RetrogeneDB ID: | retro_cjac_4227 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | Y:170056..171079(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSCJAG00000023103 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | CAB39 | ||
| Ensembl ID: | ENSCJAG00000013349 | ||
| Aliases: | None | ||
| Description: | calcium binding protein 39 [Source:HGNC Symbol;Acc:20292] |
Retrocopy-Parental alignment summary:
>retro_cjac_4227
ATGCGGTTCCCGTTCGGGAAGTCTCACAAATCTCCAGCAGACACTGTGAAGGATCTGAAGGAAAGCATGGCCGTTCTGGA
AGAGCAAGACATTTCTGACAAAAAAGCAGAAAAGGCTACAGAAGAAGTTTCCAAAAATCTGGTTGCCATGAAAGAAATTC
TGTATGGCACAAATGAAAAAGAGCCTCAGACAGAAGCAGTGGCCCAGCTTGCTCACGAACTCTGTAATAGTGGGCTTCTT
AGCACCCTGGTAGCTGATTTACAGCTCGTTGACTTTGAGGGCAAAAAAGACGTGGCTCAAATTTTCAACAATGTTCTCAG
AAGACAAATTGGTACAAGAACTCCTACTGTTGAATACATCTGCACCCAACAGAATATTTTGTTCGTGTTATTGAAAGGGT
ATGAATCTCCAGAAATAGCTTTAAATTGTGGAATAATGTTAAGAGAATGCATCAGACATGAACCACTTGCAAAAATCATT
TTGTGGTCAGAACAGGTTTCTGATTTCTTCAGATATGTCGAAATGTCAACGTTTGACATAGCTTCAGATGCATTTGCCAC
ATTCAAGGATTTACTTACAAGACATAAATTGCTCAGTGCAGAATTTTTGGAACAGCATTATGATAGATTTTTGAGTGAAT
ATGAGAAGTTACTTCATTCAGAAAATTACGTGACAAAAAGAAAGTCACTCAAGCTTCTCGGTGAACTACTACTAGACAGA
CACAACTTCACAATTATGACAAAATACATCAGTAAACCTGAGAACCTCAAGTTAATGATGAACCTGCTGCGAGACAAAAG
TCGCAACATCCAGTTGGAGGCCTTTCACGTTTTTAAGGTGTTTGTAGCCAATCCTAACAAGACACAGCCCATCCTAGACA
TCCTCCTCAAGAACCAGACCAAACTCATAGAGTCCCTCAGCAAGTTTCAGAATGACAGGACGGAGGATGAGCAGTTTAAT
GACGAGAAGACCTATTTAGTTAAACAGATCAGGGATTTGAAGAGACCAGCTCAGCAAGAAGCT
ORF - retro_cjac_4227 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 95.6 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | MPFPFGKSHKSPADIVKNLKESMAVLEKQDISDKKAEKATEEVSKNLVAMKEILYGTNEKEPQTEAVAQL |
| M.FPFGKSHKSPAD.VK.LKESMAVLE.QDISDKKAEKATEEVSKNLVAMKEILYGTNEKEPQTEAVAQL | |
| Retrocopy | MRFPFGKSHKSPADTVKDLKESMAVLEEQDISDKKAEKATEEVSKNLVAMKEILYGTNEKEPQTEAVAQL |
| Parental | AQELYNSGLLSTLVADLQLIDFEGKKDVAQIFNNILRRQIGTRTPTVEYICTQQNILFMLLKGYESPEIA |
| A.EL.NSGLLSTLVADLQL.DFEGKKDVAQIFNN.LRRQIGTRTPTVEYICTQQNILF.LLKGYESPEIA | |
| Retrocopy | AHELCNSGLLSTLVADLQLVDFEGKKDVAQIFNNVLRRQIGTRTPTVEYICTQQNILFVLLKGYESPEIA |
| Parental | LNCGIMLRECIRHEPLAKIILWSEQFYDFFRYVEMSTFDIASDAFATFKDLLTRHKLLSAEFLEQHYDRF |
| LNCGIMLRECIRHEPLAKIILWSEQ..DFFRYVEMSTFDIASDAFATFKDLLTRHKLLSAEFLEQHYDRF | |
| Retrocopy | LNCGIMLRECIRHEPLAKIILWSEQVSDFFRYVEMSTFDIASDAFATFKDLLTRHKLLSAEFLEQHYDRF |
| Parental | FSEYEKLLHSENYVTKRQSLKLLGELLLDRHNFTIMTKYISKPENLKLMMNLLRDKSRNIQFEAFHVFKV |
| .SEYEKLLHSENYVTKR.SLKLLGELLLDRHNFTIMTKYISKPENLKLMMNLLRDKSRNIQ.EAFHVFKV | |
| Retrocopy | LSEYEKLLHSENYVTKRKSLKLLGELLLDRHNFTIMTKYISKPENLKLMMNLLRDKSRNIQLEAFHVFKV |
| Parental | FVANPNKTQPILDILLKNQTKLIEFLSKFQNDRTEDEQFNDEKTYLVKQIRDLKRPAQQEA |
| FVANPNKTQPILDILLKNQTKLIE.LSKFQNDRTEDEQFNDEKTYLVKQIRDLKRPAQQEA | |
| Retrocopy | FVANPNKTQPILDILLKNQTKLIESLSKFQNDRTEDEQFNDEKTYLVKQIRDLKRPAQQEA |
Legend:
| * | Stop codon |
| > | Forward frameshift by one nucleotide |
| < | Reverse frameshift by one nucleotide |
(Hint: click retrocopy or parental gene accession number on the plot's legend, to show / hide expression level values)
Expression validation based on RNA-Seq data:
| Library | Retrocopy expression | Parental gene expression |
|---|---|---|
| SRP051959_colon | 0 .27 RPM | 35 .37 RPM |
| SRP051959_heart | 0 .12 RPM | 31 .24 RPM |
| SRP051959_kidney | 0 .33 RPM | 33 .70 RPM |
| SRP051959_liver | 0 .09 RPM | 18 .37 RPM |
| SRP051959_lung | 0 .16 RPM | 40 .16 RPM |
| SRP051959_lymph_node | 0 .21 RPM | 37 .99 RPM |
| SRP051959_skeletal_muscle | 0 .22 RPM | 32 .69 RPM |
| SRP051959_spleen | 0 .11 RPM | 36 .05 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_4227 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_4227 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_4227 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 3 parental genes, and 3 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Callithrix jacchus | ENSCJAG00000013349 | 1 retrocopy |
retro_cjac_4227 ,
|
| Equus caballus | ENSECAG00000015288 | 1 retrocopy | |
| Otolemur garnettii | ENSOGAG00000002000 | 1 retrocopy |