RetrogeneDB ID: | retro_cjac_3074 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 8:54115580..54116354(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | RAB40C | ||
| Ensembl ID: | ENSCJAG00000036629 | ||
| Aliases: | None | ||
| Description: | RAB40C, member RAS oncogene family [Source:HGNC Symbol;Acc:18285] |
Retrocopy-Parental alignment summary:
>retro_cjac_3074
GTGGGCAAGGGCGAGATCCTGGAGAGCTTGCAGGACGGCGCGGCCGAGTCCCCGTATGCCTACAGCAACGGAATCGACTA
CAAGACCATCACCGTCCTGCTGGAAGGCCAGCGCGTGAAGCTGGCGCTCTGGGACACGTCCGGCCGGGGCTGGTTTTGCA
CCATCTTGAGGTCCTACTCCAGGGGCGCTCAGGGGATCCTCCTGGTGTTTGACGTCACCAACCTCTGGACCTTTGACAGC
ATCGACTGCTGCATCAAGGAGATCGACGAGCATGCGCCCAGAGTCCCCCGGATCTTGGTTGGAAAGAGGCTGCACCTGTC
CTTCAAGCTGCGGAGTCCTAACGGAGCAGGCCGGCGCATTCGCAGAGAAGAAGTACATGACCTTTTTTGAGGTCAACCCC
CTGTGCAACTTCAACGTCATCGAGTCCTTCACGGAGCTGTCCCGCATCGTGCTCAGGCGGCACGACATGGAGAAGATCTG
GAGGCCCAATTGAGTGTTCAGCCTGCAGGGCCTCTGTTGCTGGGCCATCGCCTCGTGCACCTCGGGGCACCTCATCGACA
AGCTTCCACTGCCCGTCCCATCAAGCCACCTCAAGTCCTTCTCAGTGGCCAACGGCATGAACGCCATCATGATGCACGGC
CGCTCCTACTCCCTGGCCAGCGGGGACGGGGTGGTGGTAGCAAGGGCAACAGCCTTAAGAGGTCCAAGCCCATCCGCCAG
CCCCAGAGCCCCTCCCGTCCCCGAAACTGCTCACGGAGAAACTGTAATATCTCC
ORF - retro_cjac_3074 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 80.84 % |
| Parental protein coverage: | 91.46 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 2 |
Retrocopy - Parental Gene Alignment:
| Parental | VGKGEILESLQDGAAESPYAYSNGIDYKTTTILLDGRRVKLELWDTSGQGRFCTIFRSYSRGAQGILLVY |
| VGKGEILESLQDGAAESPYAYSNGIDYKT.T.LL.G.RVKL.LWDTSG.G.FCTI.RSYSRGAQGILLV. | |
| Retrocopy | VGKGEILESLQDGAAESPYAYSNGIDYKTITVLLEGQRVKLALWDTSGRGWFCTILRSYSRGAQGILLVF |
| Parental | DITNRWSFDGIDRWIKEIDEHAPGVPRILVGNRLHLAFKRQVP-TEQARAYAEKNCMTFFEVSPLCNFNV |
| D.TN.W.FD.ID..IKEIDEHAP.VPRILVG.RLHL.FK...P.TEQA.A.AEK..MTFFEV.PLCNFNV | |
| Retrocopy | DVTNLWTFDSIDCCIKEIDEHAPRVPRILVGKRLHLSFKLRSP>TEQAGAFAEKKYMTFFEVNPLCNFNV |
| Parental | IESFTELSRIVLMRHGMEKIWRPNRVFSLQDLCCRAIVSCTPVHLIDKLPLPVTIKSHLKSFSMANGMNA |
| IESFTELSRIVL.RH.MEKIWRPN.VFSLQ.LCC.AI.SCT..HLIDKLPLPV...SHLKSFS.ANGMNA | |
| Retrocopy | IESFTELSRIVLRRHDMEKIWRPN*VFSLQGLCCWAIASCTSGHLIDKLPLPVP-SSHLKSFSVANGMNA |
| Parental | VMMHGRSYSLASGAG-SGGSKGNSLKRSKSIRPPQSP--PQNCSRSNCKIS |
| .MMHGRSYSLASG.G..GGSKGNSLKRSK.IR.PQSP..P.NCSR.NC.IS | |
| Retrocopy | IMMHGRSYSLASGDG<GGGSKGNSLKRSKPIRQPQSPSRPRNCSRRNCNIS |
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 | 3 .88 RPM |
| SRP051959_heart | 0 .00 RPM | 2 .98 RPM |
| SRP051959_kidney | 0 .00 RPM | 3 .26 RPM |
| SRP051959_liver | 0 .00 RPM | 1 .82 RPM |
| SRP051959_lung | 0 .00 RPM | 3 .25 RPM |
| SRP051959_lymph_node | 0 .00 RPM | 3 .13 RPM |
| SRP051959_skeletal_muscle | 0 .00 RPM | 1 .94 RPM |
| SRP051959_spleen | 0 .00 RPM | 2 .10 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_3074 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_3074 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_3074 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 | ENSCJAG00000036629 | 1 retrocopy |
retro_cjac_3074 ,
|
| Echinops telfairi | ENSETEG00000005311 | 1 retrocopy |