RetrogeneDB ID: | retro_cjac_2811 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 6:52174835..52175537(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | RAD51 | ||
| Ensembl ID: | ENSCJAG00000020821 | ||
| Aliases: | None | ||
| Description: | RAD51 recombinase [Source:HGNC Symbol;Acc:9817] |
Retrocopy-Parental alignment summary:
>retro_cjac_2811
ATGGCAATGCAGATGCAGATTGAAGCAAATGCAGATACTTCAGTGGAAGAAGAAAGCTTTGGCCCACAACCTGTTTCACG
GTTAGAGCAGTGTGGCATAAATGCCAATGATGTGAAAAAATTGGAAGAAGCTGGATTCCATACTGTGGAGGCTGTTGCCT
ATGCACCAAAGAAGGAGCTAATAAATATTAAGGGAATTAGTGAAGCCAAAGCTGATAAAATTCTGGCTGAAGCAGCCAAA
TTAGTTCCAATGGGTTTCACCGCTGCAACTGAATTCCACCAAAGGCGGTCAGAGATCATACAGATTACTACTGGCTCTAA
AGAGCTTGACAAACTACTTCAAGGTGGAATTGAGACTGGCTCTATCACAGAAATGTTTGGAGAATTCCGAACTGGGAAGA
CCCAGATCTGTCATACACTGGCTGTCACCTGCCAGCTTCCCATTGACCGGGGCAGAGGTGTAGGAAAGGCCATGTACATT
GACACCAAGGGTACCTTTAGGCCAGAACGGCTGCTAGCAGTGGCTGAGAGGTATGGTCTCTCTGGTAGTGATGTCCTGGA
TAATGTAGCATATGCTCGAGCATTCAACACAGACCACCAGACCCAGCTCCTTTAGCAAGCATCAGCCATGATGGTAGAAT
CTAGGTATGCACTGCTTATTGTAGACAGTGCCACCGCCCTTTACAGAACAGACTACTCGGGC
ORF - retro_cjac_2811 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 96.15 % |
| Parental protein coverage: | 68.93 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | MAMQMQLEANADTSVEEESFGPQPVSRLEQCGINANDVKKLEEAGFHTVEAVAYAPKKELINIKGISEAK |
| MAMQMQ.EANADTSVEEESFGPQPVSRLEQCGINANDVKKLEEAGFHTVEAVAYAPKKELINIKGISEAK | |
| Retrocopy | MAMQMQIEANADTSVEEESFGPQPVSRLEQCGINANDVKKLEEAGFHTVEAVAYAPKKELINIKGISEAK |
| Parental | ADKILAEAAKLVPMGFTTATEFHQRRSEIIQIT-GCKELDNLLQGGIETGSITEMFGEFRTGKTQICHTL |
| ADKILAEAAKLVPMGFT.ATEFHQRRSEIIQIT.G.KELD.LLQGGIETGSITEMFGEFRTGKTQICHTL | |
| Retrocopy | ADKILAEAAKLVPMGFTAATEFHQRRSEIIQITTGSKELDKLLQGGIETGSITEMFGEFRTGKTQICHTL |
| Parental | AVTCQLPIDRGGGEGKAMYIDTEGTFRPERLLAVAERYGLSGSDVLDNVAYARAFNTDHQTQLLYQASAM |
| AVTCQLPIDRG.G.GKAMYIDT.GTFRPERLLAVAERYGLSGSDVLDNVAYARAFNTDHQTQLL.QASAM | |
| Retrocopy | AVTCQLPIDRGRGVGKAMYIDTKGTFRPERLLAVAERYGLSGSDVLDNVAYARAFNTDHQTQLL*QASAM |
| Parental | MVESRYALLIVDSATALYRTDYSG |
| MVESRYALLIVDSATALYRTDYSG | |
| Retrocopy | MVESRYALLIVDSATALYRTDYSG |
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 .60 RPM | 2 .53 RPM |
| SRP051959_heart | 0 .02 RPM | 0 .32 RPM |
| SRP051959_kidney | 0 .02 RPM | 0 .27 RPM |
| SRP051959_liver | 0 .09 RPM | 0 .37 RPM |
| SRP051959_lung | 0 .08 RPM | 0 .59 RPM |
| SRP051959_lymph_node | 0 .32 RPM | 1 .14 RPM |
| SRP051959_skeletal_muscle | 0 .04 RPM | 0 .20 RPM |
| SRP051959_spleen | 0 .08 RPM | 1 .13 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_2811 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_2811 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_2811 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 3 parental genes, and 4 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Callithrix jacchus | ENSCJAG00000020821 | 2 retrocopies |
retro_cjac_2811 , retro_cjac_430,
|
| Ornithorhynchus anatinus | ENSOANG00000028534 | 1 retrocopy | |
| Otolemur garnettii | ENSOGAG00000031397 | 1 retrocopy |