Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative Cyclic AMP response element-binding protein 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_2 g5515 g5515.t4 TTS g5515.t4 10027731 10027731
chr_2 g5515 g5515.t4 isoform g5515.t4 10027974 10028566
chr_2 g5515 g5515.t4 exon g5515.t4.exon1 10027974 10028194
chr_2 g5515 g5515.t4 cds g5515.t4.CDS1 10027974 10028194
chr_2 g5515 g5515.t4 exon g5515.t4.exon2 10028251 10028364
chr_2 g5515 g5515.t4 cds g5515.t4.CDS2 10028251 10028364
chr_2 g5515 g5515.t4 exon g5515.t4.exon3 10028429 10028566
chr_2 g5515 g5515.t4 cds g5515.t4.CDS3 10028429 10028552
chr_2 g5515 g5515.t4 TSS g5515.t4 10029368 10029368

Sequences

>g5515.t4 Gene=g5515 Length=473
CAAATATTGGTCATATGATAACTTCAGATGATTCTGACGACTATTCTGATGATGATTCTC
CAAAAAAGCGTAGAGATTTATTGACGAGACGTCCTTCATATCGAAAAATTTTAAATGACC
TCGGAGGAGGTGAAATGGGGGGAACAATATTGACACAAGCTGGAAATCCAAATGATCATG
CGATTCATGGTGGAAGTACGATTGTACAATATAATAATCAGGATGGATCAGGTTTGGTGT
CATATGTCCCTGTAAATTTGGTTGGAAATAATGTGATAGCAGAAGACCAGTCCAGAAAAC
GTGAGATGAGGTTACTTAAAAATAGAGAAGCAGCTCGAGAATGTCGTCGAAAAAAGAAGG
AATACATAAAGTGCCTGGAAAATAGAGTAGCAGTACTTGAAAATCAAAATAAGGCATTAA
TCGAAGAGTTAAAGAGTTTAAAAGAGTTATATTGTCAACAGAAGAATGATTGA

>g5515.t4 Gene=g5515 Length=152
MITSDDSDDYSDDDSPKKRRDLLTRRPSYRKILNDLGGGEMGGTILTQAGNPNDHAIHGG
STIVQYNNQDGSGLVSYVPVNLVGNNVIAEDQSRKREMRLLKNREAARECRRKKKEYIKC
LENRVAVLENQNKALIEELKSLKELYCQQKND

Protein features from InterProScan

Transcript Database ID Name Start End E.value
12 g5515.t4 CDD cd14690 bZIP_CREB1 95 148 3.97355E-26
11 g5515.t4 Coils Coil Coil 111 145 -
10 g5515.t4 Gene3D G3DSA:1.20.5.170 - 95 149 3.3E-21
15 g5515.t4 MobiDBLite mobidb-lite consensus disorder prediction 1 26 -
16 g5515.t4 MobiDBLite mobidb-lite consensus disorder prediction 11 26 -
4 g5515.t4 PANTHER PTHR45879:SF3 CYCLIC AMP RESPONSE ELEMENT-BINDING PROTEIN B 4 43 6.2E-54
6 g5515.t4 PANTHER PTHR45879 CYCLIC AMP RESPONSE ELEMENT-BINDING PROTEIN B 4 43 6.2E-54
3 g5515.t4 PANTHER PTHR45879:SF3 CYCLIC AMP RESPONSE ELEMENT-BINDING PROTEIN B 74 150 6.2E-54
5 g5515.t4 PANTHER PTHR45879 CYCLIC AMP RESPONSE ELEMENT-BINDING PROTEIN B 74 150 6.2E-54
7 g5515.t4 PRINTS PR00041 cAMP response element binding (CREB) protein signature 13 35 1.2E-6
8 g5515.t4 PRINTS PR00041 cAMP response element binding (CREB) protein signature 110 126 1.2E-6
2 g5515.t4 Pfam PF02173 pKID domain 12 40 2.5E-15
1 g5515.t4 Pfam PF00170 bZIP transcription factor 93 150 1.6E-18
14 g5515.t4 ProSitePatterns PS00036 Basic-leucine zipper (bZIP) domain signature. 99 113 -
18 g5515.t4 ProSiteProfiles PS50953 KID domain profile. 1 55 13.436
17 g5515.t4 ProSiteProfiles PS50217 Basic-leucine zipper (bZIP) domain profile. 93 144 11.519
13 g5515.t4 SMART SM00338 brlzneu 89 152 9.7E-8
9 g5515.t4 SUPERFAMILY SSF57959 Leucine zipper domain 95 146 1.05E-12

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

Data is missing for g5515/g5515.t4; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5515.t4.fa.iupred3.txt does not exist

GO terms from InterProScan

GOID TERM ONTOLOGY
GO:0005634 nucleus CC
GO:0003677 DNA binding MF
GO:0005515 protein binding MF
GO:0006355 regulation of transcription, DNA-templated BP
GO:0003700 DNA-binding transcription factor activity MF

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