RetrogeneDB ID: | retro_pabe_320 | ||
Retrocopy location | Organism: | Orangutan (Pongo abelii) | |
| Coordinates: | 1:174744633..174745701(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | WDR48 | ||
| Ensembl ID: | ENSPPYG00000014001 | ||
| Aliases: | None | ||
| Description: | WD repeat-containing protein 48 [Source:UniProtKB/Swiss-Prot;Acc:Q5RAW8] |
Retrocopy-Parental alignment summary:
>retro_pabe_320
ATGGCGGCCCATCACCGGCAGAAGACAGCAGGGCGGAGGAAAGTGCAGGTTTCCTATGTTATTCAAGATGAAGTGGAGAA
GTACAACCGAAATGGAGTCAATGCTCTGCAGCTGGATCCAGCACTAAATAGACTTTTCACAGCCGGTCGAGACTCTATCA
TAAGAATATGGAGTGTCAATCAGCACAAGCAAGATCCGTATATAGCATCTATGGAACACCATACTGATTGGGTAAATGAC
ATTGTACTCTGTTGTAATGGGAAAACATTAATATCTGCTTCTTCTGACACAACAGTAAAAGTATGGAATGCACACAAGGG
ATTTTTCATGTCAACATTAAGGACACATAAGGATTACGTAAAGGCCTTAGCATATGCCAAGGATAAAGAACTAGTAGCAT
CAGCTGGGTTGGACAGATAAATATTCCTTTTGGATGTGAATACTCTAACAGCATTGACTGCCTCAAATAACACTGTCACA
ACTTCTTCTTTAAGTGGAAACAAAGATTCCATTTATAGCCTGGCCATGAATCAACTGGGAACAATCATTGTATCAGGGTC
CACTGAAAAGGTGTTAAGGGTATGGGATCCAAGAACATGTGCAAAACTAATGAAGCTTAAAGGGCACATGGATAATGTGA
AGGCATTGCTATTAAACAGAGATGGCACGCAATGCCTTTCAGGCAGTTCTGATGGGACAATTCGCCTTTGGTCCCTTGGC
CAGCAGAGATATATAGCAACATACCGAGTCCATGATGAAGGTGTTTGGGCGCTGCAAGTCAATGATGCCTTCACATATGT
GTATTCTGGTGGAAGGGACAGGAAGATTTATTGTACAGACCTAAGAAACCCTGACATTCGGGTGCTAATTTGTGAAGAAA
AAGCACCAGTTCTCAAGATGGAGCTTGATAGATCAGCTGATCCTCCTCCTGCAATTTGGGTTGCAACAACTAAGTCTACA
GTAAATAAATGGACTTTGAAAGGAATTCATAATTTTAGAGCCTCTGGAGATTATGACAATGACTGTACAAATCCTATAAC
ACCTCTTTGTACACAACCTGACCAGGTT
ORF - retro_pabe_320 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 97.47 % |
| Parental protein coverage: | 52.58 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | MAAHHRQNTAGRRKVQVSYVIRDEVEKYNRNGVNALQLDPALNRLFTAGRDSIIRIWSVNQHKQDPYIAS |
| MAAHHRQ.TAGRRKVQVSYVI.DEVEKYNRNGVNALQLDPALNRLFTAGRDSIIRIWSVNQHKQDPYIAS | |
| Retrocopy | MAAHHRQKTAGRRKVQVSYVIQDEVEKYNRNGVNALQLDPALNRLFTAGRDSIIRIWSVNQHKQDPYIAS |
| Parental | MEHHTDWVNDIVLCCNGKTLISASSDTTVKVWNAHKGFCMSTLRTHKDYVKALAYAKDKELVASAGLDRQ |
| MEHHTDWVNDIVLCCNGKTLISASSDTTVKVWNAHKGF.MSTLRTHKDYVKALAYAKDKELVASAGLDR. | |
| Retrocopy | MEHHTDWVNDIVLCCNGKTLISASSDTTVKVWNAHKGFFMSTLRTHKDYVKALAYAKDKELVASAGLDR* |
| Parental | IFLWDVNTLTALTASNNTVTTSSLSGNKDSIYSLAMNQLGTIIVSGSTEKVLRVWDPRTCAKLMKLKGHT |
| IFL.DVNTLTALTASNNTVTTSSLSGNKDSIYSLAMNQLGTIIVSGSTEKVLRVWDPRTCAKLMKLKGH. | |
| Retrocopy | IFLLDVNTLTALTASNNTVTTSSLSGNKDSIYSLAMNQLGTIIVSGSTEKVLRVWDPRTCAKLMKLKGHM |
| Parental | DNVKALLLNRDGTQCLSGSSDGTIRLWSLGQQRCIATYRVHDEGVWALQVNDAFTHVYSGGRDRKIYCTD |
| DNVKALLLNRDGTQCLSGSSDGTIRLWSLGQQR.IATYRVHDEGVWALQVNDAFT.VYSGGRDRKIYCTD | |
| Retrocopy | DNVKALLLNRDGTQCLSGSSDGTIRLWSLGQQRYIATYRVHDEGVWALQVNDAFTYVYSGGRDRKIYCTD |
| Parental | LRNPDIRVLICEEKAPVLKMELDRSADPPPAIWVATTKSTVNKWILKGIHNFRASGDYDNDCTNPITPLC |
| LRNPDIRVLICEEKAPVLKMELDRSADPPPAIWVATTKSTVNKW.LKGIHNFRASGDYDNDCTNPITPLC | |
| Retrocopy | LRNPDIRVLICEEKAPVLKMELDRSADPPPAIWVATTKSTVNKWTLKGIHNFRASGDYDNDCTNPITPLC |
| Parental | TQPDQV |
| TQPDQV | |
| Retrocopy | TQPDQV |
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 .00 RPM | 28 .20 RPM |
| SRP007412_cerebellum | 0 .00 RPM | 34 .17 RPM |
| SRP007412_heart | 0 .00 RPM | 13 .94 RPM |
| SRP007412_kidney | 0 .00 RPM | 19 .56 RPM |
| SRP007412_liver | 0 .00 RPM | 13 .01 RPM |
Pongo abelii was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_pabe_320 retrocopy.
Pongo abelii was not studied using FANTOM5 data.
retro_pabe_320 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_pabe_320 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 3 parental genes, and 4 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Pongo abelii | ENSPPYG00000007796 | 1 retrocopy | |
| Pongo abelii | ENSPPYG00000014001 | 2 retrocopies |
retro_pabe_320 , retro_pabe_321,
|
| Pongo abelii | ENSPPYG00000019140 | 1 retrocopy |