RetrogeneDB ID: | retro_cjac_682 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 10:44333816..44334412(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | MIS18A | ||
| Ensembl ID: | ENSCJAG00000009090 | ||
| Aliases: | None | ||
| Description: | MIS18 kinetochore protein homolog A (S. pombe) [Source:HGNC Symbol;Acc:1286] |
Retrocopy-Parental alignment summary:
>retro_cjac_682
GAGTAGGGTGACAAGGGCAAGTGCAGTGACTCCTTGCTGTTGAGCAAGAGGCTCTCTGAAGACTCAAGCTGCCACCAGGT
GCTGCAGAAGTCGACGAATATGTGGCGCTCCACAAGTGAGGACGCGTCGGTGGCCAACAAGGAGAAGGCGCGGCTCGAGG
AGGTGGAGGCGGCAGAGGAGAGGCTGCTGGTGTTCCTGTGCTCCAGCTGCTGGCGGCCGCTGGGTGACTCGCGAGCTGGG
TGACCAGCCAAAAGGACACCAACTGTATCCTGCTGCACTGTGTTTCCTGTAATGTTTCTGTGGGTAAGGAACAGAAGTTA
TCCACATGTGAAAAGGAAAATGGTTGCATCCTTGAAACTTTGTACTGCACGGGGTGCTCACTCAACCTTGGCTACGTGTA
TAGATGCACACCCAAGAATCTTGATTACAAGAGAGACTTGTTTTGCCTCAGTATTGAAGCCATCAAAAGCTATGTTTTAG
GGTCCTCTGAAAAGCAAATTGTGTCAGAAGATAAAGAACTTTTTAATCTTGAAAGCCGTGTTGAAATAGAAAAGTCTCTA
AAACAGATGGAAGATGTCTTGCAAAAGTACAGATTG
ORF - retro_cjac_682 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 88.0 % |
| Parental protein coverage: | 85.78 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | EYGDKGKCSDSSLLSKRLSEDSSRHQLLQKWTNMWRSTSEDASVADTEKARLEEAAAAEERPLVFLCSSC |
| E.GDKGKCSDS.LLSKRLSEDSS.HQ.LQK.TNMWRSTSEDASVA..EKARLEE..AAEER.LVFLCSSC | |
| Retrocopy | E*GDKGKCSDSLLLSKRLSEDSSCHQVLQKSTNMWRSTSEDASVANKEKARLEEVEAAEERLLVFLCSSC |
| Parental | RRPLGDS-LSWVTSQEDTNCILLRCVSCNVSVDKEQKLSKREKENGCILETLYCTGCSLNLGYVYRCTPK |
| .RPLGDS..SWVTSQ.DTNCILL.CVSCNVSV.KEQKLS..EKENGCILETLYCTGCSLNLGYVYRCTPK | |
| Retrocopy | WRPLGDS<ASWVTSQKDTNCILLHCVSCNVSVGKEQKLSTCEKENGCILETLYCTGCSLNLGYVYRCTPK |
| Parental | NLDYKRDLFCLSVEAIESYVLGSSEKQIVSEDKELFNLESRVEIEKSLKQMEDVLQALQM |
| NLDYKRDLFCLS.EAI.SYVLGSSEKQIVSEDKELFNLESRVEIEKSLKQMEDVLQ.... | |
| Retrocopy | NLDYKRDLFCLSIEAIKSYVLGSSEKQIVSEDKELFNLESRVEIEKSLKQMEDVLQKYRL |
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 | 1 .18 RPM |
| SRP051959_heart | 0 .00 RPM | 1 .44 RPM |
| SRP051959_kidney | 0 .00 RPM | 1 .02 RPM |
| SRP051959_liver | 0 .00 RPM | 0 .56 RPM |
| SRP051959_lung | 0 .00 RPM | 1 .90 RPM |
| SRP051959_lymph_node | 0 .00 RPM | 1 .80 RPM |
| SRP051959_skeletal_muscle | 0 .00 RPM | 0 .50 RPM |
| SRP051959_spleen | 0 .00 RPM | 2 .71 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_682 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_682 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_682 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 2 parental genes, and 2 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Callithrix jacchus | ENSCJAG00000009090 | 1 retrocopy |
retro_cjac_682 ,
|
| Ictidomys tridecemlineatus | ENSSTOG00000004511 | 1 retrocopy |