RetrogeneDB ID: | retro_cjac_3861 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | GL285268.1:47863..49144(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSCJAG00000021874 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | ZFP64 | ||
| Ensembl ID: | ENSCJAG00000000596 | ||
| Aliases: | None | ||
| Description: | ZFP64 zinc finger protein [Source:HGNC Symbol;Acc:15940] |
Retrocopy-Parental alignment summary:
>retro_cjac_3861
ATGTCACGGCGCAAGCAGGCCAAGCCTCAGCATCTCAACTCCGAGGAGCCGCGGCCTGTGCGCCGGGAGTGCGCGGAGGT
GGCCCCGCAGGTGGGGGGGGCGGGGAGCCCGCTTCGGAACTTGATAATGATGTTCCAAAAGCGACCTGCCTCTCCACTGA
AGGCAGTGACCCTCAGAAGGCCCCTGTCATCACTCTTGCCTCAGAGTCAAGGGAACAAACCGCCACCCTTGGAGAGAGGA
CATTCAACTGTTGCTACCCAGGTCGCCACTTCAAAACTATGCATGGCATGAAAGACTTGGACCGCCATCTTAGAATCCAC
ACGGGAGACAAACCGCACAAGTGTGACTTCTGTGACAAGTTCTTCAGCCGGAAGGACAACCTGATCATGCACGTGCGGTG
CCACACCAGTGTGAAGCCACACAAGCGTGACGTGTGCGACTGCACCGCCGTGGACAGTGGCAGCCTCAAGAAGCACCTGG
GGATCCACTCGGAGGAGCGGCCATACAAATGCCAGCTCTGCCCCTATGCCAGCCGCAACTCCAGCCAGCTCACCGTCCAC
CTGCGGTCCCACACGGGGGATACCCCCTTCCAGTGCTGGCTGTGTAGTGCCAAGTTCAAAATCAGCTCGACTTGAAAAAG
CACATGATCGTGCACTCTGGGGAGCAGCCTTTCACGTGCGAGTTCTGTGACGTCCACTGCACCATGAAGGCGAACCTCAA
ATCGCACATCCGCATCAAGCACACCTTCAAGTGTCTGCACTGTGCCTTCCAGGTCCGGGACCGGGCTGACCTCCTGGAGC
ACAGCCGGCTGCACCAGGCTGACCACCCGGAGAAGTGTCCTGAGTGCAGCTACTCCTGCTCCAGCGCGGCCATCCTGCGC
GTGCACAGCAGAGTCCACTGTAAGGACCATCCCTTCAAGTGTGACTTCTGCAGCTTTGACATAAAGCGGCCCAGCAGCCT
GGCCAAGCACATGGACAAGGTGCACAGGGACGAGGCCAAGATGGAGAACTGGGCCCCTCTGGGCAAAGAAGTGCCCAGAT
AGAGCAGCTCCCAACACAAGGCCAAGATCGTGACACAGAGAGCTTTTCGCTGTGAGACCCGTGGCGCCTCCTTCGCCAGG
GATGAGTCTCTGAGATGCCCCAAGCAGCAGCATAGTGATCAGAGTGAGAACAGGAACTCAGACTTGGTCACCTTCCCACC
CGAAAGCTGCGCCTCAGGGCAGCTCAGCACCCTGGTCTCTGTGGGCAGCTCGAGGCCCCCCTAGAACCCAGCTAAGACCT
C
ORF - retro_cjac_3861 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 89.33 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 2 |
| Number of frameshifts detected: | 3 |
Retrocopy - Parental Gene Alignment:
| Parental | MSRRKQANPQHLNSEEPRPARRECAEVAPQV--AGEP-ASELDNDVPKATCLSTEGSDPQKAPVIALASE |
| MSRRKQA.PQHLNSEEPRP.RRECAEVAPQV..AG.P.ASELDNDVPKATCLSTEGSDPQKAPVI.LASE | |
