RetrogeneDB ID: | retro_cjac_4145 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | X:26638314..26639059(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | CDCA5 | ||
| Ensembl ID: | ENSCJAG00000002502 | ||
| Aliases: | None | ||
| Description: | cell division cycle associated 5 [Source:HGNC Symbol;Acc:14626] |
Retrocopy-Parental alignment summary:
>retro_cjac_4145
ATGTCTTGGAGGCGAACGCGGCCCAGAGGGGCCGCGCAGCGCTCCGGGCCAAGGGCCCCATCTCCTACTAAGTCTGTGCG
GAGGTCCCAACAGAAATCAGGCTCTGATCTCCCAAGCATGCCCCCTGAAATCTGGCCGAAGACACCCAGTGCGGCTGCAA
TCAGAAAGCCCATCGTCTTGGAGATCGTGGCCCAAGATGTAGACGTCCCAGCTGTTCCCTTGCCTCGCAGGAGCCCTAGG
ATTGCCTTTTTCTTGGAGAAGGAAAACAAGCCCCCTTGCAAGGAGCTGACTAAGGAGGACCTTTCCAAGATACAGCCTCC
CTGCCACTCCTAACACTTCTCCTGTGCTCAACCCTGAGGCTGAGTCCAGCTCCAAGGAGAGAGAGCTGGAGGCCAAATAC
TTGGAAATGTTTAAGAAAGTCAGGGGCTCCTACAGCCGGCTGGAGACCCTGGGCTCTGCCTCCACCTCCACCCCAGGCTG
CCGGTTCTGCTTTGGCTTCCATGGGCTACTAGGGGCAGAAGATTTGTCCGGAGTCTCACCAGTGGTGTGCTCAAAATTCA
CCGAGGTCCCCAGGGTCGGTACAAAGCCCTGAGCCACAGACACAATTCTCCCTGGAATCTCTCCACCACCCGAGAAACAG
AAACAAAAGAAGATGCTAGAGATACTGAAAACGGAGCTGGATGAGAGGGCTGCAGCCATGAATGCTGAGTTTGAAGCTGC
TGAGCAGTTTGATCTCCTGGTTGAA
ORF - retro_cjac_4145 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 79.45 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 2 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | MPGRRTRSGGAAQRSGPRAPSPVKSVRRSQRKSGSDLPSIPPEIWPKTPSAAAIRKPIVLKKIVAHAVEV |
| M..RRTR..GAAQRSGPRAPSP.KSVRRSQ.KSGSDLPS.PPEIWPKTPSAAAIRKPIVL..IVA..V.V | |
| Retrocopy | MSWRRTRPRGAAQRSGPRAPSPTKSVRRSQQKSGSDLPSMPPEIWPKTPSAAAIRKPIVLE-IVAQDVDV |
| Parental | PAVHSPRRSPRIAFFLE-KENKPPCRELTKEDLSKIHSVPDTPNTSPVLNPEAESSSKERELDARDLEMF |
| PAV..PRRSPRIAFFLE.....P..R...........S.P.TPNTSPVLNPEAESSSKEREL.A..LEMF | |
| Retrocopy | PAVPLPRRSPRIAFFLE>RKTSPLARS*LRRTFPR-YSLPATPNTSPVLNPEAESSSKERELEAKYLEMF |
| Parental | KKVRRSYSRLETLGSTSTSTPGRRSCFGFEGLLGAEDLSGVSPVVCSKFIEVPRVGAKPWAPDTTLPGIS |
| KKVR.SYSRLETLGS.STSTPG.R.CFGF.GLLGAEDLSGVSPVVCSKF.EVPRVG.KP.A.DT.LPGIS | |
| Retrocopy | KKVRGSYSRLETLGSASTSTPGCRFCFGFHGLLGAEDLSGVSPVVCSKFTEVPRVGTKP*ATDTILPGIS |
| Parental | PPPEKQKRKKKKMPEILKTELDEWAAAMNAEFEAAEQFDLLVE |
| PPPEKQ..K.KKM.EILKTELDE.AAAMNAEFEAAEQFDLLVE | |
| Retrocopy | PPPEKQ--KQKKMLEILKTELDERAAAMNAEFEAAEQFDLLVE |
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 .55 RPM |
| SRP051959_heart | 0 .00 RPM | 0 .00 RPM |
| SRP051959_kidney | 0 .00 RPM | 0 .02 RPM |
| SRP051959_liver | 0 .00 RPM | 0 .11 RPM |
| SRP051959_lung | 0 .00 RPM | 0 .34 RPM |
| SRP051959_lymph_node | 0 .00 RPM | 0 .78 RPM |
| SRP051959_skeletal_muscle | 0 .00 RPM | 0 .07 RPM |
| SRP051959_spleen | 0 .00 RPM | 0 .38 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_4145 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_4145 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_4145 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 5 parental genes, and 6 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Callithrix jacchus | ENSCJAG00000002502 | 1 retrocopy |
retro_cjac_4145 ,
|
| Dasypus novemcinctus | ENSDNOG00000019033 | 1 retrocopy | |
| Felis catus | ENSFCAG00000028197 | 1 retrocopy | |
| Pteropus vampyrus | ENSPVAG00000007908 | 1 retrocopy | |
| Rattus norvegicus | ENSRNOG00000046635 | 2 retrocopies |