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.t4 TTS g3839.t4 28313381 28313381
chr_3 g3839 g3839.t4 isoform g3839.t4 28314075 28315654
chr_3 g3839 g3839.t4 exon g3839.t4.exon1 28314075 28314334
chr_3 g3839 g3839.t4 cds g3839.t4.CDS1 28314077 28314334
chr_3 g3839 g3839.t4 exon g3839.t4.exon2 28314391 28314711
chr_3 g3839 g3839.t4 cds g3839.t4.CDS2 28314391 28314711
chr_3 g3839 g3839.t4 exon g3839.t4.exon3 28314771 28315194
chr_3 g3839 g3839.t4 cds g3839.t4.CDS3 28314771 28315194
chr_3 g3839 g3839.t4 exon g3839.t4.exon4 28315262 28315407
chr_3 g3839 g3839.t4 cds g3839.t4.CDS4 28315262 28315407
chr_3 g3839 g3839.t4 exon g3839.t4.exon5 28315613 28315654
chr_3 g3839 g3839.t4 cds g3839.t4.CDS5 28315613 28315654
chr_3 g3839 g3839.t4 TSS g3839.t4 28315775 28315775

Sequences

>g3839.t4 Gene=g3839 Length=1193
ATGGCAATGACTACAAGATTTGCATCGAAAAAACGTGAAGAAAACATCCAACCATTGGTA
GGAAAATTGAAAATGGTTGATACAAAATTGTCTCAAAAAACAGGTCTGGTCGATGAGAAA
CGAAAAGCATTCGGCGAAATACATAACAGACGTGAGATTGGATCTATACTGGACAATAAT
AAGAATGGAATTGAAAAGAAAACTTCACTAGCAAATTCTCTGAGTGTTAATTCTGTCGTG
TATAAGGATATTAAACCTCGCGTTGATACTCGGTGGAAGAAGAAAGAAACGACAGTAGAA
CAAAAACCGAGTGATACTGCTTCAGTTGCCACTCAGACTAAACCTCTTTCACGTCAAAAT
TCAAAGGCCAGTGATTTAACTAAAAAGACGACTAATGTAAAAAGCATTACTGATAAAATT
TCTGCCCAAATTAAGAAAACGACATCAATTGCATCTTCTATTGATTACAAAAGAACTCAA
AATGTGCAAGAAAAGCGAATCGAGAATGTGCCTCTTATCAGATCACCAGCAAAAAGTTTG
ATTAAAAATTTTCATAAACAGGATAGCGGATTACATTTCTTTGAAACTCATTCAACATTT
ATGTTGAATCAAGTTGACAATATTGACGAAACTGATAAAGAAAATCCTCAATTGCTTTCT
GAATACGTTAATGACATTTATGCATATTTGATGAAATTGGAAAAGCAATTTCCGATCCGT
GAAAATTTTTTGGATAATCAAATGGATGTAACACCAAAAATGCGCTCAGTTTTGTTGGAT
TGGATAAGTGAAGTTCATCACCAATTTGGATTGGAAATTGAAACGTTTCACATGGCTGTC
TCGATCGTTGATCGCTATCTTCAAGCGCAACAAGCAACTCCACGACGCTACTTGCAATTA
GTCGGTGTTACAGCTTTATTCATGGCATCTAAGTATGAAGAATTAATGCCACCGGAAATT
TCTGATTTTGTTTATGTAACTGATGATACATATGAAAAGAAACAAATCTTACAAATGGAA
ATGCAAATGTTTAAAACACTTGAATACTCATTGTGTAAGCCTCTTCCTATTCATTTTCTC
AGACGGTTTGCAAAAGCTGCAGGTTCTCTCGGTGATAGACAATACATTGCGGCTAAATAT
TTTATTGAATTGGCAGCTATCGATTACGAACTCACAAAGTACAATCCATCAGA

>g3839.t4 Gene=g3839 Length=397
MAMTTRFASKKREENIQPLVGKLKMVDTKLSQKTGLVDEKRKAFGEIHNRREIGSILDNN
KNGIEKKTSLANSLSVNSVVYKDIKPRVDTRWKKKETTVEQKPSDTASVATQTKPLSRQN
SKASDLTKKTTNVKSITDKISAQIKKTTSIASSIDYKRTQNVQEKRIENVPLIRSPAKSL
IKNFHKQDSGLHFFETHSTFMLNQVDNIDETDKENPQLLSEYVNDIYAYLMKLEKQFPIR
ENFLDNQMDVTPKMRSVLLDWISEVHHQFGLEIETFHMAVSIVDRYLQAQQATPRRYLQL
VGVTALFMASKYEELMPPEISDFVYVTDDTYEKKQILQMEMQMFKTLEYSLCKPLPIHFL
RRFAKAAGSLGDRQYIAAKYFIELAAIDYELTKYNPS

Protein features from InterProScan

Transcript Database ID Name Start End E.value
10 g3839.t4 CDD cd00043 CYCLIN 254 343 2.44812E-22
11 g3839.t4 CDD cd00043 CYCLIN 354 397 0.00191416
8 g3839.t4 Gene3D G3DSA:1.10.472.10 - 240 345 4.9E-37
7 g3839.t4 Gene3D G3DSA:1.10.472.10 - 346 397 3.6E-10
15 g3839.t4 MobiDBLite mobidb-lite consensus disorder prediction 94 127 -
14 g3839.t4 MobiDBLite mobidb-lite consensus disorder prediction 102 127 -
3 g3839.t4 PANTHER PTHR10177:SF193 G2/MITOTIC-SPECIFIC CYCLIN-B1 122 397 2.8E-70
4 g3839.t4 PANTHER PTHR10177 CYCLINS 122 397 2.8E-70
9 g3839.t4 PIRSF PIRSF001771 Cyclin_A_B_D_E 1 397 4.3E-82
1 g3839.t4 Pfam PF00134 Cyclin, N-terminal domain 225 352 9.7E-42
2 g3839.t4 Pfam PF02984 Cyclin, C-terminal domain 354 397 4.5E-7
12 g3839.t4 ProSitePatterns PS00292 Cyclins signature. 255 286 -
13 g3839.t4 SMART SM00385 cyclin_7 260 345 2.0E-25
6 g3839.t4 SUPERFAMILY SSF47954 Cyclin-like 214 351 4.19E-47
5 g3839.t4 SUPERFAMILY SSF47954 Cyclin-like 354 397 1.63E-6

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