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.t6 TTS g5515.t6 10027731 10027731
chr_2 g5515 g5515.t6 isoform g5515.t6 10027974 10029024
chr_2 g5515 g5515.t6 exon g5515.t6.exon1 10027974 10028194
chr_2 g5515 g5515.t6 cds g5515.t6.CDS1 10027974 10028194
chr_2 g5515 g5515.t6 exon g5515.t6.exon2 10028251 10028364
chr_2 g5515 g5515.t6 cds g5515.t6.CDS2 10028251 10028364
chr_2 g5515 g5515.t6 exon g5515.t6.exon3 10028438 10028579
chr_2 g5515 g5515.t6 cds g5515.t6.CDS3 10028438 10028579
chr_2 g5515 g5515.t6 exon g5515.t6.exon4 10028655 10028792
chr_2 g5515 g5515.t6 cds g5515.t6.CDS4 10028655 10028792
chr_2 g5515 g5515.t6 exon g5515.t6.exon5 10028902 10029024
chr_2 g5515 g5515.t6 cds g5515.t6.CDS5 10028902 10029024
chr_2 g5515 g5515.t6 TSS g5515.t6 10029368 10029368

Sequences

>g5515.t6 Gene=g5515 Length=738
ATGGATCCTATTGAAGAAAACTCTTCAAATATTGAAACTTCTGTTTCATCTGCAACATCA
GGAACCACAAATATTGTCCATCATCTAATTCCGCCATCACAAGTGAATCCTTCAGCACAT
CAAGCCCACGTTCAATCTTCATCTGTAATACAACCAAATCAACAATCAGTTATAACCGCT
ACTGGAGTGCAACTTGTAAAAAGTGTTTTGCTGGTGAATAGTAAACCAAATTCTGTCATT
CATACGACTCAAGCTATTCAAATAAAACCTGAACCAAATATTGGTCATATGATAACTTCA
GATGATTCTGACGACTATTCTGATGATGATTCTCCAAAAAAGCGTAGAGATTTATTGACG
AGACGTCCTTCATATCGAAAAATTTTAAATGACCTCGGAGGAGGGGGAACAATATTGACA
CAAGCTGGAAATCCAAATGATCATGCGATTCATGGTGGAAGTACGATTGTACAATATAAT
AATCAGGATGGATCAGGTTTGGTGTCATATGTCCCTGTAAATTTGGTTGGAAATAATGTG
ATAGCAGAAGACCAGTCCAGAAAACGTGAGATGAGGTTACTTAAAAATAGAGAAGCAGCT
CGAGAATGTCGTCGAAAAAAGAAGGAATACATAAAGTGCCTGGAAAATAGAGTAGCAGTA
CTTGAAAATCAAAATAAGGCATTAATCGAAGAGTTAAAGAGTTTAAAAGAGTTATATTGT
CAACAGAAGAATGATTGA

>g5515.t6 Gene=g5515 Length=245
MDPIEENSSNIETSVSSATSGTTNIVHHLIPPSQVNPSAHQAHVQSSSVIQPNQQSVITA
TGVQLVKSVLLVNSKPNSVIHTTQAIQIKPEPNIGHMITSDDSDDYSDDDSPKKRRDLLT
RRPSYRKILNDLGGGGTILTQAGNPNDHAIHGGSTIVQYNNQDGSGLVSYVPVNLVGNNV
IAEDQSRKREMRLLKNREAARECRRKKKEYIKCLENRVAVLENQNKALIEELKSLKELYC
QQKND

Protein features from InterProScan

Transcript Database ID Name Start End E.value
12 g5515.t6 CDD cd14690 bZIP_CREB1 188 241 1.28704E-31
11 g5515.t6 Coils Coil Coil 204 238 -
10 g5515.t6 Gene3D G3DSA:1.20.5.170 - 188 242 8.1E-21
15 g5515.t6 MobiDBLite mobidb-lite consensus disorder prediction 1 20 -
4 g5515.t6 PANTHER PTHR45879:SF3 CYCLIC AMP RESPONSE ELEMENT-BINDING PROTEIN B 12 134 4.6E-59
6 g5515.t6 PANTHER PTHR45879 CYCLIC AMP RESPONSE ELEMENT-BINDING PROTEIN B 12 134 4.6E-59
3 g5515.t6 PANTHER PTHR45879:SF3 CYCLIC AMP RESPONSE ELEMENT-BINDING PROTEIN B 167 243 4.6E-59
5 g5515.t6 PANTHER PTHR45879 CYCLIC AMP RESPONSE ELEMENT-BINDING PROTEIN B 167 243 4.6E-59
8 g5515.t6 PRINTS PR00041 cAMP response element binding (CREB) protein signature 109 131 2.4E-6
7 g5515.t6 PRINTS PR00041 cAMP response element binding (CREB) protein signature 203 219 2.4E-6
2 g5515.t6 Pfam PF02173 pKID domain 108 134 1.0E-14
1 g5515.t6 Pfam PF00170 bZIP transcription factor 186 243 4.2E-18
14 g5515.t6 ProSitePatterns PS00036 Basic-leucine zipper (bZIP) domain signature. 192 206 -
17 g5515.t6 ProSiteProfiles PS50953 KID domain profile. 92 151 12.65
16 g5515.t6 ProSiteProfiles PS50217 Basic-leucine zipper (bZIP) domain profile. 186 237 11.519
13 g5515.t6 SMART SM00338 brlzneu 182 245 9.7E-8
9 g5515.t6 SUPERFAMILY SSF57959 Leucine zipper domain 188 239 2.67E-12

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

Data is missing for g5515/g5515.t6; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5515.t6.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