Gene loci information

Transcript annotation

  • This transcript has been annotated as Cyclin-T.

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_2 g7980 g7980.t1 TSS g7980.t1 27457718 27457718
chr_2 g7980 g7980.t1 isoform g7980.t1 27457821 27460106
chr_2 g7980 g7980.t1 exon g7980.t1.exon1 27457821 27457960
chr_2 g7980 g7980.t1 cds g7980.t1.CDS1 27457821 27457960
chr_2 g7980 g7980.t1 TTS g7980.t1 27458189 27458189
chr_2 g7980 g7980.t1 exon g7980.t1.exon2 27458359 27458476
chr_2 g7980 g7980.t1 cds g7980.t1.CDS2 27458359 27458476
chr_2 g7980 g7980.t1 exon g7980.t1.exon3 27458590 27458800
chr_2 g7980 g7980.t1 cds g7980.t1.CDS3 27458590 27458800
chr_2 g7980 g7980.t1 exon g7980.t1.exon4 27458880 27459016
chr_2 g7980 g7980.t1 cds g7980.t1.CDS4 27458880 27459016
chr_2 g7980 g7980.t1 exon g7980.t1.exon5 27459085 27459249
chr_2 g7980 g7980.t1 cds g7980.t1.CDS5 27459085 27459249
chr_2 g7980 g7980.t1 exon g7980.t1.exon6 27459309 27460106
chr_2 g7980 g7980.t1 cds g7980.t1.CDS6 27459309 27460106

Sequences

>g7980.t1 Gene=g7980 Length=1569
ATGAGTGAAAAATGGTACTTCACAGAAGAACAGTTAGCAAACTCGCCAAGTCGACGAACA
GGAATAAACGCAGAAATGGAACTTTCTTACAGACAAAGAGCTGCAAATCTGATCCAAGAA
ATGGGACAGCGATTACAAGTATCACAACTCTGCATAAATACAGCAATTGTGTATATGCAT
CGGTTTTACGCATTTCACTCTTTCACGATGTTTCACAGAAATAGTATAGCTGCTGCAGCT
TTTTTTCTCGCAGCCAAGGTAGAGGAGCAACCGCGTAAATTAGAACATGTTATAAAAATA
TTAAATATATGTTTGGAAAAAACTGATTCGAGAGAATCGTATGCAGAACAAGCACAAGAA
TTAGTATTTAATGAAAATATCCTACTTCAAACTCTTGGATTTGATGTTGCTATTGATCAT
CCACATACTCATGTCGTTAAAGCATGTCAACTTTTTAATATTGTGACAGTTTCTAGAGAA
TTAAGACAAACTTGTTATTTTATGGCCTCCAACAGTTTACATTTGACAACTATGTGTCTC
AAGTATCGTCCAACAGTCGTTGCTGCCTTTTGTATTTATATTGCATGCAAATGGTCTCGT
TGGGAGATACCTGATTCAAGTGAGGGAAAAGCTTGGTACAGCTATGTTGACGAAAGCGTG
ACTTTAGATACACTTAAGAAATTGACTGAAGAATATTTACAAATATTAGAACGTAGTCCT
TCAAAATTCAAAAGCAAGATGAAAGCAATCACATCAAATGGACAAACAGGAATGAATCAA
ACTCCAAGTTTTTCTGGTGAATCTTCATCTGCTTCTCGACACAACAATCAACACCATCAT
CATCATCATCATCATCGTAATAATTCTGCTTCGAGTAGCTCTACATCAGGCATGAATGTA
TCAAATAGTAATGGAAATAGTCGAAATCCATCTTCATCCACCTCATCATCGTCAAAAGCT
CAAATGCATCAAATGTCAAACTCACAGGCCTATAAGCAACAAGTTCCTTCACAGCAGCAG
CAACCTATTCCTGCTGTCTCTGCATCGTCCTCTCATATGCATCGTCCAAGACCGTCATCA
TCTTCATCATCAAGTGCACAGCAGCAACAACAAATGTATGGTAGTAACAGTAGTAGCCAA
CAAAAACCCGAAGAAAGACAAAGAATGATGCATCAAGATGGTTCCTATTATAGTTCATCA
TCATCATCTGCTCAAAGAATGTCAGATCATAATAAACATCGTTTGAGTTCTTCTCAGCAA
CAGCAGCAACAACAACAACAAGTTCAATCTCAACATCTACAACAAACTTCTTACATGAAA
CAACCTATTGTAAACGATCAAAAACAACAACATAATGCAATAATGAATAGTGCAAAACAA
CAACAGCAGCAACAAAATTCAGCATATCCAATGGATATGCATCAGAAGAGCATGAGTCGA
AGTAGTTCAGGGAGTAATAATAGTAGCAGCACTGGAAATAATGCAGGCCAATTGCCTCAA
CACGTTAGTCAATCACAAAAGAAACCTCCATGGATGCAGCAGCAGCAACAACAACAAACA
CAACAGTAA

