Gene loci information

Transcript annotation

  • This transcript has been annotated as C-terminal-binding protein.

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 g2029 g2029.t1 TTS g2029.t1 14576881 14576881
chr_3 g2029 g2029.t1 isoform g2029.t1 14577254 14579253
chr_3 g2029 g2029.t1 exon g2029.t1.exon1 14577254 14577319
chr_3 g2029 g2029.t1 cds g2029.t1.CDS1 14577254 14577319
chr_3 g2029 g2029.t1 exon g2029.t1.exon2 14577390 14577574
chr_3 g2029 g2029.t1 cds g2029.t1.CDS2 14577390 14577574
chr_3 g2029 g2029.t1 exon g2029.t1.exon3 14577821 14578019
chr_3 g2029 g2029.t1 cds g2029.t1.CDS3 14577821 14578019
chr_3 g2029 g2029.t1 exon g2029.t1.exon4 14578138 14578278
chr_3 g2029 g2029.t1 cds g2029.t1.CDS4 14578138 14578278
chr_3 g2029 g2029.t1 exon g2029.t1.exon5 14578371 14578631
chr_3 g2029 g2029.t1 cds g2029.t1.CDS5 14578371 14578631
chr_3 g2029 g2029.t1 exon g2029.t1.exon6 14578701 14579006
chr_3 g2029 g2029.t1 cds g2029.t1.CDS6 14578701 14579006
chr_3 g2029 g2029.t1 exon g2029.t1.exon7 14579068 14579253
chr_3 g2029 g2029.t1 cds g2029.t1.CDS7 14579068 14579253
chr_3 g2029 g2029.t1 TSS g2029.t1 NA NA

Sequences

>g2029.t1 Gene=g2029 Length=1344
ATGTTGCCAAAACGTCCACGACTTGATGCCGTTCGCGGCCCAATATCATCGAACGGTCCT
CTGCAATCGCGGCCCCTTGTAGCTTTATTAGATGGTAGAGATTGCTCCATTGAAATGCCA
ATACTAAAAGATGTTGCAACAGTTGCATTTTGTGATGCTCAGAGTACGTCTGAAATTCAT
GAAAAAGTATTAAATGAAGCCGTTGGTGCTTTGATGTGGCATACAATAATTTTAACGAAA
GAAGATCTCGAGAAATTCAAAGCACTTCGAATTATTGTTCGCATTGGTAGTGGTGTAGAC
AATATTGATGTTAAAGCGGCTGGTGAATTGGGAATAGCTGTTTGTAATGTGCCCGGCTAT
GGCGTCGAAGAAGTGGCAGACACGACGCTCTGTCTCATCCTAAATCTCTACCGAAGAACC
TATTGGCTAGCGAATATGGTTCGTGAAGGAAAGAAATTCACAGGTCCCGAACAAGTCCGA
GATGCAGCACAAGGCTGTGCAAGAATACGTGGCGACACATTGGGTATTGTTGGTCTTGGA
CGTATAGGCAGTGCAGTCGCGTTAAGAGCGAAAGCATTTGGCTTTAATGTCAGTTTCTAT
GATCCTTATTTACCAGATGGCATTGAAAAATCTTTAGGTCTAAATCGTGTCTATACACTT
CAAGAACTACTCTTCCACTCTGACTGTGTCTCATTGCATTGTACATTAAACGAACATAAT
CATCATCTTATTAATGACTACACAATTAAACAGATGAGACCCGGAGCATTCATTGTGAAC
ACGGCTAGAGGCGGTTTAGTTGACGATGAGGCACTCGCGCAAGCTTTAAAACAAGGCAGA
ATACGAGCGGCTGCATTGGATGTGCACGAGAATGAGCCATATAATGTATTTCAGGGTGCT
CTGAAAGATGCACCAAATCTTCTCTGCACGCCGCATGCCGCCTTTTACAGTGAAGCCGCC
ACAACAGAGCTCCGCGAAATGGCCGCCAGTGAAATTCGACGCGCAATCATCGGGACCATT
CCTGATTGTCTCAGAAATTGTGTGAATAAAGAATATTTTATGAGATCATCGTCAGGCGCA
GGATATTCAGAAGCTGGAATTAACGGTGGATATTATTCAGGTGGATTACATACACAAGTA
CATAGCACGACACCATTAGAAGCGCCACATAGTGCAGGATCAACACATGCCTCGGCAGCT
AGTGCACCACCATCTCAATCAGCTTCAGCTCCTCCGACTTCTGCACCACCTGGTATACAC
GGGTTGGTTAGTAAATCGCCTCTTAGTGCCCCTGATCCTAATCATCATTCAGCCAATAAG
CCAGAGTCATCGGAAGTTCACTAG

>g2029.t1 Gene=g2029 Length=447
MLPKRPRLDAVRGPISSNGPLQSRPLVALLDGRDCSIEMPILKDVATVAFCDAQSTSEIH
EKVLNEAVGALMWHTIILTKEDLEKFKALRIIVRIGSGVDNIDVKAAGELGIAVCNVPGY
GVEEVADTTLCLILNLYRRTYWLANMVREGKKFTGPEQVRDAAQGCARIRGDTLGIVGLG
RIGSAVALRAKAFGFNVSFYDPYLPDGIEKSLGLNRVYTLQELLFHSDCVSLHCTLNEHN
HHLINDYTIKQMRPGAFIVNTARGGLVDDEALAQALKQGRIRAAALDVHENEPYNVFQGA
LKDAPNLLCTPHAAFYSEAATTELREMAASEIRRAIIGTIPDCLRNCVNKEYFMRSSSGA
GYSEAGINGGYYSGGLHTQVHSTTPLEAPHSAGSTHASAASAPPSQSASAPPTSAPPGIH
GLVSKSPLSAPDPNHHSANKPESSEVH

Protein features from InterProScan

Transcript Database ID Name Start End E.value
13 g2029.t1 CDD cd05299 CtBP_dh 25 343 9.34586E-152
12 g2029.t1 Gene3D G3DSA:3.40.50.720 - 39 341 3.0E-137
11 g2029.t1 Gene3D G3DSA:3.40.50.720 - 122 315 3.0E-137
9 g2029.t1 MobiDBLite mobidb-lite consensus disorder prediction 386 408 -
10 g2029.t1 MobiDBLite mobidb-lite consensus disorder prediction 386 447 -
3 g2029.t1 PANTHER PTHR46029:SF7 C-TERMINAL-BINDING PROTEIN 16 439 5.9E-240
4 g2029.t1 PANTHER PTHR46029 C-TERMINAL-BINDING PROTEIN 16 439 5.9E-240
2 g2029.t1 Pfam PF00389 D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain 35 349 3.6E-29
1 g2029.t1 Pfam PF02826 D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain 131 314 2.2E-54
7 g2029.t1 ProSitePatterns PS00065 D-isomer specific 2-hydroxyacid dehydrogenases NAD-binding signature. 174 201 -
8 g2029.t1 ProSitePatterns PS00671 D-isomer specific 2-hydroxyacid dehydrogenases signature 3. 252 268 -
6 g2029.t1 SUPERFAMILY SSF52283 Formate/glycerate dehydrogenase catalytic domain-like 24 140 2.27E-59
5 g2029.t1 SUPERFAMILY SSF51735 NAD(P)-binding Rossmann-fold domains 124 314 1.97E-54

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:0016616 oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor MF
GO:0003714 transcription corepressor activity MF
GO:0051287 NAD binding MF
GO:0055114 NA NA

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