RetrogeneDB ID: | retro_cjac_2664 | ||
Retrocopylocation | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 5:127464706..127465035(-) | ||
| Located in intron of: | None | ||
Retrocopyinformation | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental geneinformation | Parental gene summary: | ||
| Parental gene symbol: | MED9 | ||
| Ensembl ID: | ENSCJAG00000008916 | ||
| Aliases: | None | ||
| Description: | mediator complex subunit 9 [Source:HGNC Symbol;Acc:25487] |
Retrocopy-Parental alignment summary:
>retro_cjac_2664
ATGGCCTCTGCTGGGGAGGCCACCAGGCACAGACCGAGGGATGCCTCACCTTCACTGTCAACCACAGCAGCTGCCTGCCC
TCAGGAGGGAGGAAGGGGACAACTCCTTTTCACTTCTGCGCACAACGTCATCAAACACATAGACAAGGAGGGCCCTGGTG
TCCACCTGGACCTGAACACCCTCAAAACCGAGTTCCAGGAGCTTCAAAAGCTCATGGGCACTGGGCCCCCGCACCCTCCC
CAGCCTGAGCAGCAGCCACAGCCCCATAGCCTCCGGGAGCAAGTCAGGACCAGAACAAGCTTCTGCAAAAATTTGAGTCT
CTGTGCATT
ATGGCCTCTGCTGGGGAGGCCACCAGGCACAGACCGAGGGATGCCTCACCTTCACTGTCAACCACAGCAGCTGCCTGCCC
TCAGGAGGGAGGAAGGGGACAACTCCTTTTCACTTCTGCGCACAACGTCATCAAACACATAGACAAGGAGGGCCCTGGTG
TCCACCTGGACCTGAACACCCTCAAAACCGAGTTCCAGGAGCTTCAAAAGCTCATGGGCACTGGGCCCCCGCACCCTCCC
CAGCCTGAGCAGCAGCCACAGCCCCATAGCCTCCGGGAGCAAGTCAGGACCAGAACAAGCTTCTGCAAAAATTTGAGTCT
CTGTGCATT
ORF - retro_cjac_2664 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 55.17 % |
| Parental protein coverage: | 94.96 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected | 3 |
Retrocopy - Parental Gene Alignment:
| Parental | MASAGVAAGRQAEDALPPTSD-QPLPDSARAREEENYSFLPL-VHNIIKCMDKDSPEVHQDLNTLKTKFQ |
| MASAG.A......DA.P..S..Q.LP..A..REE...SF..L..HN.IK..DK..P.VH.DLNTLKT.FQ | |
| Retrocopy | MASAGEATRHRPRDASPSLST>QQLP--ALRREEGDNSFSLL<AHNVIKHIDKEGPGVHLDLNTLKTEFQ |
| Parental | EMRKLISTMPGIHLSPEQQQQQLHSLRDQVRTK-NELLQKYKSLCM |
| E..KL..T.P.....PEQQ.Q..HSLR.QVRT..N.LLQK..SLC. | |
| Retrocopy | ELQKLMGTGPPHPPQPEQQPQP-HSLREQVRTR<NKLLQKFESLCI |
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 .04 RPM | 4 .77 RPM |
| SRP051959_heart | 0 .05 RPM | 6 .38 RPM |
| SRP051959_kidney | 0 .07 RPM | 6 .10 RPM |
| SRP051959_liver | 0 .02 RPM | 5 .46 RPM |
| SRP051959_lung | 0 .02 RPM | 5 .04 RPM |
| SRP051959_lymph_node | 0 .02 RPM | 4 .61 RPM |
| SRP051959_skeletal_muscle | 0 .00 RPM | 7 .75 RPM |
| SRP051959_spleen | 0 .02 RPM | 4 .35 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_2664 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_2664 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_2664 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 | ENSCJAG00000008916 | 1 retrocopy |
retro_cjac_2664 ,
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