RetrogeneDB ID: | retro_cjac_1605 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 17:58694104..58695538(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | SWAP70 | ||
| Ensembl ID: | ENSCJAG00000011252 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_cjac_1605
AAAAAAAACCTCACAAAAGAATCCCCTGCTCATTACAGAAGATGATGCATTTAAAGTATGGGTTATTTTCAACTTTGTAT
CTGAGGCCAAGTATCCATTAATTATTGTGACAGAAGAGATTGAATACCTGCTTAAGAAGCTTACAGAAGCTATGGGAGGA
GGTTGGCAGCAAGAACAATTTGAACATTATAAAGTCAACTTTGATGACAGTAAAGATGGCGTGGGAACTTATCGAGCTTA
TTGGAAATGGACAGTTTAGCAAAGGCATGGATTGGCAGACTGTGTCTCTGGCAATTAATGAAGTCTTTAATGAACTTATA
CTAGATGTATTAAAACAGGGTTACATGATGAAAAAGGGCCACAGACTGAAAAACTGGACTGAACGATGGTCTGTACTAAA
ACGCAACATAATTTCTTACTATGTGAGTGAGGACCTGAATGATAAGAAAGGAGACATTCTCTTGGATGAAAACTGCTGTT
TAGAGTCCTTGCCTGACAAAGATGGAAAGAAATGCCTTTTTCTCGTAAAATGTTTTGATAAGACTTTTGAAATTGGTGCT
TCAGCTAAGAAGAAGAAACAGGAGTGGATAAAAGCCATTCATTCTACTATTCATCTGTTGAAGCTGGGCAGCCCTCCACC
ACACAAAGAAGCCTGACAGCGTCTGAAGGAACTCCGGAAGAAGCAACTGGCTGAACAAGAGGAAGTGGAGCGACAAATGA
AGGAGCTCCAGGCCGCCAACGAAAGCAGGCAGCTGGAGCTGGAGGCCGTGCGGAAGAAACAAGGAAGCAGCATCCCGTGC
AGCAGAAGAGGAAAAGAAACGCCTTCAGACTCAACTGGAACTTCAGGCCAGGTTCAGCACAGAGCTGGAAAGAAAGAAGC
TTATTAAACAGCAGATGGAAGGACAGGTTGCTCCAAAGTCCTCTGAACTGGGACAGTATTTACAGCGAGTACGGGAGCTG
GAAGACATGTACCTAAGGCTGCAAGAGGCTCTTGAGGATGAGAGACAGGCCCGGCAAGATGATGAGACGGTGCGGAAGCT
TCAGGCCAGGTTGTTGGAGGAAGAGTCTTCCAAGAGGGCTGAACTAGAAAAGTGGCACTTGGAGCAGCAGCAGGCCATTC
AGACGACTGAGACAGAGAAGCAGGAGTTGGAGAATCAGCGTGTCCTGGAGAAGCGGGCCCTGCAAGAAGCCATGGAGCAG
CTGGAGTTGGAACGGAAACAAGCACTTGAGCAGTACTAGGAAGTTAAAAAGAAGCTGGAGATGGCAACTAATAAGACCAA
GAGTTGGAAGGACGACGTGGCCCATCGTGAAGGATTAATTCAACTGATAGAACCAGGTTCAAAGAACCCTCACCTGATCA
CTAACTGGGGACCTGCTACTTTCGTTGAGGCAGAACTTGAAGAGAGAACTGGAAAGAGAAAAAGACCACGGAGT
ORF - retro_cjac_1605 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 87.27 % |
| Parental protein coverage: | 82.74 % |
| Number of stop codons detected: | 2 |
| Number of frameshifts detected: | 3 |
Retrocopy - Parental Gene Alignment:
| Parental | KKNLTK-NPLLITEEDAFKVWVIFNFLSEDKYPLIIVTEEIEYLLKKLTEAMGGGWQQEQFEHYKVNFDD |
| KKNLTK.NPLLITE.DAFKVWVIFNF.SE.KYPLIIVTEEIEYLLKKLTEAMGGGWQQEQFEHYKVNFDD | |
| Retrocopy | KKNLTK>NPLLITEDDAFKVWVIFNFVSEAKYPLIIVTEEIEYLLKKLTEAMGGGWQQEQFEHYKVNFDD |
| Parental | SKDGLSAW-ELIELIGNGQFSKGMDRQTVSMAINEVFNELILDVLKQGYMMKKGHRRKNWTERWFVLKPN |
