RetrogeneDB ID: | retro_cjac_1917 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 2:65484350..65485591(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | MKNK2 | ||
| Ensembl ID: | ENSCJAG00000000539 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_cjac_1917
CAGCCAGCCCATTGACATCCCGGACGCCAAGAAGAGGGGCAAGAAGAAGAAGCGCGGCCGGGCCACCAACAGCTTCTTGG
GCAGGTTTGAAGACATCCACTGGCTACGGGAGGATGTTCTGGGTGAGGGCGCCCATGCCCACCTGCAGACCTGCATCAAC
CTGATCACCAGCCAGGATTACGCTGTCAAGATCATTGAGAAGCAGCCAGGCCACATTCGGAGCAGGGTTTTCCGGGAGGT
GGAGATGCTGTACCAGTGCCAGGGACACAGGAACGTTCTAGAGCTGATTGAGTTCTTCGAGGAGGAGGACCGCTTCTACC
TGGTATTTGAGAAGATGCAGGAGGCTCCATCCTGAGCCACAACCACAAGCGCCGGCACTTCAACGAGCTGGAGGCCAGTG
TGGTGGTGCAGGACGTGGCCAGTGCCTTGGACTTTTTGCACAACAAAGGCATCACCCACAGGGACCTAAAGCCGAAAAAC
ATCCTCTGTGAGCACCCCAACGGGGTCTTCCCCGTGAAGATCTGTGACTTCTACCTGGGCAGCGGCATCAAACTCAACAG
GGACTGCTCCCCCATCTCCACCCCGGAGCTGCTCACCCTGTGCGGCTCGGCGGAGTACATGGCCCCGGAGGTGGTGGAGG
TCTTCAGCAAGGAGGCCAACATCTACAACAAGTGCTGCGACCTGTGGAGCCTGATCGTCATCCTGTACATCCTGCTCAGC
GGCTACCCACCCTTTGTGGGCTGCTGCGGCGGCAACTGAGGCTGGTTCCACGGCGAGGCCTGCACTGCCTGCCAGAACAT
GCTGTTTGAGAGCATCCAGGAGGGCAAGTACGAGTTTCCCGACAAGGACTGGGCCCACATCTCCTGCGCCACCAAAGACC
TCATCTCCAAGCTGCTTGTCTGCGACTCCAAGCAGAGGCTGAGCGCTGCCCAAGTCCTGCAACATCCCTGGGTTCAAGGG
TGTGCCCCGGAGAACACTCTGCCCACTCCCATGGTCCTGCAGAGGAACAGCTGTGCCAAAGACCTCACGTCCTTCGCAGC
AGAGCTCATCGCCATGAATCGGCAGCTGGCCCAGCGCGACGAGGACCTGGTGGAGGAGGAGGCTGCGGGGCAGGGCCAGC
CTGTCCTGGTCCGAGCTACCTCATGCTGCCTGCAGCTGTCACCGCCTCTGAGTCCAAGCTGGCCCAGCGGCAGCAAAGGG
CCAGCCTGTCCTCGGCCCCCGCGGTGTTGGTGGGAGACCGC
ORF - retro_cjac_1917 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 89.45 % |
| Parental protein coverage: | 89.59 % |
| Number of stop codons detected: | 2 |
| Number of frameshifts detected: | 3 |
Retrocopy - Parental Gene Alignment:
| Parental | QPAHRHP-DAKKRGKKKKRGRATDSFSGRFEDVYQLQEDVLGEGAHARVQ-CINLITSQEYAVKIIEKQP |
| QPAH.HP.DAKKRGKKKKRGRAT.SF.GRFED...L.EDVLGEGAHA..Q.CINLITSQ.YAVKIIEKQP | |
| Retrocopy | QPAH*HP>DAKKRGKKKKRGRATNSFLGRFEDIHWLREDVLGEGAHAHLQTCINLITSQDYAVKIIEKQP |
| Parental | GHIRSRVFREVEMLYQCQGHRNVLELIEFFEEEDRFYLVFEKMR-GGSILSHIHKRRHFNELEASVVVQD |
| GHIRSRVFREVEMLYQCQGHRNVLELIEFFEEEDRFYLVFEKM..GGSILSH.HKRRHFNELEASVVVQD | |
| Retrocopy | GHIRSRVFREVEMLYQCQGHRNVLELIEFFEEEDRFYLVFEKMQ<GGSILSHNHKRRHFNELEASVVVQD |
| Parental | VASALDFLHNKGIAHRDLKPENILCEHPNQVSPVKICDFDLGSGIKLNGDCSPISTPELLTPCGSAEYMA |
| VASALDFLHNKGI.HRDLKP.NILCEHPN.V.PVKICDF.LGSGIKLN.DCSPISTPELLT.CGSAEYMA | |
| Retrocopy | VASALDFLHNKGITHRDLKPKNILCEHPNGVFPVKICDFYLGSGIKLNRDCSPISTPELLTLCGSAEYMA |
| Parental | PEVVEAFSEEASIYDKRCDLWSLGVILYILLSGYPPFVGRCGSDCGWDRGEACPACQNMLFESIQEGKYE |
| PEVVE.FS.EA.IY.K.CDLWSL.VILYILLSGYPPFVG.CG...GW..GEAC.ACQNMLFESIQEGKYE | |
| Retrocopy | PEVVEVFSKEANIYNKCCDLWSLIVILYILLSGYPPFVGCCGGN*GWFHGEACTACQNMLFESIQEGKYE |
| Parental | FPDKDWAHISCAAKDLISKLLVRDAKQRLSAAQVLQHPWVQGCAPENTLPTPMVLQRNSCAKDLTSFAAE |
| FPDKDWAHISCA.KDLISKLLV.D.KQRLSAAQVLQHPWVQGCAPENTLPTPMVLQRNSCAKDLTSFAAE | |
| Retrocopy | FPDKDWAHISCATKDLISKLLVCDSKQRLSAAQVLQHPWVQGCAPENTLPTPMVLQRNSCAKDLTSFAAE |
| Parental | AIAMNRQLAQRDEDLAEEEAAGQGQPVLVRATSRCLQLSPP-SESKLAQRRQRASLSSAPVVLVGDR |
| .IAMNRQLAQRDEDL.EEEAAGQGQPVLVRATS.CLQLSPP.SESKLAQR.QRASLSSAP.VLVGDR | |
| Retrocopy | LIAMNRQLAQRDEDLVEEEAAGQGQPVLVRATSCCLQLSPP<SESKLAQRQQRASLSSAPAVLVGDR |
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 .13 RPM | 11 .23 RPM |
| SRP051959_heart | 0 .28 RPM | 23 .47 RPM |
| SRP051959_kidney | 0 .24 RPM | 32 .84 RPM |
| SRP051959_liver | 0 .43 RPM | 27 .90 RPM |
| SRP051959_lung | 0 .29 RPM | 25 .80 RPM |
| SRP051959_lymph_node | 0 .34 RPM | 25 .00 RPM |
| SRP051959_skeletal_muscle | 0 .55 RPM | 62 .78 RPM |
| SRP051959_spleen | 0 .17 RPM | 28 .15 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_1917 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_1917 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_1917 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 1 parental gene, and 1 retrocopy.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Callithrix jacchus | ENSCJAG00000000539 | 1 retrocopy |
retro_cjac_1917 ,
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