RetrogeneDB ID: | retro_ptro_1602 | ||
Retrocopy location | Organism: | Chimpanzee (Pan troglodytes) | |
| Coordinates: | 2A:60267047..60268704(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | KLHL5 | ||
| Ensembl ID: | ENSPTRG00000015989 | ||
| Aliases: | None | ||
| Description: | kelch-like family member 5 [Source:HGNC Symbol;Acc:6356] |
Retrocopy-Parental alignment summary:
>retro_ptro_1602
AGCCCGACGCGGACTTCCAATAGTAGTCAGACATTATCATCCTGTCATACTATGGAGCCATGTACATCAGATGAATTTTT
CCAAGCCCTTAATCATGCCGAGCAAACATTTAAAAAAATGGAAAACTATTTGAGACATAAACAGTTGTGCGATGTAATTT
TAGTCGCTGGTGATCGCAGAATTCCAGCTCACAGATTGGTGCTCTCCTCTGTCTCAGACTATTTTGCTGCCATGTTTACT
AATGATGTCAGAGAGGCAAGACAAGAAGAAATAAAAATGGAAGGTGTAGAACCAAATTCATTGTGGTCCTTGATCCAGTA
TGCTTATACAGGCCGCCTTGAATTAAAAGAAGATAATATTGAGTGCCTGTTATCTACAGCTTGCCTTCTTCAGCTTTCAC
AGGTTGTAGAAGCATGCTGTAAGTTTTTAATGAAACAGCTTCATCCATCCAACTGTCTTGGAATTCGTTCTTTTGCTGAT
GCCCAAGGTTGTACAGATTTGCATAAAGTGGCTCACAATTATACTATGGATCATTTCATGGAAGTAATCAGAAACCAGGA
ATTTGTATTATTACCAGCCAGTGAAATTGCAAAGCTCTTGGCTAGTGATGACATGAACATTCCTAATGAGGAGACAATAT
TGAATGCACTTCTTACTTGGGTCCGTCATGATTTGGAACAGAGACGGAAAGATCTAAGTAAACTTTTGGCTTATATTAGG
CTACCTCTTCTTGCACCACAGTTCCTGGCAGACATGGAAAATAATGCACTTTTTCGGGATGATATAGAATGTCAGAAACT
CATTATGGAAGCAATGAAGTACCATTTATTACCAGAGAGACGACCCATGTTACAAAGTCCTCGGACAAAACCTAGGAAGT
CAACTGTTGGTACATTATTTGCAGTTGGGGGAATGGATTCAACAAAAGGAGCAACAAGCATTTGAAAGTATGACTTCCGT
ACAAATATGTGGACTCCAGTAACAAATATGAATGGGAGGAGGCTACAGTCCGGTGGTCCAGTGCTAGATGACAAACTGTA
TGTGGTTGGAGGAAGAGATGGACTGAAGACTTTGAATACTGTAGAGTGCTACAACCCCAAAACAAAAACTTGGAGTGTGA
TGCCACCTATGTCCACACATAGACATGGCCTTGGTGTGGCTGTACTGGAAGGTCCCATGTATGCCGTAGGAGGACATGAT
GGCTGGAGCTATCTGAACACAGTGGAAAGATGGGACCCTCAGGCTCGCCAGTGGAATTTTGTTGCCACTATGTCTACCCC
TAGGAGTACAGTAGGTGTGGCAGTACTAAGTGGAAAACTTTATGCAGTTGGTGGTCGTGATGGAAGTTCTTGTCTCAAAT
CAGTAGAATGTTTTGATCCTCATACTACTAAGTGGACACTGTGTGCACAGATGTCAAAAAGGAGAGGTGGCGTAGGAGTG
ACGACCTGGAATGGACTGCTGTATGCTATAGGGGGGCACGATGCTCCCGCATCCAACTTGACTTCCAGACTCTCAGACTG
TGTGTAAAGATATGATCCCAAAACAGACATGTGGACTGCAGTAGCATCCATGAGCATCAGCAGAGATGCAGTCGGGGTCT
GTTTACTTGGTGATAAAGTTAATATGCTTGTTGGGGGGTTATGATGGACAGGCATAC
ORF - retro_ptro_1602 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 97.11 % |
| Parental protein coverage: | 72.98 % |
| Number of stop codons detected: | 2 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | SSCRTSNSSQTLSSCHTMEPCTSDEFFQALNHAEQTFKKMENYLRHKQLCDVILVAGDRRIPAHRLVLSS |
| S..RTSNSSQTLSSCHTMEPCTSDEFFQALNHAEQTFKKMENYLRHKQLCDVILVAGDRRIPAHRLVLSS | |
| Retrocopy | SPTRTSNSSQTLSSCHTMEPCTSDEFFQALNHAEQTFKKMENYLRHKQLCDVILVAGDRRIPAHRLVLSS |
