RetrogeneDB ID: | retro_cjac_2466 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 4:116017214..116017557(-) | ||
| Located in intron of: | ENSCJAG00000004553 | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | NIP7 | ||
| Ensembl ID: | ENSCJAG00000015364 | ||
| Aliases: | None | ||
| Description: | NIP7, nucleolar pre-rRNA processing protein [Source:HGNC Symbol;Acc:24328] |
Retrocopy-Parental alignment summary:
>retro_cjac_2466
GGGACCTGCTTCAGAAAATCCACCAAGATCCGTAAGTTTCAGTTGCACAACACAGCTCTGGATTACCCTGCACCCTATGT
CAACACAAAGCGCGGCTAAAAACTGGAGCAGAGCAGTCCTTCCCATATGGGAACCATATGCTAAAATCTGGTCTGAGTTG
AATCATGAAAAATAACTTCACCAGGCCAGGGAGTGGTGGTGTACACCATGGCAGACATCCCTTTGGGTTTTGGGGTGGCA
GCAAAATTTATGCAAAACTGCAGAAAAGCAGACCCCGTGGCAATTTGTGGTATTTCATCGAGCAGACATTGGTGAATATG
TGTGGCATGAAGAGACGTTGACT
ORF - retro_cjac_2466 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 70.94 % |
| Parental protein coverage: | 63.69 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 3 |
Retrocopy - Parental Gene Alignment:
| Parental | GTCFGKFTKTHKFRLHVTALDYLAPYA-KYKVWIKPGAEQSFLYGNHVLKSGLGRITEN-TSQYQGVVVY |
| GTCF.K.TK..KF.LH.TALDY.APY....K...K.GAEQSF.YGNH.LKSGL..I..N.TS..QGVVVY | |
| Retrocopy | GTCFRKSTKIRKFQLHNTALDYPAPYV<QHKARLKTGAEQSFPYGNHMLKSGLS*IMKN>TSPGQGVVVY |
| Parental | SMADVPLGFGVAAKSTQDCRKVDPMAI-VVFHQADIGEYVRHEETLT |
| .MAD.PLGFGVAAK..Q.CRK.DP.AI.VVFH.ADIGEYV.HEETLT | |
| Retrocopy | TMADIPLGFGVAAKFMQNCRKADPVAI>VVFHRADIGEYVWHEETLT |
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 .73 RPM | 2 .33 RPM |
| SRP051959_heart | 0 .42 RPM | 2 .32 RPM |
| SRP051959_kidney | 0 .73 RPM | 1 .89 RPM |
| SRP051959_liver | 0 .24 RPM | 2 .23 RPM |
| SRP051959_lung | 1 .02 RPM | 2 .44 RPM |
| SRP051959_lymph_node | 0 .98 RPM | 2 .83 RPM |
| SRP051959_skeletal_muscle | 0 .22 RPM | 3 .63 RPM |
| SRP051959_spleen | 1 .16 RPM | 2 .67 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_2466 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_2466 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_2466 has 5 orthologous retrocopies within eutheria group .| Species | RetrogeneDB ID |
|---|---|
| Homo sapiens | retro_hsap_3648 |
| Pan troglodytes | retro_ptro_2473 |
| Gorilla gorilla | retro_ggor_2464 |
| Pongo abelii | retro_pabe_2995 |
| Macaca mulatta | retro_mmul_1801 |