General information for g2894.t1
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.t1 | TTS | g2894.t1 | 20953520 | 20953520 |
| chr_3 | g2894 | g2894.t1 | isoform | g2894.t1 | 20954393 | 20966788 |
| chr_3 | g2894 | g2894.t1 | exon | g2894.t1.exon1 | 20954393 | 20954636 |
| chr_3 | g2894 | g2894.t1 | cds | g2894.t1.CDS1 | 20954393 | 20954636 |
| chr_3 | g2894 | g2894.t1 | exon | g2894.t1.exon2 | 20954693 | 20954912 |
| chr_3 | g2894 | g2894.t1 | cds | g2894.t1.CDS2 | 20954693 | 20954912 |
| chr_3 | g2894 | g2894.t1 | exon | g2894.t1.exon3 | 20954974 | 20955986 |
| chr_3 | g2894 | g2894.t1 | cds | g2894.t1.CDS3 | 20954974 | 20955986 |
| chr_3 | g2894 | g2894.t1 | exon | g2894.t1.exon4 | 20956057 | 20956172 |
| chr_3 | g2894 | g2894.t1 | cds | g2894.t1.CDS4 | 20956057 | 20956172 |
| chr_3 | g2894 | g2894.t1 | exon | g2894.t1.exon5 | 20956299 | 20956411 |
| chr_3 | g2894 | g2894.t1 | cds | g2894.t1.CDS5 | 20956299 | 20956411 |
| chr_3 | g2894 | g2894.t1 | exon | g2894.t1.exon6 | 20957287 | 20957404 |
| chr_3 | g2894 | g2894.t1 | cds | g2894.t1.CDS6 | 20957287 | 20957404 |
| chr_3 | g2894 | g2894.t1 | exon | g2894.t1.exon7 | 20966771 | 20966788 |
| chr_3 | g2894 | g2894.t1 | cds | g2894.t1.CDS7 | 20966771 | 20966788 |
| chr_3 | g2894 | g2894.t1 | TSS | g2894.t1 | 20967308 | 20967308 |
Sequences
>g2894.t1 Gene=g2894 Length=1842
ATGCCATCATTGCAACAGACATCAACATTTAAAGATTGTAATCTGTCATCAGAAATTCTT
CAAAAACATTCAATAAACTCTATTAATTCACTCTTAAATAACGAAGATGGCTTGATTTTA
TCTCCTCATTCAGAAGATCCTAATCTAATTTTTGGTGACATGTTTCACACAGCTACTCCA
AAAGGATATTCATCACCTGACAGGAACTATATTCAGACAACTCCACCAAAAATGTTTGAA
AATTTTCAGTTTGACAATCGTTCAATACAACGAAATTTAAGTTTTGACTGCAATGTCACA
ACTCCGACTTCACCGGGAACACCTAGTTCTTTTAAAGCATACATGAATTCACCGTCTTCA
TATGGAAATGATTCGGGATTTTACAACAACAGTCGATCTGATTCGCCAACGATGTTGATT
AATGATTCGCAAGATCTCTTTGGCTCGTCAAACTTTTCGCAAACACAATCGGAAAGTTTG
TCAGACATTATGAATTACTTGAATATAAATACATCATCTATTCAACAATCAAATCACATA
CAGCAGCAGCATCAGCATCAGCGCTTTGAAAATCAAAGGAAGCATGAGCAACAGGCTTAT
CAAAATGAGCTAAAACAAATGCAGTATCAATTGCTTCAACAGCAACACATGTCGCAACCA
ATCAATCATCATTTGTTGCAACAACAATTTTTAAATCGCTACAATAATCAAAATTTAGTG
AACTGGCGTCAGCAACAACATTTTTCGTCGAATAATTTTAACAATGGAAGCTCATTAGAT
CATGCTGCTAAATACCATCGTTCTTCAGCTGCTCTTTTCGATCCAAGCTGTACTTGGAGT
GGTAATCTTCCACCACGTATTCATCGATTTGTTACGTATTCACCTAAAGTTTTTCTCGGA
GGTCTTCCTTGGAACACCTCAGAACAAACGCTGATGCAAATCTTTAAGCCTTTTGGTAAT
ATCAAAGTTGAATGGCCCGGAAAAGAACAAAATGCTGTTCAACCAAAAGGTTATGTTTAT
GTGATTTTTGAATCTGAGAAGCAGGTAAAAGCTTTGTTGCAAGCCTGCAGTATTCAAGAT
AATTTTTCAAACAATTTATCAAATTCTAACCATGGTGATTCAATGGACACCATGTCATCT
TCTGCGGGCATTCCCTGTTTTGGTGGAAATTATTACTATAAAATATCCTCAAATCGCATT
AAGGAAAAAGAAGTTGAAGTTATTCCGTGGATCATTGCAGATTCTAATTACATCAAATCT
GCAAATCAAAAAATTGAATCAGCAAAAACTGTTTTTGTTGGTGCACTTCATGGAAAGACA
ACTGCGGAGGGACTTGCAAAAATAATGAATGACCTTTTTGATGGAGTAATTTATGCAGGA
ATTGACACTGACAAATACAAATATCCGATTGGATCAGGACGTGTTACATTTAATAACACA
