RetrogeneDB ID: | retro_cjac_2942 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 7:125748654..125748986(+) | ||
| Located in intron of: | ENSCJAG00000001934 | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | None | ||
| Ensembl ID: | ENSCJAG00000010709 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_cjac_2942
ATGGCGTCCGCCACCCGTATCGTCCAGCGGCTGCGGAACTGGGCGTCCGGGCATGACCTGCTGGCGAAGCTGCAGCTGCA
TTACCAGGAGATCTCCAAGTGAACTCAGCCTCTTCCCAAGCTCCCTGTGGGTCCCAACCGCAAGCTCTCCAACAATTACT
ATTGTACTCGCGATGGCTGCCAGGAATCTGTGCCCCCTTCCAACATCATGTCCTCGCAGAAGGTGCTGGTGTCAGGCAAG
CCAGCAGAGAGCTCTGCTGTAGCAGCCACTGAGAAGAAGGCGGTGACTCTAGCGCCTCCCATAAGAGGTGGGAGCTGTCC
TCGGACCAGCCC
ORF - retro_cjac_2942 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 91.07 % |
| Parental protein coverage: | 98.23 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | MASATRIVQRLRNWASGHDLQAKLQLRYQEISKRTQPPPKLPVGPNHKLSNNYYCTRDGRRESVPPSIIM |
| MASATRIVQRLRNWASGHDL.AKLQL.YQEISK.TQP.PKLPVGPN.KLSNNYYCTRDG..ESVPPS.IM | |
| Retrocopy | MASATRIVQRLRNWASGHDLLAKLQLHYQEISK*TQPLPKLPVGPNRKLSNNYYCTRDGCQESVPPSNIM |
| Parental | SSQKVLVSGKPAESSAVAATEKKAVTPAPPI-KRWELSSDQP |
| SSQKVLVSGKPAESSAVAATEKKAVT.APPI.KRWELSSDQP | |
| Retrocopy | SSQKVLVSGKPAESSAVAATEKKAVTLAPPI<KRWELSSDQP |
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 .07 RPM | 5 .57 RPM |
| SRP051959_heart | 0 .40 RPM | 10 .37 RPM |
| SRP051959_kidney | 0 .09 RPM | 8 .76 RPM |
| SRP051959_liver | 0 .04 RPM | 10 .12 RPM |
| SRP051959_lung | 0 .34 RPM | 5 .60 RPM |
| SRP051959_lymph_node | 0 .84 RPM | 4 .45 RPM |
| SRP051959_skeletal_muscle | 0 .15 RPM | 24 .98 RPM |
| SRP051959_spleen | 0 .36 RPM | 4 .45 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_2942 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_2942 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_2942 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 5 parental genes, and 9 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Choloepus hoffmanni | ENSCHOG00000000685 | 1 retrocopy | |
| Callithrix jacchus | ENSCJAG00000010709 | 2 retrocopies |
retro_cjac_2942 , retro_cjac_956,
|
| Dipodomys ordii | ENSDORG00000012324 | 1 retrocopy | |
| Macropus eugenii | ENSMEUG00000015637 | 3 retrocopies | |
| Rattus norvegicus | ENSRNOG00000006939 | 2 retrocopies |