RetrogeneDB ID: | retro_cjac_2256 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 3:109497136..109498590(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | XRCC5 | ||
| Ensembl ID: | ENSCJAG00000012291 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_cjac_2256
TGGCCCTGCCGACTGACCATTGGCTCCAATTTGTCTATAGGAATTGCATCCTATAAATTGATTCTACGGGTGAGAGAGTT
TAAAAGACCTGGGCAGTTGTGGATGCAAAAACCCTAAAAAAAAAAAGAAGATATACAAAAAGAAACAGTTTATTGCTTAA
ATGATGATGATGAAACTGGAGTTTTAAAAGAGGATATTATTCAAGTGTTCCTCTATGGAAGTGATATAGCTCCTTTCTCT
AAAGTGGATGAGGAACAAATGAAATATAAATTGGAAGGCAAGTGCTTCTCTGTTTTGAGATTTTGTAAATCTTCTCAGGT
TTAGAGAAGATTCTTCAAGGGAAATCAAGTTCTAAAGGTCTTTGCAGCAAGAGACGATGAGGCAGCAGCAGTTGCACTTT
CCTCCCTGATTTATGCTTTGGATGAGTTAGATGTGGTGGCCATAGTTTGATATGCTTATGACAAAAGAACTAATCCTCAA
GTCGGCATGGCTTTTCCTCACATCAAGCATAATCATGAGTGTTTAGTGTATGTGCAGCCACCTTTCATGGAAGACTTGCT
GCAATATCTGTTTTCATCCTTGAAAAACAGTGAGAAATATGCTCCCACCGAGGCACAGTTGAATGCTGTTGATGCTTCTA
TTGACTCCATGAGCTTGGTAAAGAAAGATGGGAAGACAGATACTCTTGAAGACTTGTTTCCAACCACCCAAATCTCAAAT
CCTCTATTTCACAGATTATTTCGGTGTCTGCTGCACAAAGCTTTACATCCCCAGGAGCCTCTACCCCCAACTCAGCAGCA
TATTTAGAATATGCTGAATCCTCCCACTGAGGTGACAGCAAAATGTCAAATTTCTCTCTCTAAAATAAAGACCCTTTTCC
CTCTGATGGAAGCCAAGAAAAAGGATCAAGTAACCATTCAGGACATTTTCCAAGACAACCATACAAATGGACCCATCTCT
AAAAAATTAATGACTGAGGAAGAGGGAGCCCACTTCAGCGTCTCCAGCCTGGCTGAAGACAGTGTCACCTCTGCTGGAAG
TGTGAATCCTACTGAAAACTTTCGTGTTCTAGTGAAACAGAAAAATGCCAGCTTTGAGGAAGCGAGTGTTCAGCTCATAA
ATCACATCAAACAGTTTTTGGATAATAATGGAACACAATATTTTACGAAGAGCAGGGACTGCATCAGAGCCTTCCAGAAA
GAAGCCATTAAGTTTCAAAAGAGCAGTGCTTTAACAACTTCCTGTAAGCGCTTTGAGAGAAAGTGGAAATTAAACAATTA
AATCATTTATGGGAAATTGTTGTTCAGGATGGAATTACTCTGATCACCAAAGAGGAAGCCTCTGGAAGATCTGTCACAGC
TGAGGAAGCCAAAAAGTTTCTGGCCGCCAAAGTAAAACCAAGTGAAGACACAGCAGCCGTATTTGAAGAAGGTGCTTATG
GGAACGATTTACTG
ORF - retro_cjac_2256 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 80.45 % |
| Parental protein coverage: | 65.98 % |
| Number of stop codons detected: | 6 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | WPCRLTIGSNLSIRIAAYKSILQER-VKKTWTVVDAKTLKK-EDIQKETVYCLNDDDETEILKEDIIQGF |
| WPCRLTIGSNLSI.IA.YK.IL..R..K........K..KK.EDIQKETVYCLNDDDET..LKEDIIQ.F | |
| Retrocopy | WPCRLTIGSNLSIGIASYKLILRVREFKRPGQLWMQKP*KKKEDIQKETVYCLNDDDETGVLKEDIIQVF |
