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.t1 TTS g3839.t1 28313381 28313381
chr_3 g3839 g3839.t1 isoform g3839.t1 28313741 28315654
chr_3 g3839 g3839.t1 exon g3839.t1.exon1 28313741 28314013
chr_3 g3839 g3839.t1 cds g3839.t1.CDS1 28313741 28314013
chr_3 g3839 g3839.t1 exon g3839.t1.exon2 28314074 28314334
chr_3 g3839 g3839.t1 cds g3839.t1.CDS2 28314074 28314334
chr_3 g3839 g3839.t1 exon g3839.t1.exon3 28314391 28314711
chr_3 g3839 g3839.t1 cds g3839.t1.CDS3 28314391 28314711
chr_3 g3839 g3839.t1 exon g3839.t1.exon4 28314771 28315194
chr_3 g3839 g3839.t1 cds g3839.t1.CDS4 28314771 28315194
chr_3 g3839 g3839.t1 exon g3839.t1.exon5 28315262 28315407
chr_3 g3839 g3839.t1 cds g3839.t1.CDS5 28315262 28315407
chr_3 g3839 g3839.t1 exon g3839.t1.exon6 28315613 28315654
chr_3 g3839 g3839.t1 cds g3839.t1.CDS6 28315613 28315654
chr_3 g3839 g3839.t1 TSS g3839.t1 28315775 28315775

Sequences

>g3839.t1 Gene=g3839 Length=1467
ATGGCAATGACTACAAGATTTGCATCGAAAAAACGTGAAGAAAACATCCAACCATTGGTA
GGAAAATTGAAAATGGTTGATACAAAATTGTCTCAAAAAACAGGTCTGGTCGATGAGAAA
CGAAAAGCATTCGGCGAAATACATAACAGACGTGAGATTGGATCTATACTGGACAATAAT
AAGAATGGAATTGAAAAGAAAACTTCACTAGCAAATTCTCTGAGTGTTAATTCTGTCGTG
TATAAGGATATTAAACCTCGCGTTGATACTCGGTGGAAGAAGAAAGAAACGACAGTAGAA
CAAAAACCGAGTGATACTGCTTCAGTTGCCACTCAGACTAAACCTCTTTCACGTCAAAAT
TCAAAGGCCAGTGATTTAACTAAAAAGACGACTAATGTAAAAAGCATTACTGATAAAATT
TCTGCCCAAATTAAGAAAACGACATCAATTGCATCTTCTATTGATTACAAAAGAACTCAA
AATGTGCAAGAAAAGCGAATCGAGAATGTGCCTCTTATCAGATCACCAGCAAAAAGTTTG
ATTAAAAATTTTCATAAACAGGATAGCGGATTACATTTCTTTGAAACTCATTCAACATTT
ATGTTGAATCAAGTTGACAATATTGACGAAACTGATAAAGAAAATCCTCAATTGCTTTCT
GAATACGTTAATGACATTTATGCATATTTGATGAAATTGGAAAAGCAATTTCCGATCCGT
GAAAATTTTTTGGATAATCAAATGGATGTAACACCAAAAATGCGCTCAGTTTTGTTGGAT
TGGATAAGTGAAGTTCATCACCAATTTGGATTGGAAATTGAAACGTTTCACATGGCTGTC
TCGATCGTTGATCGCTATCTTCAAGCGCAACAAGCAACTCCACGACGCTACTTGCAATTA
GTCGGTGTTACAGCTTTATTCATGGCATCTAAGTATGAAGAATTAATGCCACCGGAAATT
TCTGATTTTGTTTATGTAACTGATGATACATATGAAAAGAAACAAATCTTACAAATGGAA
ATGCAAATGTTTAAAACACTTGAATACTCATTGTGTAAGCCTCTTCCTATTCATTTTCTC
AGACGGTTTGCAAAAGCTGCAGGTTCTCTCGGTGATAGACAATACATTGCGGCTAAATAT
TTTATTGAATTGGCAGCTATCGATTACGAACTCACAAAGTACAATCCATCAGAGATTGCC
GCTGCTGCAATTTATTTATCACTTTTTATAACAAACAAAATGAAGAGCGATAATGATCTT
TGGACACCAACATTGCAATTCTATTCTACTTATAAAATCGAAAACATAATGCCTGTGGTT
AAACGTTTAGCTCTCCTTGTTTCAACTGCACATGAAGTAAAACTGAAGTCCGTTTATACC
AAGTATGCACATGCACATTTTAAGTTCACCTCAACAATGTCTGAAATGACAGGCTCAAAA
ATTCGCGAATTGGCAAGATATGCTTAA

>g3839.t1 Gene=g3839 Length=488
MAMTTRFASKKREENIQPLVGKLKMVDTKLSQKTGLVDEKRKAFGEIHNRREIGSILDNN
KNGIEKKTSLANSLSVNSVVYKDIKPRVDTRWKKKETTVEQKPSDTASVATQTKPLSRQN
SKASDLTKKTTNVKSITDKISAQIKKTTSIASSIDYKRTQNVQEKRIENVPLIRSPAKSL
IKNFHKQDSGLHFFETHSTFMLNQVDNIDETDKENPQLLSEYVNDIYAYLMKLEKQFPIR
ENFLDNQMDVTPKMRSVLLDWISEVHHQFGLEIETFHMAVSIVDRYLQAQQATPRRYLQL
VGVTALFMASKYEELMPPEISDFVYVTDDTYEKKQILQMEMQMFKTLEYSLCKPLPIHFL
RRFAKAAGSLGDRQYIAAKYFIELAAIDYELTKYNPSEIAAAAIYLSLFITNKMKSDNDL
WTPTLQFYSTYKIENIMPVVKRLALLVSTAHEVKLKSVYTKYAHAHFKFTSTMSEMTGSK
IRELARYA

Protein features from InterProScan

Transcript Database ID Name Start End E.value
11 g3839.t1 CDD cd00043 CYCLIN 254 343 1.8001E-21
10 g3839.t1 CDD cd00043 CYCLIN 354 443 2.00037E-11
8 g3839.t1 Gene3D G3DSA:1.10.472.10 - 225 469 3.4E-85
7 g3839.t1 Gene3D G3DSA:1.10.472.10 - 239 352 3.4E-85
17 g3839.t1 MobiDBLite mobidb-lite consensus disorder prediction 94 127 -
16 g3839.t1 MobiDBLite mobidb-lite consensus disorder prediction 102 127 -
3 g3839.t1 PANTHER PTHR10177:SF193 G2/MITOTIC-SPECIFIC CYCLIN-B1 121 485 5.2E-83
4 g3839.t1 PANTHER PTHR10177 CYCLINS 121 485 5.2E-83
9 g3839.t1 PIRSF PIRSF001771 Cyclin_A_B_D_E 1 486 2.3E-103
1 g3839.t1 Pfam PF00134 Cyclin, N-terminal domain 225 352 1.4E-41
2 g3839.t1 Pfam PF02984 Cyclin, C-terminal domain 354 475 2.7E-28
12 g3839.t1 ProSitePatterns PS00292 Cyclins signature. 255 286 -
14 g3839.t1 SMART SM00385 cyclin_7 260 345 2.0E-25
13 g3839.t1 SMART SM01332 Cyclin_C_2 354 476 1.9E-27
15 g3839.t1 SMART SM00385 cyclin_7 358 445 3.5E-11
6 g3839.t1 SUPERFAMILY SSF47954 Cyclin-like 214 351 4.35E-47
5 g3839.t1 SUPERFAMILY SSF47954 Cyclin-like 354 474 1.25E-29

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

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