RetrogeneDB ID: | retro_cjac_1188 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 14:14916216..14916707(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | None | ||
| Ensembl ID: | ENSCJAG00000011259 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_cjac_1188
ATGAAAGCCTGGGATTGGTGGCCCTGCTTCTGGGGGCCATGCTGGGAACTGCCTGGGCTCGGAGGAGCCAGGATCTCCCC
TATGGAGTGTGCAGGGCTCTGGTGGATGAACTAGAATGGGAAATTGCCAAGGTGGACCCCAAGAAAACCATTCAGATGGG
ACCTTTCCGTATCAATCCAGATGGCAGCCAGTCAGCGGTGGACGTGCCTTATGCCCTCTCAGAGGCCCACCGCACAGAGC
TGCTGGAGGAGATATCTGACCGGATGAAGGAGTATGGGGAACAGATTGATCCTTCCACCCATCGCAAGAACTATGTACGT
GTAGTGAGCCGGAATGGAGAATCCAGTGAACTGGACCTACAAGGCATCTGAATTGACTCAGGTATCAGTGGCACCCTCAA
GTTTGCGTGTGAGAGCGTTGTGGAGGAATACGAGGATGAACTCATTGAATTCTTTTCCCGAGAGGCTGACAATGTTAAAG
ACAAACTTTGC
ORF - retro_cjac_1188 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 89.7 % |
| Parental protein coverage: | 90.11 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | MKGWGW-LALLLGALLGTAWARRSQDLHCGACRALVDELEWEIAKVDPKKTIQMGSFRINPDGSQSVVEV |
| MK.W.W..ALLLGA.LGTAWARRSQDL..G.CRALVDELEWEIAKVDPKKTIQMG.FRINPDGSQS.V.V | |
| Retrocopy | MKAWDW<VALLLGAMLGTAWARRSQDLPYGVCRALVDELEWEIAKVDPKKTIQMGPFRINPDGSQSAVDV |
| Parental | PYARSEAHLTELLEEICDRMKEYGEQIDPSTHRKNYVRVVSRNGESSELDLQGIRIDSDISGTLKFACES |
| PYA.SEAH.TELLEEI.DRMKEYGEQIDPSTHRKNYVRVVSRNGESSELDLQGI.IDS.ISGTLKFACES | |
| Retrocopy | PYALSEAHRTELLEEISDRMKEYGEQIDPSTHRKNYVRVVSRNGESSELDLQGI*IDSGISGTLKFACES |
| Parental | IVEEYEDELIEFFSREADNVKDKLC |
| .VEEYEDELIEFFSREADNVKDKLC | |
| Retrocopy | VVEEYEDELIEFFSREADNVKDKLC |
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 .00 RPM | 12 .25 RPM |
| SRP051959_heart | 0 .00 RPM | 11 .44 RPM |
| SRP051959_kidney | 0 .00 RPM | 20 .32 RPM |
| SRP051959_liver | 0 .00 RPM | 21 .23 RPM |
| SRP051959_lung | 0 .03 RPM | 13 .63 RPM |
| SRP051959_lymph_node | 0 .02 RPM | 13 .22 RPM |
| SRP051959_skeletal_muscle | 0 .02 RPM | 7 .42 RPM |
| SRP051959_spleen | 0 .00 RPM | 16 .76 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_1188 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_1188 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_1188 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 4 parental genes, and 4 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Callithrix jacchus | ENSCJAG00000011259 | 1 retrocopy |
retro_cjac_1188 ,
|
| Dasypus novemcinctus | ENSDNOG00000010925 | 1 retrocopy | |
| Mustela putorius furo | ENSMPUG00000001366 | 1 retrocopy | |
| Ictidomys tridecemlineatus | ENSSTOG00000015971 | 1 retrocopy |