General information for g11516.t4
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Cytoplasmic FMR1-interacting protein.
Parent gene
- The parent gene g11516 is located on chr_1: 16754336..16756174 (- 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_1 | g11516 | g11516.t4 | isoform | g11516.t4 | 16754336 | 16756174 |
| chr_1 | g11516 | g11516.t4 | exon | g11516.t4.exon1 | 16754336 | 16755134 |
| chr_1 | g11516 | g11516.t4 | cds | g11516.t4.CDS1 | 16754337 | 16755134 |
| chr_1 | g11516 | g11516.t4 | exon | g11516.t4.exon2 | 16755198 | 16755377 |
| chr_1 | g11516 | g11516.t4 | cds | g11516.t4.CDS2 | 16755198 | 16755377 |
| chr_1 | g11516 | g11516.t4 | exon | g11516.t4.exon3 | 16755451 | 16755577 |
| chr_1 | g11516 | g11516.t4 | cds | g11516.t4.CDS3 | 16755451 | 16755577 |
| chr_1 | g11516 | g11516.t4 | exon | g11516.t4.exon4 | 16755637 | 16755722 |
| chr_1 | g11516 | g11516.t4 | cds | g11516.t4.CDS4 | 16755637 | 16755719 |
| chr_1 | g11516 | g11516.t4 | exon | g11516.t4.exon5 | 16755967 | 16756174 |
| chr_1 | g11516 | g11516.t4 | TSS | g11516.t4 | NA | NA |
| chr_1 | g11516 | g11516.t4 | TTS | g11516.t4 | NA | NA |
Sequences
>g11516.t4 Gene=g11516 Length=1400
TGTTTGCGCTTTGTTTATAAACCGAAGTCGTTAAAAATTTAAAACAGAATTCGTTCGTCA
GTGATGTAAATTATACGAAAAATTTTTAAACAAGGTGAGAGGAAAAAAAATATTGTTTTC
CAATTTCTTTGTGGTTTTAGCTACTATTTTTAGTAGTATTTATTATATAAAAGCTATTAA
AAGCACATAATTACGAAAAAAGTTGAAGGAAATGGCAAATGAACGAGTTACTTTAGCGGA
TGCTTTGAGTAATGTTGAGATTTTAGACGAAAGACCACTCCCAGATGAACAACCACTCAT
AGAAGCTTCAACTTGTTCAATCACATATCAGGCAAATTTTGATACAAACTTTGAAGATCG
TAATGGCTTCGTCACAGGCATTGCAAAATACATCGAAGAAGCAACAACTCATGCAAATCT
AAATATTCTACTTGAAGAAGGTCAAAAACATGCAGTTATGTTGTATACTTGGCGTTGTTG
TTCACGTGCAATTCCTCAACCAAAGTCAAACGAACAACCGAATCGAGTTGAAATTTATGA
AAAAACTGTTGAAGTACTTGCGCCAGAAGTGAACAAACTCCTCAATTTCATGTACTTTCA
GAAAAAAGCTATTGAAGTCTTCTCAGCTGAAGTTAAACGTTTATGTCATGCCGAAAAACG
TAAAGATTTTGTCTCAGAAGCTTACTTATTGACTCTTGGTAAATTCATCAACATGTTTGC
CGTGTTGGATGAGTTGAAAAATATGAAAAGTTCTGTGAAGAATGATTATTCAACTTATCG
TCGTGCCGCTCAATTTTTAAAAGTTATGTCTGATTCTCATACACTGCAAGAATCACAAAA
TTTGTCAATGTTTTTGGCTACTCAAAATAAGATTCGCGATACTGTAAAGGATACACTTGA
AAAGATTCCTGGTTTCGAGGAACTAATTTGTGAAGTCGTTAATATATGTGTACATATGTT
TGAACAAAAGATGTTTCTTACACCAGAAGAGAAGCATATGCTTGTGAAAGTTTGTGGTTT
TGGATTGTTTTTGATGGATTCGGAAATGTGCAATATCAATAAACTCGATCAGAAAAAGAA
ATTACGATTGGATCGCATTGACAGAATTTTTAAAAATTTAGAAGTTGTACCACTTTTTGG
TGATATGCAAATTAATCCTTTTAACTATGTTAGAAAAAGTAAACATTTTGATGCAAGCAA
ATGGCCACTTTCAACTTCGCAAGCAATCAGTCCTCAAGCAGATCTCATGGTACACTTGCC
AAATATAAGAGAAGAGCATGTCAAATATATTTCAGAACTGTCTCGATATAGCAATGAAGT
TACAACAACATATACATATAAGGAAAATCATTCTGATTCAGAAAATCGAGCTGTATCAGA
TCTTGCTTTACGTGGCTTAC
>g11516.t4 Gene=g11516 Length=396
MANERVTLADALSNVEILDERPLPDEQPLIEASTCSITYQANFDTNFEDRNGFVTGIAKY
IEEATTHANLNILLEEGQKHAVMLYTWRCCSRAIPQPKSNEQPNRVEIYEKTVEVLAPEV
NKLLNFMYFQKKAIEVFSAEVKRLCHAEKRKDFVSEAYLLTLGKFINMFAVLDELKNMKS
SVKNDYSTYRRAAQFLKVMSDSHTLQESQNLSMFLATQNKIRDTVKDTLEKIPGFEELIC
EVVNICVHMFEQKMFLTPEEKHMLVKVCGFGLFLMDSEMCNINKLDQKKKLRLDRIDRIF
KNLEVVPLFGDMQINPFNYVRKSKHFDASKWPLSTSQAISPQADLMVHLPNIREEHVKYI
SELSRYSNEVTTTYTYKENHSDSENRAVSDLALRGL
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g11516.t4 | Coils | Coil | Coil | 172 | 192 | - |
| 2 | g11516.t4 | PANTHER | PTHR12195:SF2 | CYTOPLASMIC FMR1-INTERACTING PROTEIN 1 | 3 | 396 | 7.4E-211 |
| 3 | g11516.t4 | PANTHER | PTHR12195 | CYTOPLASMIC FMR1-INTERACTING PROTEIN-RELATED | 3 | 396 | 7.4E-211 |
| 9 | g11516.t4 | PIRSF | PIRSF008153 | CYFIP | 2 | 396 | 7.7E-177 |
| 4 | g11516.t4 | PRINTS | PR01698 | Cytoplasmic fragile X mental retardation protein interacting protein signature | 45 | 62 | 1.8E-42 |
| 7 | g11516.t4 | PRINTS | PR01698 | Cytoplasmic fragile X mental retardation protein interacting protein signature | 100 | 116 | 1.8E-42 |
| 5 | g11516.t4 | PRINTS | PR01698 | Cytoplasmic fragile X mental retardation protein interacting protein signature | 140 | 169 | 1.8E-42 |
| 6 | g11516.t4 | PRINTS | PR01698 | Cytoplasmic fragile X mental retardation protein interacting protein signature | 261 | 276 | 1.8E-42 |
| 1 | g11516.t4 | Pfam | PF07159 | Protein of unknown function (DUF1394) | 62 | 268 | 2.2E-11 |
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:0031267 | small GTPase binding | MF |
| GO:0030833 | regulation of actin filament polymerization | BP |
KEGG
Orthology
This gene did not have any KEGG ortholog annotations (KAAS, GHOSTZ).
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.
