RetrogeneDB ID: | retro_cjac_2187 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 3:137214037..137214357(+) | ||
| Located in intron of: | ENSCJAG00000018115 | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | MRPL22 | ||
| Ensembl ID: | ENSCJAG00000007325 | ||
| Aliases: | None | ||
| Description: | mitochondrial ribosomal protein L22 [Source:HGNC Symbol;Acc:14480] |
Retrocopy-Parental alignment summary:
>retro_cjac_2187
GACAAGATGTGGTATTTGGCAAAATTGGTATGAGACATGTCCACTGACCAGGCTTAGCTCAACTGGGATTCAGCAACAAA
ATGGGACCCAAATCATTAAAGACGTCCTTTTAGAAACACAAGACTTGGCAGTGAGAGACCACAATGTGGAATTCAGATCC
ATTTATATATAACTGAGTCCACCTCAGGCGGAGGCTAGTGCCTGACAGGTTTCTGCTACCAAGGTAGAGGTTGCTTTGGG
ATCATGAAGGTTTACTGCCATTATTTTGTGAAGTTGGTGGAAGGACCTCCCCATCTCCATGTGAGGCACCAAAGATGGCG
ORF - retro_cjac_2187 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 73.45 % |
| Parental protein coverage: | 52.43 % |
| Number of stop codons detected: | 2 |
| Number of frameshifts detected: | 4 |
Retrocopy - Parental Gene Alignment:
| Parental | DKMWYLAKLIRGMSIDQA-LAQLEFSDKKGAK-IIKEVLLEAQDMAVRDHNVEFRS-NLYIAESTSGRGQ |
| DKMWYLAKL...MS.DQA.LAQL.FS.K.G.K.IIK.VLLE.QD.AVRDHNVEFRS..LYI.ESTSG.G. | |
| Retrocopy | DKMWYLAKLV*DMSTDQA<LAQLGFSNKMGPK<IIKDVLLETQDLAVRDHNVEFRS<HLYITESTSGGG* |
| Parental | CLKRIRYHGRGYFGIMEKVYCHYFVKLVEGPP-PPP-EPPKTA |
| CL....Y.GRG.FGIM.KVYCHYFVKLVEGPP.P.P.E.PK.A | |
| Retrocopy | CLTGFCYQGRGCFGIM-KVYCHYFVKLVEGPP<PSPCEAPKMA |
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 .60 RPM | 5 .13 RPM |
| SRP051959_heart | 0 .00 RPM | 6 .12 RPM |
| SRP051959_kidney | 0 .00 RPM | 8 .43 RPM |
| SRP051959_liver | 0 .00 RPM | 7 .58 RPM |
| SRP051959_lung | 0 .02 RPM | 6 .56 RPM |
| SRP051959_lymph_node | 0 .00 RPM | 5 .80 RPM |
| SRP051959_skeletal_muscle | 0 .00 RPM | 5 .42 RPM |
| SRP051959_spleen | 0 .02 RPM | 6 .34 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_2187 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_2187 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_2187 has 5 orthologous retrocopies within eutheria group .| Species | RetrogeneDB ID |
|---|---|
| Homo sapiens | retro_hsap_3041 |
| Pan troglodytes | retro_ptro_1997 |
| Gorilla gorilla | retro_ggor_2095 |
| Pongo abelii | retro_pabe_2436 |
| Macaca mulatta | retro_mmul_1889 |
Parental genes homology:
Parental genes homology involve 8 parental genes, and 9 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Anolis carolinensis | ENSACAG00000003875 | 1 retrocopy | |
| Callithrix jacchus | ENSCJAG00000007325 | 2 retrocopies |
retro_cjac_2187 , retro_cjac_2558,
|
| Homo sapiens | ENSG00000082515 | 1 retrocopy | |
| Gorilla gorilla | ENSGGOG00000010232 | 1 retrocopy | |
| Mus musculus | ENSMUSG00000020514 | 1 retrocopy | |
| Nomascus leucogenys | ENSNLEG00000016692 | 1 retrocopy | |
| Pongo abelii | ENSPPYG00000015979 | 1 retrocopy | |
| Pan troglodytes | ENSPTRG00000017453 | 1 retrocopy |