CGTTCATATATGCGAGCCGTAGCAGCTGCATTCATTGAAATCAAATCGCAAAAGTTTAAT
AAAAAGGTTCAAATTGATCCTTATCTTGAAGATTCGTTATGTTCATTATGTAATGTACAA
CATGGTCCATATTATTGCAGAGATCTGTCTTGCTTCCGATATTTCTGCCGTCAATGCTGG
CAAATGAGACACAATAATGATTCTCATTTACGAAATCACAAACCATTAACGCGAAATTCA
AAATCACAACAACAAATTCACTCTTCGGTATTTTACAATAATCCGTTTAGTAGCAGCAGC
TCTGCAGGATCCACAGGATCAAGCAATCCAGGTTCACCGAGTTCTTCTGAAACTTTATTG
TCGTCATCACCGCCATCGTTAATTAATTTTTCAATGAAATAA
>g2894.t1 Gene=g2894 Length=613
MPSLQQTSTFKDCNLSSEILQKHSINSINSLLNNEDGLILSPHSEDPNLIFGDMFHTATP
KGYSSPDRNYIQTTPPKMFENFQFDNRSIQRNLSFDCNVTTPTSPGTPSSFKAYMNSPSS
YGNDSGFYNNSRSDSPTMLINDSQDLFGSSNFSQTQSESLSDIMNYLNINTSSIQQSNHI
QQQHQHQRFENQRKHEQQAYQNELKQMQYQLLQQQHMSQPINHHLLQQQFLNRYNNQNLV
NWRQQQHFSSNNFNNGSSLDHAAKYHRSSAALFDPSCTWSGNLPPRIHRFVTYSPKVFLG
GLPWNTSEQTLMQIFKPFGNIKVEWPGKEQNAVQPKGYVYVIFESEKQVKALLQACSIQD
NFSNNLSNSNHGDSMDTMSSSAGIPCFGGNYYYKISSNRIKEKEVEVIPWIIADSNYIKS
ANQKIESAKTVFVGALHGKTTAEGLAKIMNDLFDGVIYAGIDTDKYKYPIGSGRVTFNNT
RSYMRAVAAAFIEIKSQKFNKKVQIDPYLEDSLCSLCNVQHGPYYCRDLSCFRYFCRQCW
QMRHNNDSHLRNHKPLTRNSKSQQQIHSSVFYNNPFSSSSSAGSTGSSNPGSPSSSETLL
SSSPPSLINFSMK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 11 | g2894.t1 | CDD | cd12725 | RRM2_CPEB1 | 429 | 511 | 3.70069E-54 |
| 10 | g2894.t1 | CDD | cd19757 | Bbox1 | 513 | 557 | 1.8286E-7 |
| 9 | g2894.t1 | Coils | Coil | Coil | 186 | 206 | - |
| 6 | g2894.t1 | Gene3D | G3DSA:3.30.70.330 | - | 296 | 409 | 1.0E-22 |
| 7 | g2894.t1 | Gene3D | G3DSA:3.30.70.330 | - | 413 | 505 | 6.9E-28 |
| 8 | g2894.t1 | Gene3D | G3DSA:3.30.40.130 | - | 506 | 566 | 5.2E-25 |
| 16 | g2894.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 581 | 613 | - |
| 3 | g2894.t1 | PANTHER | PTHR12566 | CYTOPLASMIC POLYADENYLATION ELEMENT BINDING PROTEIN CPEB | 76 | 568 | 2.5E-177 |
| 4 | g2894.t1 | PANTHER | PTHR12566:SF9 | CYTOPLASMIC POLYADENYLATION ELEMENT-BINDING PROTEIN 1 | 76 | 568 | 2.5E-177 |
| 2 | g2894.t1 | Pfam | PF16367 | RNA recognition motif | 294 | 409 | 2.8E-21 |
| 1 | g2894.t1 | Pfam | PF16366 | Cytoplasmic polyadenylation element-binding protein ZZ domain | 501 | 559 | 1.5E-27 |
| 15 | g2894.t1 | ProSitePatterns | PS00028 | Zinc finger C2H2 type domain signature. | 526 | 549 | - |
| 14 | g2894.t1 | ProSitePatterns | PS00028 | Zinc finger C2H2 type domain signature. | 531 | 553 | - |
| 18 | g2894.t1 | ProSiteProfiles | PS50102 | Eukaryotic RNA Recognition Motif (RRM) profile. | 295 | 382 | 11.077 |
| 17 | g2894.t1 | ProSiteProfiles | PS50102 | Eukaryotic RNA Recognition Motif (RRM) profile. | 429 | 510 | 8.518 |
| 12 | g2894.t1 | SMART | SM00360 | rrm1_1 | 296 | 370 | 2.7E-5 |
| 13 | g2894.t1 | SMART | SM00360 | rrm1_1 | 430 | 502 | 0.25 |
| 5 | g2894.t1 | SUPERFAMILY | SSF54928 | RNA-binding domain, RBD | 295 | 488 | 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.
