Gene loci information

Transcript annotation

  • This transcript has been annotated as G2/mitotic-specific cyclin-B.

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_3 g3839 g3839.t3 TTS g3839.t3 28313381 28313381
chr_3 g3839 g3839.t3 isoform g3839.t3 28314075 28314773
chr_3 g3839 g3839.t3 exon g3839.t3.exon1 28314075 28314334
chr_3 g3839 g3839.t3 cds g3839.t3.CDS1 28314077 28314334
chr_3 g3839 g3839.t3 exon g3839.t3.exon2 28314391 28314711
chr_3 g3839 g3839.t3 cds g3839.t3.CDS2 28314391 28314633
chr_3 g3839 g3839.t3 exon g3839.t3.exon3 28314771 28314773
chr_3 g3839 g3839.t3 TSS g3839.t3 28315409 28315409

Sequences

>g3839.t3 Gene=g3839 Length=584
CAAGTTGACAATATTGACGAAACTGATAAAGAAAATCCTCAATTGCTTTCTGAATACGTT
AATGACATTTATGCATATTTGATGAAATTGGAAAAGCAATTTCCGATCCGTGAAAATTTT
TTGGATAATCAAATGGATGTAACACCAAAAATGCGCTCAGTTTTGTTGGATTGGATAAGT
GAAGTTCATCACCAATTTGGATTGGAAATTGAAACGTTTCACATGGCTGTCTCGATCGTT
GATCGCTATCTTCAAGCGCAACAAGCAACTCCACGACGCTACTTGCAATTAGTCGGTGTT
ACAGCTTTATTCATGGCATCTAAGTATGAAGAATTAATGCCACCGGAAATTTCTGATTTT
GTTTATGTAACTGATGATACATATGAAAAGAAACAAATCTTACAAATGGAAATGCAAATG
TTTAAAACACTTGAATACTCATTGTGTAAGCCTCTTCCTATTCATTTTCTCAGACGGTTT
GCAAAAGCTGCAGGTTCTCTCGGTGATAGACAATACATTGCGGCTAAATATTTTATTGAA
TTGGCAGCTATCGATTACGAACTCACAAAGTACAATCCATCAGA

>g3839.t3 Gene=g3839 Length=167
MKLEKQFPIRENFLDNQMDVTPKMRSVLLDWISEVHHQFGLEIETFHMAVSIVDRYLQAQ
QATPRRYLQLVGVTALFMASKYEELMPPEISDFVYVTDDTYEKKQILQMEMQMFKTLEYS
LCKPLPIHFLRRFAKAAGSLGDRQYIAAKYFIELAAIDYELTKYNPS

Protein features from InterProScan

Transcript Database ID Name Start End E.value
12 g3839.t3 CDD cd00043 CYCLIN 24 113 7.17636E-22
11 g3839.t3 CDD cd00043 CYCLIN 124 167 0.00383172
10 g3839.t3 Gene3D G3DSA:1.10.472.10 - 10 115 6.3E-38
9 g3839.t3 Gene3D G3DSA:1.10.472.10 - 116 167 8.2E-11
3 g3839.t3 PANTHER PTHR10177:SF193 G2/MITOTIC-SPECIFIC CYCLIN-B1 2 167 1.3E-55
4 g3839.t3 PANTHER PTHR10177 CYCLINS 2 167 1.3E-55
1 g3839.t3 Pfam PF00134 Cyclin, N-terminal domain 3 122 1.2E-40
2 g3839.t3 Pfam PF02984 Cyclin, C-terminal domain 124 167 1.2E-7
8 g3839.t3 ProSitePatterns PS00292 Cyclins signature. 25 56 -
7 g3839.t3 SMART SM00385 cyclin_7 30 115 2.0E-25
6 g3839.t3 SUPERFAMILY SSF47954 Cyclin-like 2 121 9.41E-42
5 g3839.t3 SUPERFAMILY SSF47954 Cyclin-like 124 167 4.22E-7

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

GO terms from InterProScan

There are no GO annotations for this transcript.

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