General information for g2894.t2
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Cytoplasmic polyadenylation element-binding protein 1-A.
Parent gene
- The parent gene g2894 is located on chr_3: 20955967..20966788 (- strand)
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 | g2894 | g2894.t2 | TTS | g2894.t2 | 20953520 | 20953520 |
| chr_3 | g2894 | g2894.t2 | isoform | g2894.t2 | 20954393 | 20966788 |
| chr_3 | g2894 | g2894.t2 | exon | g2894.t2.exon1 | 20954393 | 20954636 |
| chr_3 | g2894 | g2894.t2 | cds | g2894.t2.CDS1 | 20954393 | 20954636 |
| chr_3 | g2894 | g2894.t2 | exon | g2894.t2.exon2 | 20954693 | 20954912 |
| chr_3 | g2894 | g2894.t2 | cds | g2894.t2.CDS2 | 20954693 | 20954912 |
| chr_3 | g2894 | g2894.t2 | exon | g2894.t2.exon3 | 20954974 | 20955986 |
| chr_3 | g2894 | g2894.t2 | cds | g2894.t2.CDS3 | 20954974 | 20955986 |
| chr_3 | g2894 | g2894.t2 | exon | g2894.t2.exon4 | 20956057 | 20956172 |
| chr_3 | g2894 | g2894.t2 | cds | g2894.t2.CDS4 | 20956057 | 20956172 |
| chr_3 | g2894 | g2894.t2 | exon | g2894.t2.exon5 | 20956299 | 20956414 |
| chr_3 | g2894 | g2894.t2 | cds | g2894.t2.CDS5 | 20956299 | 20956414 |
| chr_3 | g2894 | g2894.t2 | exon | g2894.t2.exon6 | 20957287 | 20957404 |
| chr_3 | g2894 | g2894.t2 | cds | g2894.t2.CDS6 | 20957287 | 20957404 |
| chr_3 | g2894 | g2894.t2 | exon | g2894.t2.exon7 | 20966771 | 20966788 |
| chr_3 | g2894 | g2894.t2 | cds | g2894.t2.CDS7 | 20966771 | 20966788 |
| chr_3 | g2894 | g2894.t2 | TSS | g2894.t2 | 20967308 | 20967308 |
Sequences
>g2894.t2 Gene=g2894 Length=1845
ATGCCATCATTGCAACAGACATCAACATTTAAAGATTGTAATCTGTCATCAGAAATTCTT
CAAAAACATTCAATAAACTCTATTAATTCACTCTTAAATAACGAAGATGGCTTGATTTTA
TCTCCTCATTCAGAAGTAGATCCTAATCTAATTTTTGGTGACATGTTTCACACAGCTACT
CCAAAAGGATATTCATCACCTGACAGGAACTATATTCAGACAACTCCACCAAAAATGTTT
GAAAATTTTCAGTTTGACAATCGTTCAATACAACGAAATTTAAGTTTTGACTGCAATGTC
ACAACTCCGACTTCACCGGGAACACCTAGTTCTTTTAAAGCATACATGAATTCACCGTCT
TCATATGGAAATGATTCGGGATTTTACAACAACAGTCGATCTGATTCGCCAACGATGTTG
ATTAATGATTCGCAAGATCTCTTTGGCTCGTCAAACTTTTCGCAAACACAATCGGAAAGT
TTGTCAGACATTATGAATTACTTGAATATAAATACATCATCTATTCAACAATCAAATCAC
ATACAGCAGCAGCATCAGCATCAGCGCTTTGAAAATCAAAGGAAGCATGAGCAACAGGCT
TATCAAAATGAGCTAAAACAAATGCAGTATCAATTGCTTCAACAGCAACACATGTCGCAA
CCAATCAATCATCATTTGTTGCAACAACAATTTTTAAATCGCTACAATAATCAAAATTTA
GTGAACTGGCGTCAGCAACAACATTTTTCGTCGAATAATTTTAACAATGGAAGCTCATTA
GATCATGCTGCTAAATACCATCGTTCTTCAGCTGCTCTTTTCGATCCAAGCTGTACTTGG
AGTGGTAATCTTCCACCACGTATTCATCGATTTGTTACGTATTCACCTAAAGTTTTTCTC
GGAGGTCTTCCTTGGAACACCTCAGAACAAACGCTGATGCAAATCTTTAAGCCTTTTGGT
AATATCAAAGTTGAATGGCCCGGAAAAGAACAAAATGCTGTTCAACCAAAAGGTTATGTT
TATGTGATTTTTGAATCTGAGAAGCAGGTAAAAGCTTTGTTGCAAGCCTGCAGTATTCAA
GATAATTTTTCAAACAATTTATCAAATTCTAACCATGGTGATTCAATGGACACCATGTCA
TCTTCTGCGGGCATTCCCTGTTTTGGTGGAAATTATTACTATAAAATATCCTCAAATCGC
ATTAAGGAAAAAGAAGTTGAAGTTATTCCGTGGATCATTGCAGATTCTAATTACATCAAA
TCTGCAAATCAAAAAATTGAATCAGCAAAAACTGTTTTTGTTGGTGCACTTCATGGAAAG
ACAACTGCGGAGGGACTTGCAAAAATAATGAATGACCTTTTTGATGGAGTAATTTATGCA
GGAATTGACACTGACAAATACAAATATCCGATTGGATCAGGACGTGTTACATTTAATAAC
ACACGTTCATATATGCGAGCCGTAGCAGCTGCATTCATTGAAATCAAATCGCAAAAGTTT
