RetrogeneDB ID: | retro_cjac_698 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 10:70325419..70326541(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | ZNF277 | ||
| Ensembl ID: | ENSCJAG00000016891 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_cjac_698
ATGGTTGCTCCCAAGACCTAGGGAGCTGCAGCCCGACTGGAGGAAGACTGTGATAGGAGCTGCAGCACAGTTGGGGGTGT
AGGTTATGGGGGCAGTAAGGATTGTATCCTGGAGCCACTTTCCCTGCCAGAAAGTCCAGGTCGCACCACCACTTTAGAAG
GTTCTCCATCTGTGCCTTGTATTTTCTGTGAAGAACGTTTTCCTGTGGCTGAACAAGAGAAACTTCTGAAGCACATGAGT
ATTGAGCATAAGATTGCCATAGCTGATGTCAAATTGGTGGCTGATTTCCAAAGGTACCTTTATATTGGAGGAAGAGGTTC
ACTGAACAGCCCATCGCAGATTTTTGTAGTGTGATAAGAATTAATTCTGCTGCTCCATTTGAAGAACAAGATAATTATTT
TTTGTTATGTGATGTTTTACCAGAGGATAGAATTCTTCGAGAAGAGCTTCAGAAACAGAGACTGAAAGAAATTCTGGAAC
AACAGCAGCAAGAACAAAATGATACCAATTTTCATGGCATTTGTATATTTTGCAATGAAGAGTTCCTTGGAAACAGATCT
GTTCTTTTGGACCACATGGCAAGTGAATATGCTTCAACATTGGATTGCCAGACAACATCATAAACTGCAATGATTTTTGT
GTACATTACAGAAAAAGCTTGACAATTTGCAGTTCTTGTACTGTGAGAAGACCTTCAAGGAAAAAAATATGCTTAAAGAT
CACACGAGGAAACAATAGCCTCATAAGATTAATCCTAAGAACAGAGAATATGATCGATTTTATGTCATCAATTATTTGGA
ACTTGGAAAATCATGGGAAGAAGTTCAGTTGGAAGATGATCGGGAATTGCTGGACCATCATGAAGATGACTGGTCTGACT
GGGAAGAACACCCTGACTCTGCCATCTGCTTATTTGGTGAAAAGCAAGTTGAAACAATTGAGAAATTGTATGTCCACATG
GAGGATGCACATGAATTCGATCTCAAAATAGAGTCAGAAATTAGATTAAATTTCTATCAGCAAGTGAAACTGGTCAGTTT
TATTCGGAGGCAAGTTCACCAATGCAGATCTTTTGGCTGCCATGTGAAGTTCAAATCCAAAGCAGACTTAAGGACTCACA
TG
ORF - retro_cjac_698 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 86.28 % |
| Parental protein coverage: | 83.37 % |
| Number of stop codons detected: | 2 |
| Number of frameshifts detected: | 3 |
Retrocopy - Parental Gene Alignment:
| Parental | MAVPKTQGAVARLEEDRDGSCSTVGGVGYGDSKDCILEPLSLPESPGGTTTLEGSPSVPCIFCEEHFHVA |
| M..PKT.GA.ARLEED.D.SCSTVGGVGYG.SKDCILEPLSLPESPG.TTTLEGSPSVPCIFCEE.F.VA | |
| Retrocopy | MVAPKT*GAAARLEEDCDRSCSTVGGVGYGGSKDCILEPLSLPESPGRTTTLEGSPSVPCIFCEERFPVA |
| Parental | EQDKLLKHMIIEHKIVIADVKLVADFQRYI-LYWRKRFTEQPITDFCSVIRINSTAPFEEQENYFLLCDV |
| EQ.KLLKHM.IEHKI.IADVKLVADFQRY..LYWRKRFTEQPI.DFCSVIRINS.APFEEQ.NYFLLCDV | |
| Retrocopy | EQEKLLKHMSIEHKIAIADVKLVADFQRYL<LYWRKRFTEQPIADFCSVIRINSAAPFEEQDNYFLLCDV |
| Parental | LPEDRILREELQKQKLKEILEQQQQERNDNNFHGICMFCNEEFLGNRSVLLNHMAREHA-FNIGLPDNIV |
| LPEDRILREELQKQ.LKEILEQQQQE.ND.NFHGIC.FCNEEFLGNRSVLL.HMA.E.A.FNIGLPDNI. | |
| Retrocopy | LPEDRILREELQKQRLKEILEQQQQEQNDTNFHGICIFCNEEFLGNRSVLLDHMASEYA<FNIGLPDNII |
| Parental | NCNEF-LCTLQKKLDNLQCLYCEKTFRDKNTLKDHMRKKQHRKINPKNREYDRFYVINYLELGKSWEEVQ |
| NCN.F.LCTLQKKLDNLQ.LYCEKTF..KN.LKDH.RK....KINPKNREYDRFYVINYLELGKSWEEVQ | |
| Retrocopy | NCNDF<LCTLQKKLDNLQFLYCEKTFKEKNMLKDHTRKQ*PHKINPKNREYDRFYVINYLELGKSWEEVQ |
| Parental | LEDDRELLDNQEDDWSDWEEHPASAVCLFCEKQAETIEKLYVHMEDAHEFNLLKIKSELGLNFYQQVKLV |
| LEDDRELLD..EDDWSDWEEHP.SA.CLF.EKQ.ETIEKLYVHMEDAHEF..LKI.SE..LNFYQQVKLV | |
| Retrocopy | LEDDRELLDHHEDDWSDWEEHPDSAICLFGEKQVETIEKLYVHMEDAHEFD-LKIESEIRLNFYQQVKLV |
| Parental | NFIRRQVHQCRCYGCHVKFKSKADLRTHM |
| .FIRRQVHQCR..GCHVKFKSKADLRTHM | |
| Retrocopy | SFIRRQVHQCRSFGCHVKFKSKADLRTHM |
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 | 6 .79 RPM |
| SRP051959_heart | 0 .05 RPM | 9 .79 RPM |
| SRP051959_kidney | 0 .00 RPM | 15 .18 RPM |
| SRP051959_liver | 0 .06 RPM | 15 .05 RPM |
| SRP051959_lung | 0 .02 RPM | 13 .83 RPM |
| SRP051959_lymph_node | 0 .02 RPM | 7 .49 RPM |
| SRP051959_skeletal_muscle | 0 .00 RPM | 9 .06 RPM |
| SRP051959_spleen | 0 .04 RPM | 12 .54 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_698 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_698 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_698 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 3 parental genes, and 4 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Callithrix jacchus | ENSCJAG00000016891 | 2 retrocopies |
retro_cjac_558, retro_cjac_698 ,
|
| Mus musculus | ENSMUSG00000055917 | 1 retrocopy | |
| Otolemur garnettii | ENSOGAG00000005326 | 1 retrocopy |