RetrogeneDB ID: | retro_cjac_744 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 10:125268482..125269148(+) | ||
| Located in intron of: | ENSCJAG00000006717 | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | REEP4 | ||
| Ensembl ID: | ENSCJAG00000020323 | ||
| Aliases: | None | ||
| Description: | receptor accessory protein 4 [Source:HGNC Symbol;Acc:26176] |
Retrocopy-Parental alignment summary:
>retro_cjac_744
GTGCGGTGGATGATGTACTGGATCGTTTTTGCACTCTTCATGGTAGCAGAGATCGTCACCGACATTTTTATCTCCTGGTT
CCCTTTCTACTATGAGATCAAGATGGCCTTTGTGCTGTGGCTGCTCTCGCCCTACACCAAGGGCGCCAGCCTGCTTTACC
TCAAGTTTGTCCACCCATCCCTGTCCCGCCACGAGAAGGAGATCGACGCATACCTCGTGGAGGCCAAGGAGCGCAGCTAC
GAGACCATGCTTAGCTTCGGGAAGCGGGGCCTCAACATTGCCGCCTCGGCTGCTGTGCAGGCTGCCAGCAAGAGTCAGGG
GGCGCTGGCCGGCAGGCTGCTGAGCTTCTCCATGCAGGACCTGCGCTCCATCCCCGATGCACCCGCTCCTGCCTAACAGG
ACGCCCTCTACCCAGAGGACCAGGTGCTCCACCGGAGGCCACCCATTGGGTACCGGGACGGGGGCCTGCAGGACAGCAAC
ACGGAGGATGACTGTTGGTCAGATACTGAGGCGGTCCCCCGGATGCCAGCCCGGCCCCGAGAGAAGCCCCTGAGCCGCAG
CCAGAGCCTGCGTGTGATCAAGAGGAAGCCACTGGTGCGGGAGGGCACCTCGCGCTCCCTAAAGGTTCGGACGAGGAAAA
AGACTGTGCCCTCAGACATGGACAGC
ORF - retro_cjac_744 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 96.85 % |
| Parental protein coverage: | 86.38 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | VRWMMYWIVFALFMAAEIVTDIFISWFPFYYEIKMAFVLWLLSPYTKGASLLYRKFVHPSLSRHEKEIDA |
| VRWMMYWIVFALFM.AEIVTDIFISWFPFYYEIKMAFVLWLLSPYTKGASLLY.KFVHPSLSRHEKEIDA | |
| Retrocopy | VRWMMYWIVFALFMVAEIVTDIFISWFPFYYEIKMAFVLWLLSPYTKGASLLYLKFVHPSLSRHEKEIDA |
| Parental | YLVQAKERSYETMLSFGKRGLNMAASAAVQAATKSQGALAGRLRSFSMQDLRSIPDAPAPAYQDALYPED |
| YLV.AKERSYETMLSFGKRGLN.AASAAVQAA.KSQGALAGRL.SFSMQDLRSIPDAPAPA.QDALYPED | |
| Retrocopy | YLVEAKERSYETMLSFGKRGLNIAASAAVQAASKSQGALAGRLLSFSMQDLRSIPDAPAPA*QDALYPED |
| Parental | QVLHRRPPIGYRDGGLQDSNTEDDCWSDTEAVPRMPARPREKPLSRSQSLRVIKRKPLVREGTSRSLKVR |
| QVLHRRPPIGYRDGGLQDSNTEDDCWSDTEAVPRMPARPREKPLSRSQSLRVIKRKPLVREGTSRSLKVR | |
| Retrocopy | QVLHRRPPIGYRDGGLQDSNTEDDCWSDTEAVPRMPARPREKPLSRSQSLRVIKRKPLVREGTSRSLKVR |
| Parental | TRKKTVPSDMDS |
| TRKKTVPSDMDS | |
| Retrocopy | TRKKTVPSDMDS |
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 .87 RPM | 3 .15 RPM |
| SRP051959_heart | 0 .53 RPM | 0 .89 RPM |
| SRP051959_kidney | 0 .98 RPM | 1 .44 RPM |
| SRP051959_liver | 0 .48 RPM | 1 .86 RPM |
| SRP051959_lung | 0 .99 RPM | 3 .07 RPM |
| SRP051959_lymph_node | 0 .94 RPM | 2 .81 RPM |
| SRP051959_skeletal_muscle | 0 .46 RPM | 0 .63 RPM |
| SRP051959_spleen | 0 .74 RPM | 2 .00 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_744 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_744 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_744 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 2 parental genes, and 2 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Callithrix jacchus | ENSCJAG00000020323 | 1 retrocopy |
retro_cjac_744 ,
|
| Felis catus | ENSFCAG00000009632 | 1 retrocopy |