RetrogeneDB ID: | retro_pabe_1856 | ||
Retrocopy location | Organism: | Orangutan (Pongo abelii) | |
| Coordinates: | 21:32529134..32530219(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | BTRC | ||
| Ensembl ID: | ENSPPYG00000002583 | ||
| Aliases: | None | ||
| Description: | F-box/WD repeat-containing protein 1A [Source:RefSeq peptide;Acc:NP_001124974] |
Retrocopy-Parental alignment summary:
>retro_pabe_1856
CAGATAAGTAATGGAACATCATTTGTGATCATCTCCAGAAAGAGGCCATCAGAAGGAAACTATCAAAAAGAAAAAGACTT
GTATATTCAATATTTTAACCAGTGGTCTGAATCAGATCAATTGGAATTTGTGGGACATCTTATTTCACAAATGTGTCATT
ATCAGCATGGACGTATTAACTCTTACCTGAAGCCCATGTTGCAGCAGGACTTTATTACTGCTTTACTCGAGCAAGGCTTA
AATCACATAGCAGAAAACACTCTTTCGTACCTGGATGCCAGGTCTCTGTGTGCAGCAGAGCTGGTATGTAAAGAATGGCA
GGGAGTGATCTCAGAACCAATGCTTTGGAAGAAGCTGATTGAACGAATGGTACACACTGATCCCCTATGGAAAGGACTTT
CAGAAGGAAGAGGGTGGGATCAGTACCTGTTTCAAAACAGACCCACAGCTAGCCCTCCAAATTCATTTTACAGGTCATTA
TACCCAAAGATTATCCAGGATATAGAGACTATAGAATCCACCTAGCGGTGTGGCTGACACAGCTTGCAGAGGATTCAGTA
CCGCTCTGAAAATAGTAAAGGTGTCTATGGTTTACAGTACGATGATGAAAAAATTATCAGTGGCCTACAAGATAATTATA
TTAAGATTTGGGATAAAACCAGCCTGGAATGTTTGAAAGTGTTAACGGCCACACAGGCTCTGTCCTCTGTCTGCAGTAGG
ATGAGCGTGTCATTGTAACTGGCTCTTCAGATTCTACGGTGAGAGTGTGGGAAGTGAACACGGGTGAAGTTCTTAACACA
TTAATCCACCACAGTGAGGATGTACTGCACTTACGCTTCAGCAGTGGACTGATGGTGACCTGTTCCAAGGACCGCTCCAT
TGCTGTGTGGGACATGGCTTCTGCGACCGATATCACTTTACGTGGTGTCCTGGTTGGCCACTGAGCTGCTGTCAACGTAG
TAGACTTTGACGAGAAATACATCGTGTCTGCCTCTGGTGACAGGACCATCAAAGTCTGGAGCATGAGCACCTGTGAATTT
GTTTGTACTCTCAATGGGCACAAGCGAGTCTTGTCTCTAGTACAG
ORF - retro_pabe_1856 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 75.62 % |
| Parental protein coverage: | 60.17 % |
| Number of stop codons detected: | 4 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | KLANGTSSMIVPKQRKLSASYEKEKELCVKYFEQWSESDQVEFVEHLISQMCHYQHGHINSYLKPMLQRD |
| ...NGTS..I....R.....Y.KEK.L...YF.QWSESDQ.EFV.HLISQMCHYQHG.INSYLKPMLQ.D | |
| Retrocopy | QISNGTSFVIISRKRPSEGNYQKEKDLYIQYFNQWSESDQLEFVGHLISQMCHYQHGRINSYLKPMLQQD |
| Parental | FITALPARGLDHIAENILSYLDAKSLCAAELVCKEWYRVTSDGMLWRKLIERMVRTDSLWRGLAERRGWG |
| FITAL...GL.HIAEN.LSYLDA.SLCAAELVCKEW..V.S..MLW.KLIERMV.TD.LW.GL.E.RGW. | |
| Retrocopy | FITALLEQGLNHIAENTLSYLDARSLCAAELVCKEWQGVISEPMLWKKLIERMVHTDPLWKGLSEGRGWD |
| Parental | QYLFKNKPPDGNAAPNSFYRALYPKIIQDIETIESNWRCGRHSLQRIHCRSETSKGVYCLQYDDQKIVSG |
| QYLF.N.P......PNSFYR.LYPKIIQDIETIES..RCG.HSLQRI..RSE.SKGVY.LQYDD.KI.SG | |
| Retrocopy | QYLFQNRPTA--SPPNSFYRSLYPKIIQDIETIEST*RCG*HSLQRIQYRSENSKGVYGLQYDDEKIISG |
| Parental | LRDNTIKIWDKNTLECKRILT-GHTGSVLCLQYDERVIITGSSDSTVRVWDVNTGEMLNTLIHHCEAVLH |
| L.DN.IKIWDK..LEC...LT.GHTGSVLCLQ.DERVI.TGSSDSTVRVW.VNTGE.LNTLIHH.E.VLH | |
| Retrocopy | LQDNYIKIWDKTSLECLKVLT<GHTGSVLCLQ*DERVIVTGSSDSTVRVWEVNTGEVLNTLIHHSEDVLH |
| Parental | LRFNNGMMVTCSKDRSIAVWDMASPTDITLRRVLVGHRAAVNVVDFDDKYIVSASGDRTIKVWNTSTCEF |
| LRF..G.MVTCSKDRSIAVWDMAS.TDITLR.VLVGH.AAVNVVDFD.KYIVSASGDRTIKVW..STCEF | |
| Retrocopy | LRFSSGLMVTCSKDRSIAVWDMASATDITLRGVLVGH*AAVNVVDFDEKYIVSASGDRTIKVWSMSTCEF |
| Parental | VRTLNGHKRGIACLQ |
| V.TLNGHKR.....Q | |
| Retrocopy | VCTLNGHKRVLSLVQ |
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 | 1 .44 RPM | 118 .82 RPM |
| SRP007412_cerebellum | 3 .28 RPM | 97 .28 RPM |
| SRP007412_heart | 0 .75 RPM | 21 .13 RPM |
| SRP007412_kidney | 0 .93 RPM | 23 .24 RPM |
| SRP007412_liver | 0 .64 RPM | 16 .40 RPM |
Pongo abelii was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_pabe_1856 retrocopy.
Pongo abelii was not studied using FANTOM5 data.
retro_pabe_1856 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_pabe_1856 has 2 orthologous retrocopies within eutheria group .| Species | RetrogeneDB ID |
|---|---|
| Gorilla gorilla | retro_ggor_1576 |
| Macaca mulatta | retro_mmul_1596 |
Parental genes homology:
Parental genes homology involve 3 parental genes, and 3 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Macropus eugenii | ENSMEUG00000013579 | 1 retrocopy | |
| Pongo abelii | ENSPPYG00000002583 | 1 retrocopy |
retro_pabe_1856 ,
|
| Rattus norvegicus | ENSRNOG00000016280 | 1 retrocopy |