Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative DNA-directed RNA polymerase III subunit RPC10.

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_1 g10337 g10337.t1 TTS g10337.t1 8936814 8936814
chr_1 g10337 g10337.t1 isoform g10337.t1 8937700 8938102
chr_1 g10337 g10337.t1 exon g10337.t1.exon1 8937700 8937944
chr_1 g10337 g10337.t1 cds g10337.t1.CDS1 8937700 8937944
chr_1 g10337 g10337.t1 exon g10337.t1.exon2 8938021 8938102
chr_1 g10337 g10337.t1 cds g10337.t1.CDS2 8938021 8938102
chr_1 g10337 g10337.t1 TSS g10337.t1 8938224 8938224

Sequences

>g10337.t1 Gene=g10337 Length=327
ATGCTTTTATTCTGTCCAATCTGCTCCAATCTTTTATTGACGGAATTCTCTTCAACGTGC
TTGCGTTTATCGTGTTCTACTTGTCCTTATATCTCTCGAATTAAGAAAAAGATTTCAGAG
AGAACATATCCTAAACTCAAAGAAGTAGACCATGTTATGGGCGGATCAGAAGCTTGGAAA
AACGTAGATTCAACAGATGCCGTTTGCCCAACTTGCAATCATCCCAAAGCCTATTTCATG
CAAATGCAAATTCGAAGTGCTGATGAACCAATGACAACGTTCTACAGATGCTGTAATCCG
ACCTGTAATCATAATTGGCGGGATTAA

>g10337.t1 Gene=g10337 Length=108
MLLFCPICSNLLLTEFSSTCLRLSCSTCPYISRIKKKISERTYPKLKEVDHVMGGSEAWK
NVDSTDAVCPTCNHPKAYFMQMQIRSADEPMTTFYRCCNPTCNHNWRD

Protein features from InterProScan

Transcript Database ID Name Start End E.value
13 g10337.t1 CDD cd10509 Zn-ribbon_RPC11 61 108 7.59384E-28
6 g10337.t1 Gene3D G3DSA:2.20.25.10 - 55 108 2.8E-23
2 g10337.t1 PANTHER PTHR11239 DNA-DIRECTED RNA POLYMERASE 3 107 1.8E-37
3 g10337.t1 PANTHER PTHR11239:SF12 DNA-DIRECTED RNA POLYMERASE III SUBUNIT RPC10 3 107 1.8E-37
12 g10337.t1 PIRSF PIRSF005586 RNApol_RpoM 2 108 6.3E-29
1 g10337.t1 Pfam PF01096 Transcription factor S-II (TFIIS) 68 107 1.5E-19
8 g10337.t1 Phobius SIGNAL_PEPTIDE Signal peptide region 1 22 -
9 g10337.t1 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide. 1 1 -
10 g10337.t1 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide. 2 13 -
11 g10337.t1 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide. 14 22 -
7 g10337.t1 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 23 108 -
16 g10337.t1 ProSitePatterns PS00466 Zinc finger TFIIS-type signature. 69 106 -
17 g10337.t1 ProSiteProfiles PS51133 Zinc finger TFIIS-type profile. 65 107 15.358
15 g10337.t1 SMART SM00661 rpol9cneu 3 52 4.3E-5
14 g10337.t1 SMART SM00440 Cys4_2 67 108 4.6E-18
4 g10337.t1 SUPERFAMILY SSF57783 Zinc beta-ribbon 45 108 6.8E-22
5 g10337.t1 SignalP_EUK SignalP-noTM SignalP-noTM 1 16 -

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:0042779 tRNA 3’-trailer cleavage BP
GO:0008270 zinc ion binding MF
GO:0006351 transcription, DNA-templated BP
GO:0003676 nucleic acid binding 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