| Parental | VSDYFAAMFTNDVREARQEEIKMEGVEPNSLWSLIQYAYTGRLELKEDNIECLLSTACLLQLSQVVEACC |
| VSDYFAAMFTNDVREARQEEIKMEGVEPNSLWSLIQYAYTGRLELKEDNIECLLSTACLLQLSQVVEACC | |
| Retrocopy | VSDYFAAMFTNDVREARQEEIKMEGVEPNSLWSLIQYAYTGRLELKEDNIECLLSTACLLQLSQVVEACC |
| Parental | KFLMKQLHPSNCLGIRSFADAQGCTDLHKVAHNYTMEHFMEVIRNQEFVLLPASEIAKLLASDDMNIPNE |
| KFLMKQLHPSNCLGIRSFADAQGCTDLHKVAHNYTM.HFMEVIRNQEFVLLPASEIAKLLASDDMNIPNE | |
| Retrocopy | KFLMKQLHPSNCLGIRSFADAQGCTDLHKVAHNYTMDHFMEVIRNQEFVLLPASEIAKLLASDDMNIPNE |
| Parental | ETILNALLTWVRHDLEQRRKDLSKLLAYIRLPLLAPQFLADMENNALFRDDIECQKLIMEAMKYHLLPER |
| ETILNALLTWVRHDLEQRRKDLSKLLAYIRLPLLAPQFLADMENNALFRDDIECQKLIMEAMKYHLLPER | |
| Retrocopy | ETILNALLTWVRHDLEQRRKDLSKLLAYIRLPLLAPQFLADMENNALFRDDIECQKLIMEAMKYHLLPER |
| Parental | RPMLQSPRTKPRKSTVGTLFAVGGMDSTKGATSIEKYDLRTNMWTPVANMNGRRLQFGVAVLDDKLYVVG |
| RPMLQSPRTKPRKSTVGTLFAVGGMDSTKGATSI.KYD.RTNMWTPV.NMNGRRLQ.G..VLDDKLYVVG | |
| Retrocopy | RPMLQSPRTKPRKSTVGTLFAVGGMDSTKGATSI*KYDFRTNMWTPVTNMNGRRLQSGGPVLDDKLYVVG |
| Parental | GRDGLKTLNTVECYNPKTKTWSVMPPMSTHRHGLGVAVLEGPMYAVGGHDGWSYLNTVERWDPQARQWNF |
| GRDGLKTLNTVECYNPKTKTWSVMPPMSTHRHGLGVAVLEGPMYAVGGHDGWSYLNTVERWDPQARQWNF | |
| Retrocopy | GRDGLKTLNTVECYNPKTKTWSVMPPMSTHRHGLGVAVLEGPMYAVGGHDGWSYLNTVERWDPQARQWNF |
| Parental | VATMSTPRSTVGVAVLSGKLYAVGGRDGSSCLKSVECFDPHTNKWTLCAQMSKRRGGVGVTTWNGLLYAI |
| VATMSTPRSTVGVAVLSGKLYAVGGRDGSSCLKSVECFDPHT.KWTLCAQMSKRRGGVGVTTWNGLLYAI | |
| Retrocopy | VATMSTPRSTVGVAVLSGKLYAVGGRDGSSCLKSVECFDPHTTKWTLCAQMSKRRGGVGVTTWNGLLYAI |
| Parental | GGHDAPASNLTSRLSDCVERYDPKTDMWTAVASMSISRDAVGVCLLGDKL-YAVG-GYDGQAY |
| GGHDAPASNLTSRLSDCV.RYDPKTDMWTAVASMSISRDAVGVCLLGDK....VG.GYDGQAY | |
| Retrocopy | GGHDAPASNLTSRLSDCV*RYDPKTDMWTAVASMSISRDAVGVCLLGDKVNMLVG>GYDGQAY |
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 .07 RPM | 23 .15 RPM |
| SRP007412_cerebellum | 0 .14 RPM | 37 .50 RPM |
| SRP007412_heart | 0 .09 RPM | 21 .66 RPM |
| SRP007412_kidney | 0 .10 RPM | 29 .42 RPM |
| SRP007412_liver | 0 .26 RPM | 64 .39 RPM |
| SRP007412_testis | 0 .21 RPM | 41 .94 RPM |
Pan troglodytes was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ptro_1602 retrocopy.
Pan troglodytes was not studied using FANTOM5 data.
retro_ptro_1602 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_ptro_1602 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 2 parental genes, and 2 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Pan troglodytes | ENSPTRG00000001861 | 1 retrocopy | |
| Pan troglodytes | ENSPTRG00000015989 | 1 retrocopy |
retro_ptro_1602 ,
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