RetrogeneDB ID: | retro_cjac_4013 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | GL288339.1:3437..4206(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | METT11D1 | ||
| Ensembl ID: | ENSCJAG00000009609 | ||
| Aliases: | METTL17, METT11D1 | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_cjac_4013
ACTACCTACCATTGGCAAGAACTGAGCTACAGTGAGGGACTGAGCCTGGTGTATATGGCAGCAAGACTGGATGGTGGCTT
TGCAGCAGTCTCCAGAGCATTCCATGAGATCCAGGCTCAAAATCAAGCATTTCAGCCACAAACTTTAATGGACTTTGGCT
CGGGTACTGGTTCTGTCACCTGGGCTGCTCACAGTGTTTGGGGTCAGACCCTACGTGAATATATGTGTGTGGACAGATCA
ACTGCCATGTTGGTTTTGGCAGAAAAGCTACTGAAAGGTGGTTCAGAATCTGGGGAGCCTTATATTCCAGGGGTATTTTT
CAGACAGTTTCTACCTGTATCACCCAAGGTGCAGTTTGATATAGTCATATCAGCCTTTTCCTTAAGTGAACTGCCCAGCA
AGGCTGACCGTAATGAAGTAGTTCAAACCTTATGGCGTAAGACACATCATTTCCTGGTGCTGGTGGAGAATGGAACAAAA
GCTGGGCACAGCCTTCTCATGGATGCCAGGGATCTGGTCCTTAACGGAAATGAGAAGTCACCTTTGGACCCTCCACCTGG
TTTTGTCTTTGCCCCATGTCCCCATGAACTCCCTTGTCCCCAGTTGACAACCTCTAAGCCCCTGGCTTGTAGCATCTCAC
AGGCGTACCATCCCATCCCCTTCAGCTGGAACAAGAAACCAAAGGAAGAAAAGTTCTCTTTGGTGATCCTTGCTTGGTGG
TCTCCAGATGAGGCTAATCACTGGGCCCCGTATCACTCAACCTGTCCTT
ORF - retro_cjac_4013 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 97.28 % |
| Parental protein coverage: | 55.77 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | TTYHWQELSYSEGLSLVYMAARLDGGFAAVSRAFHEIQAQNQAFQPQTLMDFGSGTGSVTWAAHSVWGQT |
| TTYHWQELSYSEGLSLVYMAARLDGGFAAVSRAFHEIQAQNQAFQPQTLMDFGSGTGSVTWAAHSVWGQT | |
| Retrocopy | TTYHWQELSYSEGLSLVYMAARLDGGFAAVSRAFHEIQAQNQAFQPQTLMDFGSGTGSVTWAAHSVWGQT |
| Parental | LREYMCVDRSTAMLVLAEKLLKGGSESGEPYIPGVFFRQFLPVSPKVQFDIVVSAFSLSELPSKADRNEV |
| LREYMCVDRSTAMLVLAEKLLKGGSESGEPYIPGVFFRQFLPVSPKVQFDIV.SAFSLSELPSKADRNEV | |
| Retrocopy | LREYMCVDRSTAMLVLAEKLLKGGSESGEPYIPGVFFRQFLPVSPKVQFDIVISAFSLSELPSKADRNEV |
| Parental | VQTLWRKTHHFLVLVENGTKAGHSLLMDARDLVLNGNEKSPLDPRPGFVFAPCPHELPCPQLTTSKPLAC |
| VQTLWRKTHHFLVLVENGTKAGHSLLMDARDLVLNGNEKSPLDP.PGFVFAPCPHELPCPQLTTSKPLAC | |
| Retrocopy | VQTLWRKTHHFLVLVENGTKAGHSLLMDARDLVLNGNEKSPLDPPPGFVFAPCPHELPCPQLTTSKPLAC |
| Parental | SISQAYHPIPFSWNKKPKEEKFSLVILARGSPEEANRW-PRITQPVL |
| SISQAYHPIPFSWNKKPKEEKFSLVILA..SP.EAN.W.PRITQPVL | |
| Retrocopy | SISQAYHPIPFSWNKKPKEEKFSLVILAWWSPDEANHW>PRITQPVL |
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 .04 RPM | 5 .68 RPM |
| SRP051959_heart | 0 .02 RPM | 6 .49 RPM |
| SRP051959_kidney | 0 .00 RPM | 9 .96 RPM |
| SRP051959_liver | 0 .00 RPM | 6 .89 RPM |
| SRP051959_lung | 0 .00 RPM | 10 .44 RPM |
| SRP051959_lymph_node | 0 .02 RPM | 12 .56 RPM |
| SRP051959_skeletal_muscle | 0 .00 RPM | 5 .94 RPM |
| SRP051959_spleen | 0 .00 RPM | 10 .84 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_4013 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_4013 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_4013 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 | ENSCJAG00000009609 | 1 retrocopy |
retro_cjac_4013 ,
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