AATAAAAAGGTTCAAATTGATCCTTATCTTGAAGATTCGTTATGTTCATTATGTAATGTA
CAACATGGTCCATATTATTGCAGAGATCTGTCTTGCTTCCGATATTTCTGCCGTCAATGC
TGGCAAATGAGACACAATAATGATTCTCATTTACGAAATCACAAACCATTAACGCGAAAT
TCAAAATCACAACAACAAATTCACTCTTCGGTATTTTACAATAATCCGTTTAGTAGCAGC
AGCTCTGCAGGATCCACAGGATCAAGCAATCCAGGTTCACCGAGTTCTTCTGAAACTTTA
TTGTCGTCATCACCGCCATCGTTAATTAATTTTTCAATGAAATAA
>g2894.t2 Gene=g2894 Length=614
MPSLQQTSTFKDCNLSSEILQKHSINSINSLLNNEDGLILSPHSEVDPNLIFGDMFHTAT
PKGYSSPDRNYIQTTPPKMFENFQFDNRSIQRNLSFDCNVTTPTSPGTPSSFKAYMNSPS
SYGNDSGFYNNSRSDSPTMLINDSQDLFGSSNFSQTQSESLSDIMNYLNINTSSIQQSNH
IQQQHQHQRFENQRKHEQQAYQNELKQMQYQLLQQQHMSQPINHHLLQQQFLNRYNNQNL
VNWRQQQHFSSNNFNNGSSLDHAAKYHRSSAALFDPSCTWSGNLPPRIHRFVTYSPKVFL
GGLPWNTSEQTLMQIFKPFGNIKVEWPGKEQNAVQPKGYVYVIFESEKQVKALLQACSIQ
DNFSNNLSNSNHGDSMDTMSSSAGIPCFGGNYYYKISSNRIKEKEVEVIPWIIADSNYIK
SANQKIESAKTVFVGALHGKTTAEGLAKIMNDLFDGVIYAGIDTDKYKYPIGSGRVTFNN
TRSYMRAVAAAFIEIKSQKFNKKVQIDPYLEDSLCSLCNVQHGPYYCRDLSCFRYFCRQC
WQMRHNNDSHLRNHKPLTRNSKSQQQIHSSVFYNNPFSSSSSAGSTGSSNPGSPSSSETL
LSSSPPSLINFSMK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 11 | g2894.t2 | CDD | cd12725 | RRM2_CPEB1 | 430 | 512 | 3.75688E-54 |
| 10 | g2894.t2 | CDD | cd19757 | Bbox1 | 514 | 558 | 1.8137E-7 |
| 9 | g2894.t2 | Coils | Coil | Coil | 187 | 207 | - |
| 7 | g2894.t2 | Gene3D | G3DSA:3.30.70.330 | - | 297 | 410 | 1.0E-22 |
| 6 | g2894.t2 | Gene3D | G3DSA:3.30.70.330 | - | 414 | 506 | 7.0E-28 |
| 8 | g2894.t2 | Gene3D | G3DSA:3.30.40.130 | - | 507 | 567 | 5.2E-25 |
| 16 | g2894.t2 | MobiDBLite | mobidb-lite | consensus disorder prediction | 582 | 614 | - |
| 3 | g2894.t2 | PANTHER | PTHR12566 | CYTOPLASMIC POLYADENYLATION ELEMENT BINDING PROTEIN CPEB | 74 | 569 | 2.3E-177 |
| 4 | g2894.t2 | PANTHER | PTHR12566:SF9 | CYTOPLASMIC POLYADENYLATION ELEMENT-BINDING PROTEIN 1 | 74 | 569 | 2.3E-177 |
| 2 | g2894.t2 | Pfam | PF16367 | RNA recognition motif | 295 | 410 | 2.8E-21 |
| 1 | g2894.t2 | Pfam | PF16366 | Cytoplasmic polyadenylation element-binding protein ZZ domain | 502 | 560 | 1.5E-27 |
| 15 | g2894.t2 | ProSitePatterns | PS00028 | Zinc finger C2H2 type domain signature. | 527 | 550 | - |
| 14 | g2894.t2 | ProSitePatterns | PS00028 | Zinc finger C2H2 type domain signature. | 532 | 554 | - |
| 18 | g2894.t2 | ProSiteProfiles | PS50102 | Eukaryotic RNA Recognition Motif (RRM) profile. | 296 | 383 | 11.077 |
| 17 | g2894.t2 | ProSiteProfiles | PS50102 | Eukaryotic RNA Recognition Motif (RRM) profile. | 430 | 511 | 8.518 |
| 13 | g2894.t2 | SMART | SM00360 | rrm1_1 | 297 | 371 | 2.7E-5 |
| 12 | g2894.t2 | SMART | SM00360 | rrm1_1 | 431 | 503 | 0.25 |
| 5 | g2894.t2 | SUPERFAMILY | SSF54928 | RNA-binding domain, RBD | 296 | 489 | 9.51E-21 |
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:0045182 | translation regulator activity | MF |
| GO:0006417 | regulation of translation | BP |
| GO:0003730 | mRNA 3’-UTR binding | MF |
| GO:0003676 | nucleic acid binding | MF |
KEGG
Orthology
- This transcript has been annotated with K02602 (cytoplasmic polyadenylation element-binding protein)
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.
