Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative Cyclin-H.

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 g13652 g13652.t5 TSS g13652.t5 31413137 31413137
chr_1 g13652 g13652.t5 isoform g13652.t5 31413360 31414195
chr_1 g13652 g13652.t5 exon g13652.t5.exon1 31413360 31414195
chr_1 g13652 g13652.t5 cds g13652.t5.CDS1 31413452 31414195
chr_1 g13652 g13652.t5 TTS g13652.t5 NA NA

Sequences

>g13652.t5 Gene=g13652 Length=836
AAGCTTTTTTCTTGAATCCATATGAAGAAAGCATATTATTGAGGCAATATGAGCTTCAAC
TTAGAGAGTTTTGTAAGCGCTTTGAACCACCAATGCCAAAATACACAATCGGAACTGTTA
TTCAGTATTTTAAACGATTCTATCTTTATAACTCAACAATGAACTATCATCCTAAAGAAA
TATTAGCTACATGTGTTTATCTTTCTTGTAAAGTTGAAGAGTTTAATGTGTCGATTCAAC
AGTTTGTTGCAAATGTCAAAGGCGATAGAAATAAAGCCATGGACATTATTTTAAGCAATG
AACTGTTGTTAATGCAAGAATTAAATTTCAATCTCACAATTCATAATTCATTTAGACCTG
TCGAAGGCTTTTTAATTGATATAAAAACCAGATGTCATATGCAAAATCCAGATAGATTGA
GAAAAGGAATTGATGAATTTTTAGAAAAATCGTTTTTCACTGACGCATGTCTCATCTATT
CACCATCACAAATTGCTTTAGCTGCTGTGCTTCATGCTGCAAGTAAAGAACAAGAAAATC
TCGATTCATATGTTACAGAGTGTCTTTTTGCTAATGCGGGACAAATGTTAAAGCCTCTCA
TAGAAGCTGTTCGAAAGATTCGTTCGATGGTAAAAAATATTTCAGAGATGCCTGACAAAA
ATGTAATTAAAGCACTTGAAAAGAAACTCGAAAGATGCAGAAATCAAGCAAACAATCCTG
ATAGTGATGAATATAAGCAGAGGCAAATTAGAGAATTAAATGATGAAGATGACGACGGTT
TATTACCACAGCAGGATGAAGATGTTTCTATGTTAAATGCTTCAAATTTTGATTGA

>g13652.t5 Gene=g13652 Length=247
MPKYTIGTVIQYFKRFYLYNSTMNYHPKEILATCVYLSCKVEEFNVSIQQFVANVKGDRN
KAMDIILSNELLLMQELNFNLTIHNSFRPVEGFLIDIKTRCHMQNPDRLRKGIDEFLEKS
FFTDACLIYSPSQIALAAVLHAASKEQENLDSYVTECLFANAGQMLKPLIEAVRKIRSMV
KNISEMPDKNVIKALEKKLERCRNQANNPDSDEYKQRQIRELNDEDDDGLLPQQDEDVSM
LNASNFD

Protein features from InterProScan

Transcript Database ID Name Start End E.value
9 g13652.t5 CDD cd00043 CYCLIN 1 74 1.89087E-10
7 g13652.t5 Gene3D G3DSA:1.10.472.10 - 1 82 4.1E-20
8 g13652.t5 Gene3D G3DSA:1.10.472.10 - 84 182 2.1E-28
11 g13652.t5 MobiDBLite mobidb-lite consensus disorder prediction 203 247 -
12 g13652.t5 MobiDBLite mobidb-lite consensus disorder prediction 203 227 -
3 g13652.t5 PANTHER PTHR10026:SF8 CYCLIN-H 2 234 2.6E-52
4 g13652.t5 PANTHER PTHR10026 CYCLIN 2 234 2.6E-52
1 g13652.t5 Pfam PF00134 Cyclin, N-terminal domain 4 82 1.2E-9
2 g13652.t5 Pfam PF16899 Cyclin C-terminal domain 86 181 1.2E-20
10 g13652.t5 SMART SM00385 cyclin_7 1 75 0.0016
5 g13652.t5 SUPERFAMILY SSF47954 Cyclin-like 1 84 9.4E-24
6 g13652.t5 SUPERFAMILY SSF47954 Cyclin-like 87 205 6.38E-30
13 g13652.t5 TIGRFAM TIGR00569 ccl1: cyclin ccl1 1 222 4.5E-84

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:0006357 regulation of transcription by RNA polymerase II BP
GO:0070985 transcription factor TFIIK complex CC
GO:0016538 cyclin-dependent protein serine/threonine kinase regulator activity MF
GO:0006351 transcription, DNA-templated 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