>g7980.t1 Gene=g7980 Length=522
MSEKWYFTEEQLANSPSRRTGINAEMELSYRQRAANLIQEMGQRLQVSQLCINTAIVYMH
RFYAFHSFTMFHRNSIAAAAFFLAAKVEEQPRKLEHVIKILNICLEKTDSRESYAEQAQE
LVFNENILLQTLGFDVAIDHPHTHVVKACQLFNIVTVSRELRQTCYFMASNSLHLTTMCL
KYRPTVVAAFCIYIACKWSRWEIPDSSEGKAWYSYVDESVTLDTLKKLTEEYLQILERSP
SKFKSKMKAITSNGQTGMNQTPSFSGESSSASRHNNQHHHHHHHHRNNSASSSSTSGMNV
SNSNGNSRNPSSSTSSSSKAQMHQMSNSQAYKQQVPSQQQQPIPAVSASSSHMHRPRPSS
SSSSSAQQQQQMYGSNSSSQQKPEERQRMMHQDGSYYSSSSSSAQRMSDHNKHRLSSSQQ
QQQQQQQVQSQHLQQTSYMKQPIVNDQKQQHNAIMNSAKQQQQQQNSAYPMDMHQKSMSR
SSSGSNNSSSTGNNAGQLPQHVSQSQKKPPWMQQQQQQQTQQ

Protein features from InterProScan

Transcript Database ID Name Start End E.value
15 g7980.t1 CDD cd00043 CYCLIN 31 108 2.41625E-6
13 g7980.t1 Gene3D G3DSA:1.10.472.10 - 1 136 5.3E-50
14 g7980.t1 Gene3D G3DSA:1.10.472.10 - 138 255 1.6E-37
8 g7980.t1 MobiDBLite mobidb-lite consensus disorder prediction 253 522 -
11 g7980.t1 MobiDBLite mobidb-lite consensus disorder prediction 253 272 -
12 g7980.t1 MobiDBLite mobidb-lite consensus disorder prediction 289 383 -
10 g7980.t1 MobiDBLite mobidb-lite consensus disorder prediction 392 406 -
9 g7980.t1 MobiDBLite mobidb-lite consensus disorder prediction 414 522 -
2 g7980.t1 PANTHER PTHR10026:SF131 CYCLIN-T 2 452 2.7E-167
3 g7980.t1 PANTHER PTHR10026 CYCLIN 2 452 2.7E-167
1 g7980.t1 Pfam PF00134 Cyclin, N-terminal domain 6 136 3.4E-18
7 g7980.t1 SMART SM00385 cyclin_7 36 130 9.6E-17
6 g7980.t1 SMART SM00385 cyclin_7 143 234 2.7
5 g7980.t1 SUPERFAMILY SSF47954 Cyclin-like 3 137 6.0E-40
4 g7980.t1 SUPERFAMILY SSF47954 Cyclin-like 139 248 1.17E-28

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:0016538 cyclin-dependent protein serine/threonine kinase regulator activity MF
GO:0006351 transcription, DNA-templated BP

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