RetrogeneDB ID: | retro_pabe_2823 | ||
Retrocopy location | Organism: | Orangutan (Pongo abelii) | |
| Coordinates: | 5_random:9117343..9118129(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | CCDC176 | ||
| Ensembl ID: | ENSPPYG00000005979 | ||
| Aliases: | None | ||
| Description: | coiled-coil domain containing 176 [Source:HGNC Symbol;Acc:19855] |
Retrocopy-Parental alignment summary:
>retro_pabe_2823
CAGACAGAGCTGAAAAAAATAAACAAGAAAGAATGAGATGTTCTAAAGAAGAATTTAAAGAACAATTAATAGAAACATAA
GGAGACTGTTAGGACCTGGGAAGGCATGGTTTTTGAAGAAAATCATCGACTAGAACAAAAGGCTGAAAAAAGACAATGCT
GGCAATGAGGGCCCATCATGAAGTTGTCGTGCAATTGAACAATGACGGAAAAAAATGTGTTTAAAGGAACAATTATCTCC
AGAATGCTCTTGCATACCATCTGAAAGAAGTTTATGCTCTACAAAAACACTCCCAGAGATTGCAATAGAATCAAATCCTT
TTACATCAAAAGGAGATTAATGAGCTGTTGGTTAAGGAAAAGATTATGCAGCTTACCCAGTAGAAAACACAAATCCAAAC
ACTTCAGAAGAAGGTAGTAAGTTTGGAGACTGCTCTAAGTTATAGGACCAGAGTTTGAGACTGAAGCATTAAAACTGTAG
CAACAGCAATGATAGAGAACCAATCAGGTTACATATAAACTGACAAGCAGTAGCAAAGTCAGGTGAACAAAAGAAAAATG
AATTGAGTGAAGAAGCTGGCCAAGAACATACTAGGTGAGAGAACAGAATTGGACAGCTCTTTTTTAAATGCCCTACACCA
AGTGAAATAACAGATCCTATTTATCAGGAAGCATTTAAATTGAAAGCACAAGGGGCTTTCAATTACAAATGAGATCAGCA
CTTACAGGAAGAATGGAATATCCCCAAATCAGAACAATTGATGACAGAGAGCACAGCATCAATAGT
ORF - retro_pabe_2823 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 60.15 % |
| Parental protein coverage: | 50.66 % |
| Number of stop codons detected: | 12 |
| Number of frameshifts detected: | 3 |
Retrocopy - Parental Gene Alignment:
| Parental | QFQKRKIQVERELDDLKENLRNTERIHQETLRRLESRFFEEKHRLEQEAE-KKIIMLAERAHHEAIVQLN |
| Q....KI....E.D.LK.NL.N....H.ET.R..E...FEE.HRLEQ.AE.KK..MLA.RAHHE..VQLN | |
| Retrocopy | QTELKKIN-KKE*DVLKKNLKNN**KHKETVRTWEGMVFEENHRLEQKAE<KKT-MLAMRAHHEVVVQLN |
| Parental | DAGRNVFKENVYLQKALAYHLKETDALQKNSQKLQESHTLLLHQKEINDLLVKEKIMQLVQQRSQIQTLQ |
| ..G......N.YLQ.ALAYHLKE..ALQK.SQ.LQ.....LLHQKEIN.LLVKEKIMQL.Q...QIQTLQ | |
| Retrocopy | NDGKKCV*RNNYLQNALAYHLKEVYALQKHSQRLQ*NQ-ILLHQKEINELLVKEKIMQLTQ*KTQIQTLQ |
| Parental | KKVVNLETALSYMTKEFESEVLKLQQHAMIENQAGQVEIDKLQHLLQMKDREMNRVKKLAKNILDERTEV |
| KKVV.LETALSY.T........K....AMIENQ.G....DK.Q...Q...R.MN.VKKLAKNIL.ERTE. | |
| Retrocopy | KKVVSLETALSYRTRV*D*SI-KTVATAMIENQSGYI*TDK-Q*QSQVNKRKMN*VKKLAKNILGERTEL |
| Parental | ERFFLDALHQVKQQILISRKQ-YKQIAQAAFN-LKMRAACAGRTEYPKIRTFDGREHSTNS |
| ...FL.ALHQVK.QIL..RK...K..AQ.AFN.L.MR.A..GR.EYP.IRT.D.REHS.NS | |
| Retrocopy | DSSFLNALHQVK*QILFIRKH<FKLKAQGAFN<LQMRSALTGRMEYPQIRTIDDREHSINS |
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 | 4 .31 RPM |
| SRP007412_cerebellum | 0 .00 RPM | 5 .72 RPM |
| SRP007412_heart | 0 .00 RPM | 1 .63 RPM |
| SRP007412_kidney | 0 .00 RPM | 5 .10 RPM |
| SRP007412_liver | 0 .00 RPM | 2 .39 RPM |
Pongo abelii was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_pabe_2823 retrocopy.
Pongo abelii was not studied using FANTOM5 data.
retro_pabe_2823 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_pabe_2823 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 | |
|---|---|---|---|
| Pongo abelii | ENSPPYG00000005979 | 1 retrocopy |
retro_pabe_2823 ,
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