RetrogeneDB ID: | retro_cjac_1085 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 13:38425715..38426316(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | SAP25 | ||
| Ensembl ID: | ENSCJAG00000015273 | ||
| Aliases: | None | ||
| Description: | Sin3A-associated protein, 25kDa [Source:HGNC Symbol;Acc:41908] |
Retrocopy-Parental alignment summary:
>retro_cjac_1085
ATGACTCCTCCAGCACCCTGGGACCCCAAGTACGAAGCCAAAGCAGGGCCTCGGCTGGTGTGGGGGGTCAACTGTAGCTC
AGGAGCCTCCTTCTCAGGCCAGACGCTATGTCACCCCTTGTTCTGGCTGCTGTATGAGGCAGCCTCAGGTAGGGGTCCCC
GGCCTGTGGCCCCTGCCACAGGGCATGAGAATGGGCAGCAGGTGCACCCAGATGCAGGGTTCCTGGTGATGTGCCATGAA
GACCTCTTCTTCTCAGACCCTCTACTGCCCCTGGGACAGAGTGTCCCCTTATACCTTTTCGAGGCCCCCCAGCAGGTGAT
GAGCTCCCTGAAATGGCTGCCACCACCTCCCATAATGTCCCCCTGGGTCTTCCCCAGCCTGTAACCCTCCCCAGGCCACT
CCACCGCCTGGCTCAGTGGGCTGGAGCTGATAGCTCTCACTGGCCTGCTGCAGATGAGCCAGGGGGAATCCCAGGCCCAG
CTTCTCCTCCGCTGCTGGCACCCTAGACCCTGCCTCTGACCCAACCAGCCCCTGTGGTGGCTCCAGCAGTTCTCACAGTG
CTGACCCCTCTCTCCCACAGACCCCAGACACCCATTGTTCA
ORF - retro_cjac_1085 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 85.85 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | MTPLAPWDPKYEAKAGPRLVWGANCSSGASFSGRTLCHPSFWPLYEAASGRGPQPVAPATGHQNGQQAHP |
| MTP.APWDPKYEAKAGPRLVWG.NCSSGASFSG.TLCHP.FW.LYEAASGRGP.PVAPATGH.NGQQ.HP | |
| Retrocopy | MTPPAPWDPKYEAKAGPRLVWGVNCSSGASFSGQTLCHPLFWLLYEAASGRGPRPVAPATGHENGQQVHP |
| Parental | DAGFPVMCGEDVFFSDPLLPQGQRVPLYLSEAPQQVMSSLKLLPPPSIMSPWVFPSLSPSPGCSTAWLSG |
| DAGF.VMC.ED.FFSDPLLP.GQ.VPLYL.EAPQQVMSSLK.LPPP.IMSPWVFPSL.PSPG.STAWLSG | |
| Retrocopy | DAGFLVMCHEDLFFSDPLLPLGQSVPLYLFEAPQQVMSSLKWLPPPPIMSPWVFPSL*PSPGHSTAWLSG |
| Parental | PELIALTGLLQMSQGE-PRPSSSMAATPTAGPPDPASDPTSPCGGSSSSHGADPSLPQTPDTHCS |
| .ELIALTGLLQMSQGE.PRPS.S.AA....G..DPASDPTSPCGGSSSSH.ADPSLPQTPDTHCS | |
| Retrocopy | LELIALTGLLQMSQGE>PRPSFSSAA----GTLDPASDPTSPCGGSSSSHSADPSLPQTPDTHCS |
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 | 0 .35 RPM |
| SRP051959_heart | 0 .00 RPM | 0 .86 RPM |
| SRP051959_kidney | 0 .02 RPM | 2 .00 RPM |
| SRP051959_liver | 0 .00 RPM | 0 .54 RPM |
| SRP051959_lung | 0 .00 RPM | 3 .84 RPM |
| SRP051959_lymph_node | 0 .02 RPM | 6 .62 RPM |
| SRP051959_skeletal_muscle | 0 .00 RPM | 0 .68 RPM |
| SRP051959_spleen | 0 .00 RPM | 3 .09 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_1085 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_1085 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_1085 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 5 parental genes, and 5 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Callithrix jacchus | ENSCJAG00000015273 | 1 retrocopy |
retro_cjac_1085 ,
|
| Homo sapiens | ENSG00000205307 | 1 retrocopy | |
| Gorilla gorilla | ENSGGOG00000013708 | 1 retrocopy | |
| Pongo abelii | ENSPPYG00000017415 | 1 retrocopy | |
| Pan troglodytes | ENSPTRG00000019495 | 1 retrocopy |