RetrogeneDB ID: | retro_pabe_860 | ||
Retrocopy location | Organism: | Orangutan (Pongo abelii) | |
| Coordinates: | 12:70941235..70942176(+) | ||
| Located in intron of: | ENSPPYG00000004769 | ||
Retrocopy information | Ensembl ID: | ENSPPYG00000004770 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | FAHD2A | ||
| Ensembl ID: | ENSPPYG00000012057 | ||
| Aliases: | None | ||
| Description: | fumarylacetoacetate hydrolase domain-containing protein 2 [Source:RefSeq peptide;Acc:NP_001125186] |
Retrocopy-Parental alignment summary:
>retro_pabe_860
ATGCTGGTCTCTGGTAGAAGAAGGTTGCTCACAGCTCTGCTGCAGGCTCAGAAGTGGCCCTTTCAACCCTCCAGAGACAT
GAGACTAGTCCAGTTCCAGGCACCCCACCTGGTGGGGCCTCACTTGGGCCCAGAGATGGGGAATGGTGGAAGGGTTATCA
ACCTCAATGCCTTTGACTCTATGCTCCGCAAAATGATGACACAGTTCCTAGAGCAGGGAGAGGTCACCCTCTCAGTGGCA
AGAAGAGCCTTGGGTGCCCAGTTGCCAGTCCTACCATGGTTAAAAGTAACCTCCCTGGCTCCAGCCACGTGGCCAGATAA
GGTGGTGTGTGTGGGCATGAATTGTGTGGACCACTGCAAAGAATAGAATGTGCCCGTGCCCACGGAACCTTTCATCTTCA
GCAAGTTTGCCAACTCCATTGTGGAGCTCTATGATGAGATGGTCCTCCCATCAGAGAGCCAGGAGGTAGACTGGGAAGTG
GAGCAGCCGTGGTCATTGGAAAGAAAGGCAAGCACATCAAAGCCACAGATGCCATGGCCCATGTGGCTGGCTTCACTGTG
GCTCATAACGTGAGTGCTCATGACTGGCAGATGAGACATAATGGGAAACAGTGGCTGCTGGGAAAAACCTTCGACACCTT
CTGCCCTCTGGGCCCTGCCTTGGTGACCAAGGACAGTGTAGCAGATGCACACATCTTAAAGATCTGCTGCCAAGTGAATG
GGGAAGTGGTCCAGAGCAACAACACCAACCAGATAGTGGTCAAGACAGAGGAGCGGATAGCCTGGGTCTCCCAGTTTGTC
ACCTTTTACCCAGGGGATGTCATCCTGACTGGGACCTCCCCAGGTGTCGGTGTATTCAGGAAACCTCCTGTCTTTCTCAA
GAAGGGAGATGAAGTCCAGTGTGAAATTGAAGAATTAGGTGTCATCATCAGCAAGGTGGTG
ORF - retro_pabe_860 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 86.98 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | MLVSGRRRLLTALLQAQKWPFQPSRDMRLVQFQAPHLVGSHLGLETGNGGGVINLNAFDPTLPKTMTQFL |
| MLVSGRRRLLTALLQAQKWPFQPSRDMRLVQFQAPHLVG.HLG.E.GNGG.VINLNAFD..L.K.MTQFL | |
| Retrocopy | MLVSGRRRLLTALLQAQKWPFQPSRDMRLVQFQAPHLVGPHLGPEMGNGGRVINLNAFDSMLRKMMTQFL |
| Parental | EQGEATLSVARRALAAQLPVLPRSEVTFLAPVTRPDKVVCVRMNYVDHCKEQNVPVPKEPFIFSKFASSI |
| EQGE.TLSVARRAL.AQLPVLP...VT.LAP.T.PDKVVCV.MN.VDHCKE.NVPVP.EPFIFSKFA.SI | |
| Retrocopy | EQGEVTLSVARRALGAQLPVLPWLKVTSLAPATWPDKVVCVGMNCVDHCKE*NVPVPTEPFIFSKFANSI |
| Parental | VGPYDEVVLPPQSQEVDWEVE-LVVVIGKKGKHIKATDAMAHVAGFTVAHDVSARDWQMRHNGKQWLLGK |
| V..YDE.VLP..SQEVDWEVE...VVIGKKGKHIKATDAMAHVAGFTVAH.VSA.DWQMRHNGKQWLLGK | |
| Retrocopy | VELYDEMVLPSESQEVDWEVE<AAVVIGKKGKHIKATDAMAHVAGFTVAHNVSAHDWQMRHNGKQWLLGK |
| Parental | TFDTFCPLGPALVTKDSVADPHNLKICCRVNGEVVQSSNTNQMVFKTEDLIAWVSQFVTFYPGDVILTGT |
| TFDTFCPLGPALVTKDSVAD.H.LKICC.VNGEVVQS.NTNQ.V.KTE..IAWVSQFVTFYPGDVILTGT | |
| Retrocopy | TFDTFCPLGPALVTKDSVADAHILKICCQVNGEVVQSNNTNQIVVKTEERIAWVSQFVTFYPGDVILTGT |
| Parental | PPGVGVFRKPPVFLKKGDEVQCEIEELGVIINKVV |
| .PGVGVFRKPPVFLKKGDEVQCEIEELGVII.KVV | |
| Retrocopy | SPGVGVFRKPPVFLKKGDEVQCEIEELGVIISKVV |
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 .06 RPM | 30 .91 RPM |
| SRP007412_cerebellum | 0 .24 RPM | 22 .62 RPM |
| SRP007412_heart | 0 .45 RPM | 60 .30 RPM |
| SRP007412_kidney | 0 .10 RPM | 45 .28 RPM |
| SRP007412_liver | 0 .18 RPM | 53 .34 RPM |
Pongo abelii was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_pabe_860 retrocopy.
Pongo abelii was not studied using FANTOM5 data.
retro_pabe_860 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_pabe_860 has 4 orthologous retrocopies within eutheria group .| Species | RetrogeneDB ID |
|---|---|
| Homo sapiens | retro_hsap_1025 |
| Pan troglodytes | retro_ptro_700 |
| Gorilla gorilla | retro_ggor_810 |
| Macaca mulatta | retro_mmul_818 |
Parental genes homology:
Parental genes homology involve 7 parental genes, and 7 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Callithrix jacchus | ENSCJAG00000018863 | 1 retrocopy | |
| Homo sapiens | ENSG00000144199 | 1 retrocopy | |
| Gorilla gorilla | ENSGGOG00000016246 | 1 retrocopy | |
| Macaca mulatta | ENSMMUG00000012859 | 1 retrocopy | |
| Nomascus leucogenys | ENSNLEG00000000008 | 1 retrocopy | |
| Pongo abelii | ENSPPYG00000012057 | 1 retrocopy |
retro_pabe_860 ,
|
| Pan troglodytes | ENSPTRG00000012214 | 1 retrocopy |