| Retrocopy | MSRRKQAKPQHLNSEEPRPVRRECAEVAPQVGGAGSP<ASELDNDVPKATCLSTEGSDPQKAPVITLASE |
| Parental | SREQTATLGERTFNCCYPGCHFKTVHGMKDLDRHLRIHTGDKPHKCEFCDKCFSRKDNLTMHMRCHTSVK |
| SREQTATLGERTFNCCYPG.HFKT.HGMKDLDRHLRIHTGDKPHKC.FCDK.FSRKDNL.MH.RCHTSVK | |
| Retrocopy | SREQTATLGERTFNCCYPGRHFKTMHGMKDLDRHLRIHTGDKPHKCDFCDKFFSRKDNLIMHVRCHTSVK |
| Parental | PHKCHLCDYAAVDSSSLKKHLRIHSDERPYKCQLCPYASRNSSQLTVHLRSHTGDTPFQCWLCSAKFKIS |
| PHK...CD..AVDS.SLKKHL.IHS.ERPYKCQLCPYASRNSSQLTVHLRSHTGDTPFQCWLCSAKFKIS | |
| Retrocopy | PHKRDVCDCTAVDSGSLKKHLGIHSEERPYKCQLCPYASRNSSQLTVHLRSHTGDTPFQCWLCSAKFKIS |
| Parental | S-DLKRHMIVHSGEKPFKCEFCDVRCTMKANLKSHIRIKHTFKCLHCAFQGRDRADLLEHSRLHQADHPE |
| S.DLK.HMIVHSGE.PF.CEFCDV.CTMKANLKSHIRIKHTFKCLHCAFQ.RDRADLLEHSRLHQADHPE | |
| Retrocopy | S<DLKKHMIVHSGEQPFTCEFCDVHCTMKANLKSHIRIKHTFKCLHCAFQVRDRADLLEHSRLHQADHPE |
| Parental | KCPECSYSCSSAAALRVHSRVHCKDRPFKCDFCSFDTKRPSSLAKHIDKVHRDETKTENWAPPGKEVPRE |
| KCPECSYSCSSAA.LRVHSRVHCKD.PFKCDFCSFD.KRPSSLAKH.DKVHRDE.K.ENWAP.GKEVPR. | |
| Retrocopy | KCPECSYSCSSAAILRVHSRVHCKDHPFKCDFCSFDIKRPSSLAKHMDKVHRDEAKMENWAPLGKEVPR* |
| Parental | SSSQHMAKIVTQRAFRCETCGASFVRDDSLRCHKKQHSDQSENRNSDLVTFPPESSASGQLSTLVSV-GQ |
| SSSQH.AKIVTQRAFRCET.GASF.RD.SLRC.K.QHSDQSENRNSDLVTFPPES.ASGQLSTLVSV.GQ | |
| Retrocopy | SSSQHKAKIVTQRAFRCETRGASFARDESLRCPKQQHSDQSENRNSDLVTFPPESCASGQLSTLVSV<GQ |
| Parental | LEVPLESSQDL |
| LE.PLE.S.DL | |
| Retrocopy | LEAPLEPS*DL |
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 | 4 .64 RPM |
| SRP051959_heart | 0 .00 RPM | 5 .02 RPM |
| SRP051959_kidney | 0 .00 RPM | 5 .17 RPM |
| SRP051959_liver | 0 .00 RPM | 2 .38 RPM |
| SRP051959_lung | 0 .00 RPM | 6 .36 RPM |
| SRP051959_lymph_node | 0 .02 RPM | 5 .05 RPM |
| SRP051959_skeletal_muscle | 0 .00 RPM | 1 .53 RPM |
| SRP051959_spleen | 0 .17 RPM | 5 .32 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_3861 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_3861 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_3861 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 | ENSCJAG00000000596 | 1 retrocopy |
retro_cjac_3861 ,
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