RetrogeneDB ID: | retro_cjac_557 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 1:79916748..79917809(-) | ||
| Located in intron of: | ENSCJAG00000012598 | ||
Retrocopy information | Ensembl ID: | ENSCJAG00000012618 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | DND1 | ||
| Ensembl ID: | ENSCJAG00000016345 | ||
| Aliases: | None | ||
| Description: | dead end homolog 1 (zebrafish) [Source:HGNC Symbol;Acc:23799] |
Retrocopy-Parental alignment summary:
>retro_cjac_557
ATGCAGTCCAAGCGGGATTGTGAGCTGTGGTGTGAGAGGGTGAATTCAGAAAACAAGGCAGCGCTGGAGGCTTGGGTCAG
CGAGACAGGCATCCGCCTGGTGCAGGTGAATGGGCAGAGGAATATGGCAGGCCACCCCCAGGCTGGGTGGGCAGGCTGCT
GCCAGCCGGATCAGAGGTATTCATCGGGTGGCTGCCCCAGGACGTGTACGAGCACCAGCTTATCCCACTGTTCCAGCGCG
TGGGCCGCCTCTTCGAGTTCCGCCTGATGATGACCTTCAGCGGCCTGAACCGCGGCTTTGCCTATGCCAGCTACAGCTCG
TGGCGCGGCGCTCAGGCCGCCATTGCCACGCTGCACAACTACCCGCTGCAGCCGTCTTGCACGCTGCTCATGTGCCGCAG
CATCGAGAAGTGTGAGCTGAGCGTGGACTGCCTGCTGCCGAATCTGACCTGCCGCGCACTGTTACTCGTGTTGCAGTCGC
TGGGTCCTGGCCTCCAGGAGGAGCGGGTGCTGCCCAGCCCTGGACCGCTGCCCGGGCAGATCGCTCTGCTCAAATTCAGC
TCGCACCGGACCGCTACCCTGGCCAAAAAGGTGCTGGTGGAAGGGCAATCACACCTCTGTGGAGAGCCTGTCGCTGTGGA
TTGGCTCAAGCCAGACCTGAAGCAGCGACCCCGCCAGCAGCTTGTGGGTCCCTCCTTGTGGTCCCCACAGCCAGAAGGCA
GCCAGTTGGCCTTGGCAAGGGACAAGTTAGGGTCCCAAGGGGCTCGAGCTACCCTGCAGTTGCTGTGCCAACGAATGAAG
CTGGGGAGCCCTGTGTTCCTCACCAAGTGTTTGGGCACCGGGCCTGCTGGCTGGCACCGCTTCTGGTACCAGGTCGTGAT
CCCTGGGCATCCAGTACCCTTCAGTGGCCTAATCTGGGTTGTGCTGACCCTAGATGGGCAGGATGGGCATGAGGTGGCCA
AGGATGCTGTGTCTGCACAGCTGCAGCAGCAGGCACTCACTGAGTCCCGGGCCAGCCTCCTGTGGTCTGCTGGAGCTGAG
GCAGGTACCATGGTTAGACAG
ORF - retro_cjac_557 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 90.14 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | MQSKRDCELWCERVNPENKAALEAWVRETGIRLVQVNGQR-KYGGPPPGWVGRPPPAGSEVFIGRLPQDV |
| MQSKRDCELWCERVN.ENKAALEAWV.ETGIRLVQVNGQR..YG.PPPGWVGR..PAGSEVFIG.LPQDV | |
| Retrocopy | MQSKRDCELWCERVNSENKAALEAWVSETGIRLVQVNGQR<EYGRPPPGWVGRLLPAGSEVFIGWLPQDV |
| Parental | YEHQLIPLFQRVGRLYEFRLMMTFSGLNRGFAYARYSSRRGAQAAIATLHNHPLRPSCTLLVCRSTEKCE |
| YEHQLIPLFQRVGRL.EFRLMMTFSGLNRGFAYA.YSS.RGAQAAIATLHN.PL.PSCTLL.CRS.EKCE | |
| Retrocopy | YEHQLIPLFQRVGRLFEFRLMMTFSGLNRGFAYASYSSWRGAQAAIATLHNYPLQPSCTLLMCRSIEKCE |
| Parental | LSVDGLPPNLTRRALLLALQPLGPGLQEARLLPSPGPAAGQIALLKFSSHRAAALAKKALVEGQSHLCGE |
| LSVD.L.PNLT.RALLL.LQ.LGPGLQE.R.LPSPGP..GQIALLKFSSHR.A.LAKK.LVEGQSHLCGE | |
| Retrocopy | LSVDCLLPNLTCRALLLVLQSLGPGLQEERVLPSPGPLPGQIALLKFSSHRTATLAKKVLVEGQSHLCGE |
| Parental | PVAVEWLKPDLKQRLRQQLVGPSLRSPQPEGSQLALARDKLGSQGARATLQLLCQRMKLGSPVFLTKCLG |
| PVAV.WLKPDLKQR.RQQLVGPSL.SPQPEGSQLALARDKLGSQGARATLQLLCQRMKLGSPVFLTKCLG | |
| Retrocopy | PVAVDWLKPDLKQRPRQQLVGPSLWSPQPEGSQLALARDKLGSQGARATLQLLCQRMKLGSPVFLTKCLG |
| Parental | TGPAGWHRFWYQVVIPGHPVPFSGLIWVVLTLDGQDGHEVAKDAVSAQL-LQVLTESGASLLWSAGAEAR |
| TGPAGWHRFWYQVVIPGHPVPFSGLIWVVLTLDGQDGHEVAKDAVSAQL..Q.LTES.ASLLWSAGAEA. | |
| Retrocopy | TGPAGWHRFWYQVVIPGHPVPFSGLIWVVLTLDGQDGHEVAKDAVSAQLQQQALTESRASLLWSAGAEAG |
| Parental | TMVRQ |
| TMVRQ | |
| Retrocopy | TMVRQ |
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 .47 RPM | 1 .24 RPM |
| SRP051959_heart | 0 .32 RPM | 0 .84 RPM |
| SRP051959_kidney | 0 .33 RPM | 1 .29 RPM |
| SRP051959_liver | 0 .35 RPM | 1 .67 RPM |
| SRP051959_lung | 0 .49 RPM | 1 .40 RPM |
| SRP051959_lymph_node | 0 .43 RPM | 2 .83 RPM |
| SRP051959_skeletal_muscle | 0 .09 RPM | 1 .40 RPM |
| SRP051959_spleen | 0 .40 RPM | 1 .79 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_557 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_557 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_557 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 6 parental genes, and 7 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Callithrix jacchus | ENSCJAG00000016345 | 1 retrocopy |
retro_cjac_557 ,
|
| Homo sapiens | ENSG00000256453 | 1 retrocopy | |
| Macropus eugenii | ENSMEUG00000016276 | 2 retrocopies | |
| Mus musculus | ENSMUSG00000044595 | 1 retrocopy | |
| Pongo abelii | ENSPPYG00000015863 | 1 retrocopy | |
| Rattus norvegicus | ENSRNOG00000016894 | 1 retrocopy |