RetrogeneDB ID: | retro_cjac_4195 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | X:83992919..83993552(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSCJAG00000022740 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | MAD2L2 | ||
| Ensembl ID: | ENSCJAG00000013267 | ||
| Aliases: | None | ||
| Description: | MAD2 mitotic arrest deficient-like 2 (yeast) [Source:HGNC Symbol;Acc:6764] |
Retrocopy-Parental alignment summary:
>retro_cjac_4195
ATGACCACGCTTACACGGCAGGACCTCAACTTTGGCCAAGTGGTGGCCGATGTGCTCTGCGAGTTTCTGGAGGTGGCTGT
GCATCTCATCCTCTACGTGCACGAGGTCTACCCGGTGGGCATTTTCCAGAAACGTAAGAAGTACAACGTGCCGGTCCAGA
TGTCCTGCCACCCGGAGCTGAATCAGTATATCCAGGATACGCTGCACTGCGTCAAGCCACTCCTGGAGAAGAATGATGTG
GAGAAAGTGGTGGTGGTGATTTTGGATAAAGAGCACCGCCCAGTGGAGAAATTCGTCTTTGAGATCACCCAGCCTCCACT
GCTATCCATCAGCTCAGACTCCCTTTTGTCTCACGTGGAGCAGCTGCTCCGAGCCTTCATCCTGAAGATCAGCGTGTGCG
ATGCTGTCCTGCACCACAATGCCCTAGGCTGTACCTTCACAGTCCTGGTGCACACGAGAGAAGCTGCCACTCGCAACATG
GAGAAAATCCAGGTCATCAAGGATTTCCCCTGGATCCTGGCAGATGAGCAGGATGTCCACATGCATGACCCCCGGCTGAT
ACCACTGAAAACCATGACGTCGGACATTTTAAAGATGCAGCTTTACGTGGAAGAGCGCGCCCATAAAGGCAGC
ORF - retro_cjac_4195 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 98.1 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | MTTLTRQDLNFGQVVADVLCEFLEVAVHLILYVREVYPVGIFQKRKKYNVPVQMSCHPELNQYIQDTLHC |
| MTTLTRQDLNFGQVVADVLCEFLEVAVHLILYV.EVYPVGIFQKRKKYNVPVQMSCHPELNQYIQDTLHC | |
| Retrocopy | MTTLTRQDLNFGQVVADVLCEFLEVAVHLILYVHEVYPVGIFQKRKKYNVPVQMSCHPELNQYIQDTLHC |
| Parental | VKPLLEKNDVEKVVVVILDKEHRPVEKFVFEITQPPLLSISSDSLLSHVEQLLRAFILKISVCDAVLDHN |
| VKPLLEKNDVEKVVVVILDKEHRPVEKFVFEITQPPLLSISSDSLLSHVEQLLRAFILKISVCDAVL.HN | |
| Retrocopy | VKPLLEKNDVEKVVVVILDKEHRPVEKFVFEITQPPLLSISSDSLLSHVEQLLRAFILKISVCDAVLHHN |
| Parental | PPGCTFTVLVHTREAATRNMEKIQVIKDFPWILADEQDVHMHDPRLIPLKTMTSDILKMQLYVEERAHKG |
| ..GCTFTVLVHTREAATRNMEKIQVIKDFPWILADEQDVHMHDPRLIPLKTMTSDILKMQLYVEERAHKG | |
| Retrocopy | ALGCTFTVLVHTREAATRNMEKIQVIKDFPWILADEQDVHMHDPRLIPLKTMTSDILKMQLYVEERAHKG |
| Parental | S |
| S | |
| Retrocopy | S |
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 | 3 .79 RPM |
| SRP051959_heart | 0 .18 RPM | 5 .84 RPM |
| SRP051959_kidney | 0 .47 RPM | 9 .34 RPM |
| SRP051959_liver | 0 .24 RPM | 5 .89 RPM |
| SRP051959_lung | 0 .15 RPM | 5 .40 RPM |
| SRP051959_lymph_node | 0 .00 RPM | 5 .71 RPM |
| SRP051959_skeletal_muscle | 0 .15 RPM | 4 .26 RPM |
| SRP051959_spleen | 0 .06 RPM | 4 .77 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_4195 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_4195 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_4195 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 | ENSCJAG00000013267 | 1 retrocopy |
retro_cjac_4195 ,
|