| Parental | RYGSDIVPFSKVDEEQMKYKSEGKCFSVLGFCKSSQVQRRFFMGNQVLKVFAARDDEAAAVALSSLIHAL |
| .YGSDI.PFSKVDEEQMKYK.EGKCFSVL.FCKSSQV.RRFF.GNQVLKVFAARDDEAAAVALSSLI.AL | |
| Retrocopy | LYGSDIAPFSKVDEEQMKYKLEGKCFSVLRFCKSSQV*RRFFKGNQVLKVFAARDDEAAAVALSSLIYAL |
| Parental | NDLDMVAIVRYAYDKRANPQVGVAFPHIKHNYECLVYVQLPFMEDLRQYMFSSLKNSKKYAPTEAQLNAV |
| ..LD.VAIV.YAYDKR.NPQVG.AFPHIKHN.ECLVYVQ.PFMEDL.QY.FSSLKNS.KYAPTEAQLNAV | |
| Retrocopy | DELDVVAIV*YAYDKRTNPQVGMAFPHIKHNHECLVYVQPPFMEDLLQYLFSSLKNSEKYAPTEAQLNAV |
| Parental | DALIDSMSLAKKDEKTNTLEDMFPTTKIPNPRFQRLFQCLLHRALHPREPLPPIQQHIWNMLNPPTEVTK |
| DA.IDSMSL.KKD.KT.TLED.FPTT.I.NP.F.RLF.CLLH.ALHP.EPLPP.QQHI.NMLNPPTEVT. | |
| Retrocopy | DASIDSMSLVKKDGKTDTLEDLFPTTQISNPLFHRLFRCLLHKALHPQEPLPPTQQHI*NMLNPPTEVTA |
| Parental | KSQIPLSKIKTLFPLIEAKKKDQVIAQDVFQDNHEDGPTAKKLKTEEGGAHFSISSLAEGSVTSVGSVNP |
| K.QI.LSKIKTLFPL.EAKKKDQV..QD.FQDNH..GP..KKL.TEE.GAHFS.SSLAE.SVTS.GSVNP | |
| Retrocopy | KCQISLSKIKTLFPLMEAKKKDQVTIQDIFQDNHTNGPISKKLMTEEEGAHFSVSSLAEDSVTSAGSVNP |
| Parental | AENFRVLVKQKKASFEEASNQLINHIEQFLDTNETLYFMKSMDCIRAFREEAIKF-SEEQRFNNFLKALR |
| .ENFRVLVKQK.ASFEEAS.QLINHI.QFLD.N.T.YF.KS.DCIRAF..EAIKF.S.EQ.FNNFL.AL. | |
| Retrocopy | TENFRVLVKQKNASFEEASVQLINHIKQFLDNNGTQYFTKSRDCIRAFQKEAIKF<SKEQCFNNFL*AL* |
| Parental | EKVESKQLNHFWEIVVQDGITLITKEEASGSSVTAEEAKKFLAPKEKPSEDTAAAFEEGGDVEDLL |
| EKVE.KQLNH.WEIVVQDGITLITKEEASG.SVTAEEAKKFLA.K.KPSEDTAA.FEEG....DLL | |
| Retrocopy | EKVEIKQLNHLWEIVVQDGITLITKEEASGRSVTAEEAKKFLAAKVKPSEDTAAVFEEGAYGNDLL |
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 | 133 .75 RPM |
| SRP051959_heart | 0 .00 RPM | 98 .21 RPM |
| SRP051959_kidney | 0 .00 RPM | 149 .34 RPM |
| SRP051959_liver | 0 .00 RPM | 129 .51 RPM |
| SRP051959_lung | 0 .00 RPM | 120 .05 RPM |
| SRP051959_lymph_node | 0 .00 RPM | 133 .72 RPM |
| SRP051959_skeletal_muscle | 0 .00 RPM | 125 .68 RPM |
| SRP051959_spleen | 0 .00 RPM | 135 .25 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_2256 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_2256 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_2256 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 1 parental gene, and 2 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Callithrix jacchus | ENSCJAG00000012291 | 2 retrocopies |
retro_cjac_2178, retro_cjac_2256 ,
|