| SKDG.....ELI...GNGQFSKGMD.QTVS.AINEVFNELILDVLKQGYMMKKGHR.KNWTERW.VLK.N | |
| Retrocopy | SKDGVGTY>ELI---GNGQFSKGMDWQTVSLAINEVFNELILDVLKQGYMMKKGHRLKNWTERWSVLKRN |
| Parental | IISYYVSEDLNDKKGDILLDENCCVESLPDKDGKKCLFLVKCFDKTFEISASDKKKKQEWIQAIHSTIHL |
| IISYYVSEDLNDKKGDILLDENCC.ESLPDKDGKKCLFLVKCFDKTFEI.AS.KKKKQEWI.AIHSTIHL | |
| Retrocopy | IISYYVSEDLNDKKGDILLDENCCLESLPDKDGKKCLFLVKCFDKTFEIGASAKKKKQEWIKAIHSTIHL |
| Parental | LKLGSPPPHKEARQRRKELRKKQLAEQEELERQMKELQAANESKQLELEAVRKK-LEEAASRAAEEEKKR |
| LKLGSPPPHKEA.QR.KELRKKQLAEQEE.ERQMKELQAANES.QLELEAVRKK..E.A...A.EEEKKR | |
| Retrocopy | LKLGSPPPHKEA*QRLKELRKKQLAEQEEVERQMKELQAANESRQLELEAVRKK>KEAASRAA-EEEKKR |
| Parental | LQTQVELQARFSTELEREKLIRQQMEEQVAQKSSELEQYLLRVRELEDMYLRLQEALEDERQARQDEETV |
| LQTQ.ELQARFSTELER.KLI.QQME.QVA.KSSEL.QYL.RVRELEDMYLRLQEALEDERQARQD.ETV | |
| Retrocopy | LQTQLELQARFSTELERKKLIKQQMEGQVAPKSSELGQYLQRVRELEDMYLRLQEALEDERQARQDDETV |
| Parental | RKLQARLLEEESSKRAELEKWHLEQQQAIQMTEAEKQELENQRVLKEQALQEAMEQLEQLELERKQALEQ |
| RKLQARLLEEESSKRAELEKWHLEQQQAIQ.TE.EKQELENQRVL...ALQEAMEQLE...LERKQALEQ | |
| Retrocopy | RKLQARLLEEESSKRAELEKWHLEQQQAIQTTETEKQELENQRVLEKRALQEAMEQLE---LERKQALEQ |
| Parental | YEEVKKKLEMATNKTKSWKDKVAHHEGLIRLIEPGSKNPHLITNWGPAAFTEAELEEREKNWKEKKT |
| Y.EVKKKLEMATNKTKSWKD.VAH.EGLI.LIEPGSKNPHLITNWGPA.F.EAELEER....K.... | |
| Retrocopy | Y*EVKKKLEMATNKTKSWKDDVAHREGLIQLIEPGSKNPHLITNWGPATFVEAELEERTGKRKRPRS |
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 | 7 .23 RPM |
| SRP051959_heart | 0 .02 RPM | 20 .84 RPM |
| SRP051959_kidney | 0 .00 RPM | 8 .16 RPM |
| SRP051959_liver | 0 .00 RPM | 9 .29 RPM |
| SRP051959_lung | 0 .03 RPM | 14 .71 RPM |
| SRP051959_lymph_node | 0 .00 RPM | 13 .72 RPM |
| SRP051959_skeletal_muscle | 0 .00 RPM | 8 .21 RPM |
| SRP051959_spleen | 0 .04 RPM | 30 .29 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_1605 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_1605 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_1605 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 2 parental genes, and 3 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Callithrix jacchus | ENSCJAG00000011252 | 1 retrocopy |
retro_cjac_1605 ,
|
| Callithrix jacchus | ENSCJAG00000015575 | 2 retrocopies |