RetrogeneDB ID: | retro_pabe_2976 | ||
Retrocopy location | Organism: | Orangutan (Pongo abelii) | |
| Coordinates: | 6:88058075..88058906(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | RCN1 | ||
| Ensembl ID: | ENSPPYG00000003385 | ||
| Aliases: | None | ||
| Description: | reticulocalbin 1, EF-hand calcium binding domain [Source:HGNC Symbol;Acc:9934] |
Retrocopy-Parental alignment summary:
>retro_pabe_2976
CGGGCGCTGCGGGCCAAGCCCACCGTGCGCAAGGAGCGCGTGGTGCGGCCTGACTCGGAGCTGGGCGAGCGGCTCCCAGA
GGTCAACCAGAGCTTCCAGTACTGCCATGAGGCCTTCCTGGGCAAGGAGGACTCTAAGACCTTCGGCCGGCTCACCCCGG
ACAAGAGCAAGGAGAGGCTGGGGAAGATTGTTGATCGAATCAACAATGATGGAGATGGCTTTGTCACTACTGAGGAGCTG
AAAACCTGGATCAAACGGGTGCAGAAAAGATACATCTTCGATAATGTCGCCAAAGTCTGGCGGGATTACGATAGGGACAA
GGATGATAAAATTTACTAGGAAGAATACAAACAAGCCACCTGTGACCTAGGAAACCCCGCAGAGTTTCATGATTCTTCAG
TTCATCACACCTTTAAAAAGATGCTGCCACGTGAGGAGAGAAGATTCAAAGCTGCAGACCTCGATGGTGCCCTGACAGCC
ACTCAGGAGGAGTTCACTGCCTTTCTGCATCCTGAAGAGTTTGAGCATATGAAGGAAATTGTGGTTTTGGAAACCCTGGA
GGACAACGACAAGAACGGGGATGGGTTTGTGGATCGGGATGAATATATTGTGGATATGTTTTCCCATGAGGAGAATGGCT
CTGAGCCAGACTGGGTTTTATCAGAACGGGAGCAATTTAACGAATTCCGGGATCTGAACAAGGACTGGAAGTTGGACAAA
GACGAGGTTCGCCACTGGATCCTCCCTCAAGATTATGATCATGCACAGGGTGAGGCCAGGCATCTAGTATATGAGTCAGA
CAAAAACAAGGATGAGAGGCTAAAGAGGAAA
ORF - retro_pabe_2976 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 88.17 % |
| Parental protein coverage: | 84.29 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | RVLRAKPTVRKERVVRPDSELGERPPEDNQSFKYDHEAFLGKEDSKTFDQLTPDESKQRLGKIVDRIDND |
| R.LRAKPTVRKERVVRPDSELGER.PE.NQSF.Y.HEAFLGKEDSKTF..LTPD.SK.RLGKIVDRI.ND | |
| Retrocopy | RALRAKPTVRKERVVRPDSELGERLPEVNQSFQYCHEAFLGKEDSKTFGRLTPDKSKERLGKIVDRINND |
| Parental | GDGFVTTEELKTWIKRVQKRYIFDNVAKVWKDYDRDKDDKISWEEYKQATYGYYLGNPAEFHDSSDHHTF |
| GDGFVTTEELKTWIKRVQKRYIFDNVAKVW.DYDRDKDDKI..EEYKQAT....LGNPAEFHDSS.HHTF | |
| Retrocopy | GDGFVTTEELKTWIKRVQKRYIFDNVAKVWRDYDRDKDDKIY*EEYKQATCD--LGNPAEFHDSSVHHTF |
| Parental | KKMLPRDERRFKAADLNGDLTATREEFTAFLHPEEFEHMKEIVVLETLEDIDKNGDGFVDQDEYIADMFS |
| KKMLPR.ERRFKAADL.G.LTAT.EEFTAFLHPEEFEHMKEIVVLETLED.DKNGDGFVD.DEYI.DMFS | |
| Retrocopy | KKMLPREERRFKAADLDGALTATQEEFTAFLHPEEFEHMKEIVVLETLEDNDKNGDGFVDRDEYIVDMFS |
| Parental | HEENGPEPDWVLSEREQFNEFRDLNKDGKLDKDEIRHWILPQDYDHAQAEARHLVYESDKNKDEKLTKE |
| HEENG.EPDWVLSEREQFNEFRDLNKD.KLDKDE.RHWILPQDYDHAQ.EARHLVYESDKNKDE.L... | |
| Retrocopy | HEENGSEPDWVLSEREQFNEFRDLNKDWKLDKDEVRHWILPQDYDHAQGEARHLVYESDKNKDERLKRK |
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 |
|---|---|---|
| SRP007412_brain_prefrontal_cortex | 0 .22 RPM | 35 .05 RPM |
| SRP007412_cerebellum | 0 .00 RPM | 21 .77 RPM |
| SRP007412_heart | 0 .00 RPM | 16 .20 RPM |
| SRP007412_kidney | 0 .00 RPM | 31 .32 RPM |
| SRP007412_liver | 0 .00 RPM | 30 .08 RPM |
Pongo abelii was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_pabe_2976 retrocopy.
Pongo abelii was not studied using FANTOM5 data.
retro_pabe_2976 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_pabe_2976 has 1 orthologous retrocopies within eutheria group .| Species | RetrogeneDB ID |
|---|---|
| Homo sapiens | retro_hsap_3629 |
Parental genes homology:
Parental genes homology involve 4 parental genes, and 32 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Homo sapiens | ENSG00000049449 | 2 retrocopies | |
| Pongo abelii | ENSPPYG00000003385 | 1 retrocopy |
retro_pabe_2976 ,
|
| Pongo abelii | ENSPPYG00000017982 | 1 retrocopy | |
| Rattus norvegicus | ENSRNOG00000013452 | 28 retrocopies |
retro_rnor_1207, retro_rnor_1224, retro_rnor_2111, retro_rnor_2112, retro_rnor_2113, retro_rnor_2352, retro_rnor_2353, retro_rnor_2354, retro_rnor_2355, retro_rnor_2408, retro_rnor_2409, retro_rnor_2410, retro_rnor_2434, retro_rnor_2435, retro_rnor_2436, retro_rnor_2437, retro_rnor_2438, retro_rnor_2486, retro_rnor_2508, retro_rnor_2509, retro_rnor_2510, retro_rnor_2511, retro_rnor_2513, retro_rnor_2664, retro_rnor_2711, retro_rnor_2716, retro_rnor_2760, retro_rnor_797,
|