nucleoside diphosphate kinase signature 7 29 9.2E-56
11 g8645.t12 PRINTS PR01243 Nucleoside diphosphate kinase signature 51 70 9.2E-56
8 g8645.t12 PRINTS PR01243 Nucleoside diphosphate kinase signature 71 88 9.2E-56
10 g8645.t12 PRINTS PR01243 Nucleoside diphosphate kinase signature 92 108 9.2E-56
9 g8645.t12 PRINTS PR01243 Nucleoside diphosphate kinase signature 115 134 9.2E-56
1 g8645.t12 Pfam PF00334 Nucleoside diphosphate kinase 5 138 1.5E-54
15 g8645.t12 ProSitePatterns PS00469 Nucleoside diphosphate kinases active site. 115 123 -
16 g8645.t12 SMART SM00562 ndk_5 4 141 4.3E-88
12 g8645.t12 SUPERFAMILY SSF54919 Nucleoside diphosphate kinase, NDK 3 152 1.7E-63

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:0006228 UTP biosynthetic process BP
GO:0006241 CTP biosynthetic process BP
GO:0006165 nucleoside diphosphate phosphorylation BP
GO:0004550 nucleoside diphosphate kinase activity MF
GO:0006183 GTP biosynthetic process BP

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