RetrogeneDB ID: | retro_cjac_768 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 10:27500976..27501449(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | RBBP9 | ||
| Ensembl ID: | ENSCJAG00000005170 | ||
| Aliases: | None | ||
| Description: | retinoblastoma binding protein 9 [Source:HGNC Symbol;Acc:9892] |
Retrocopy-Parental alignment summary:
>retro_cjac_768
AAGTTTCTGGAGCAGATACCTGGTTTCCAGTGTTTGGCTAAAAACATGCCACACTCAATTACAGCAAGAGAGAGCATCTG
GCTGCCCTTCATGGAGGTGGGGCTGCACTGTGATGAGAAGACCATCATCAACATCCACAGTGCTGGGGCCGTCGCAGCCA
TTAGGTATGCAGAAACACATGAAGTATATGCTATTGTATTCGTGTCTGCATACATATCAGACTTGGGGATGAAAATAAGT
GTGTAAGTGAATACTTCAACTGCCCCTGGCAGTGGGAGAAGATCGGGGCCAGCTACCCTCACATTGTGTAGTTTGGCGCC
ACTGATGACCCATTCCTTCGCTGGAAGGAACAACACGAAGTAGCCGATAGGTTGGAAACCAAATTGTACAAATTCACTAA
CTGTGGCCACTTACAGAACACAGAGTTTCATGAACTGATTACTATGGTAAAGTTTTTGCTAAAAGTACCAGCA
ORF - retro_cjac_768 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 78.62 % |
| Parental protein coverage: | 84.95 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | KELEKIPGFQCLAKNMPDPITARESIWLPFMETELHCDEKTIIIGHSSGAIAAMRYAETHRVYAIVLVSA |
| K.LE.IPGFQCLAKNMP..ITARESIWLPFME..LHCDEKTII..HS.GA.AA.RYAETH.VYAIV.VSA | |
| Retrocopy | KFLEQIPGFQCLAKNMPHSITARESIWLPFMEVGLHCDEKTIINIHSAGAVAAIRYAETHEVYAIVFVSA |
| Parental | YTSDLG-DENERASGYFSRPWQWEKIKANCPYIVQFGSTDDPFLPWKEQQEVADRLETKLHKFTNRGHFQ |
| Y.SDLG.DEN...S.YF..PWQWEKI.A..P.IV.FG.TDDPFL.WKEQ.EVADRLETKL.KFTN.GH.Q | |
| Retrocopy | YISDLG<DENKCVSEYFNCPWQWEKIGASYPHIV*FGATDDPFLRWKEQHEVADRLETKLYKFTNCGHLQ |
| Parental | NTEFHELITVVKSLLKVPA |
| NTEFHELIT.VK.LLKVPA | |
| Retrocopy | NTEFHELITMVKFLLKVPA |
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 .02 RPM | 1 .82 RPM |
| SRP051959_heart | 0 .14 RPM | 1 .86 RPM |
| SRP051959_kidney | 0 .09 RPM | 4 .61 RPM |
| SRP051959_liver | 0 .09 RPM | 9 .08 RPM |
| SRP051959_lung | 0 .08 RPM | 2 .36 RPM |
| SRP051959_lymph_node | 0 .02 RPM | 2 .40 RPM |
| SRP051959_skeletal_muscle | 0 .22 RPM | 1 .35 RPM |
| SRP051959_spleen | 0 .08 RPM | 2 .73 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_768 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_768 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_768 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 | |
|---|---|---|---|
| Choloepus hoffmanni | ENSCHOG00000013286 | 1 retrocopy | |
| Callithrix jacchus | ENSCJAG00000005170 | 1 retrocopy |
retro_cjac_768 ,
|
| Macaca mulatta | ENSMMUG00000004146 | 1 retrocopy | |
| Rattus norvegicus | ENSRNOG00000007972 | 1 retrocopy |