RetrogeneDB ID: | retro_cjac_1781 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 2:42246185..42246816(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | NKX6-1 | ||
| Ensembl ID: | ENSCJAG00000005335 | ||
| Aliases: | None | ||
| Description: | NK6 homeobox 1 [Source:HGNC Symbol;Acc:7839] |
Retrocopy-Parental alignment summary:
>retro_cjac_1781
GCAGGGCTGCTGGCCAGACTGCCCCGTTTCAGCAGCCTGAGCCCGCCGCCACCGCCGCCCGGGCTCTACTTCAGCCCCAG
CGCTGCTGCCGTGGCCGCCGTGGGCCGGTACCCCAAGCCGCTAGCGGAGCTGCCCAGCCGGATGCCCATCTTCTGGCCCG
AAGTGATGCGGAGGCTGCCCTGAAGGGATGCACGCCTAGCCTGTACCCCTCATCAAGGATCCATGTTGTTGGACAAAGAC
GGGAAGAAAAAACACACACAACCCACTTTTTCCGGACTTTATTCACCCTGGAGAAGACTTTCGAACAAACAATACTTGGC
GGGGTCCGAGAGGGCTCGCTTGGCCTATTCGTTGGGGATGACGGAAAGTCAGGCCAAGGTCTGGTTCCAGAACCGCCGGA
CCAAGTGGAGGAAGAAGCACGCAGCCGAGATGGCCACGGCCAAGAAGCAGCAGGACTCGGAGACCAAGAGGCTCAATGGG
GGCCTCGGAGAAGAAGGAGGAGGACGACGACTACAAGCCTCTAGATCCCAACTCGGACGACGAGAAAATCACGCAGCTGC
TGAAGAAGCACAAGTCCAGCAGCAGCGGCGGTGGCCTCCTACTGCGCGCGTCCGAGCCCGAGAGCTCATCC
ORF - retro_cjac_1781 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 83.18 % |
| Parental protein coverage: | 58.2 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | AGLLAGLPRFSSLSPPPPPPGLYFSPSAAAVAAVGRYPKPLAELPGRTPIFWPGVMQSPPWRDARLACTP |
| AGLLA.LPRFSSLSPPPPPPGLYFSPSAAAVAAVGRYPKPLAELP.R.PIFWP.VM...P.RDARLACTP | |
| Retrocopy | AGLLARLPRFSSLSPPPPPPGLYFSPSAAAVAAVGRYPKPLAELPSRMPIFWPEVMRRLP*RDARLACTP |
| Parental | HQGSILLDKDGKRKHTRPTFSGQQIFALEKTFEQTKYLAGPERARLAYSLGMTESQVKVWFQNRRTKWRK |
| HQGS.LLDKDGK.KHT.PTFSG..............YLAG.ERARLAYSLGMTESQ.KVWFQNRRTKWRK | |
| Retrocopy | HQGSMLLDKDGKKKHTQPTFSG--LYSPWRRLSNKQYLAGSERARLAYSLGMTESQAKVWFQNRRTKWRK |
| Parental | KHAAEMATAKKKQDSETERLK-GASENEEEDDDYNKPLDPNSDDEKITQLLKKHKSSSGGGGLLLHASEP |
| KHAAEMATAKK.QDSET.RL..GASE..EEDDDY.KPLDPNSDDEKITQLLKKHKSSS.GGGLLL.ASEP | |
| Retrocopy | KHAAEMATAKKQQDSETKRLN>GASEKKEEDDDY-KPLDPNSDDEKITQLLKKHKSSSSGGGLLLRASEP |
| Parental | ESSS |
| ESSS | |
| Retrocopy | ESSS |
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 .02 RPM | 0 .00 RPM |
| SRP051959_heart | 0 .00 RPM | 0 .00 RPM |
| SRP051959_kidney | 0 .00 RPM | 0 .02 RPM |
| SRP051959_liver | 0 .00 RPM | 0 .00 RPM |
| SRP051959_lung | 0 .00 RPM | 0 .02 RPM |
| SRP051959_lymph_node | 0 .00 RPM | 0 .00 RPM |
| SRP051959_skeletal_muscle | 0 .00 RPM | 0 .00 RPM |
| SRP051959_spleen | 0 .00 RPM | 0 .00 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_1781 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_1781 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_1781 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 1 parental gene, and 1 retrocopy.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Callithrix jacchus | ENSCJAG00000005335 | 1 retrocopy |
retro_cjac_1781 ,
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