Gene loci information

Transcript annotation

  • This transcript has been annotated as hypothetical.

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 g9907 g9907.t4 TTS g9907.t4 5939142 5939142
chr_1 g9907 g9907.t4 isoform g9907.t4 5939299 5939948
chr_1 g9907 g9907.t4 exon g9907.t4.exon1 5939299 5939795
chr_1 g9907 g9907.t4 cds g9907.t4.CDS1 5939299 5939649
chr_1 g9907 g9907.t4 exon g9907.t4.exon2 5939862 5939948
chr_1 g9907 g9907.t4 TSS g9907.t4 5940329 5940329

Sequences

>g9907.t4 Gene=g9907 Length=584
ATTCGAAAAGTTGCAATAGTAATGCAGTAGTTAGTCGAACTAATAGTAATGATGTAAAAA
TTAAGATAGAAAAAACAGATGATTTCGATATAAAAAGAGAACCATTAGATATTCCCAATG
GAATAAAAATTAAAATTGAACCAGGACTAGAGACTGAAACATCAATAGAATCGCCTCCTC
CACCAATACATGAATTGTTCAATGCAGATTCAAGTCAAATATTTCTTTTTCAAATGCCAG
ATTCAATACCAGGACAAACATCTGAAGATGATGATTCATCAAAACCATGTACTAGTGCAG
AAGCAACCACTAAACCAAAATCAAGATTTTGCACACTCGAACATTTAGAAGAGGGGCCAA
TAGGGAAATTAATAAGGCACAAATCAGGAAAAATAAAATTGAAAATTGGTGACGCTGTCT
TTGACATTGATCCTGCACTAAAATGTGATTTTATTCAAAATGCTGTCACAATTGATTCCA
ATCCACAACAACGTAGTGCAAACATGTACAGTTTAGGAAAAATTCAAACAAAATACAATG
TTTCTCCTGATTGGAATTGGTTTTTTGAAAATTTAAAGTCCTAG

>g9907.t4 Gene=g9907 Length=116
MPDSIPGQTSEDDDSSKPCTSAEATTKPKSRFCTLEHLEEGPIGKLIRHKSGKIKLKIGD
AVFDIDPALKCDFIQNAVTIDSNPQQRSANMYSLGKIQTKYNVSPDWNWFFENLKS

Protein features from InterProScan

Transcript Database ID Name Start End E.value
4 g9907.t4 MobiDBLite mobidb-lite consensus disorder prediction 1 26 -
2 g9907.t4 PANTHER PTHR13408:SF0 DNA-DIRECTED RNA POLYMERASE III SUBUNIT RPC4 1 110 9.5E-26
3 g9907.t4 PANTHER PTHR13408 DNA-DIRECTED RNA POLYMERASE III 1 110 9.5E-26
1 g9907.t4 Pfam PF05132 RNA polymerase III RPC4 8 107 3.7E-25

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:0003677 DNA binding MF
GO:0005666 RNA polymerase III complex CC
GO:0006383 transcription by RNA polymerase III BP

KEGG

Orthology

This gene did not have any KEGG ortholog annotations (KAAS, GHOSTZ).

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