RetrogeneDB ID: | retro_ptro_3294 | ||
Retrocopy location | Organism: | Chimpanzee (Pan troglodytes) | |
| Coordinates: | Y:16216984..16218894(+) | ||
| Located in intron of: | ENSPTRG00000041899 | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | CDC27 | ||
| Ensembl ID: | ENSPTRG00000009326 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_ptro_3294
ATGACGGTGCTGCAGGAACCCCTCCAGCCTGCTACATGGCAAGCACTAAACCACTATGCTTACCGAGATGGGGTTTTCCC
GGCAGAATGCCTTTATGCAGAAGTACACTCAGAAGAAGCCTTGTTTTTACTGGCTACCTGTTCTTACTACCCAGGAAAGG
CCTATAACACATATAGTCTCTTCAAAGTACACAGTTTTCCTACACTGCAATGCAAATACCTGCTTGCAAAATGTTGTGTT
GATCTCAGCAAGCTTGCAGAAGGGGAACAAATCTTATCTGGTGGAGTGTTCCATAAGCAGAAAAGCCATGATGATATTGT
TACCAAGTTTGGTGATTCAGCTTGCTTTCCCCTTCCATTGTTGGGACATGTATATTGCAAGACAGATCAGCTTGTCAAAG
GATCAGAATACTACCAAAAGTGCCTTAGTTTAAATCCTTTCCTCTGGTATCCCTTGAATCATTATGTGAAATAGATGAAA
AGCCAGATCCTGACCAAACATTTAAATTCACATCTTTACAGAACTTTAGCAACTGTCTGCCCAACTCTTGCACAACACAA
GTACCTAATCATAGTTTATGTCACAAACAGTCTGAGACCTTTCTTACGGAAACACCCCAGGACACAACTGAATTAAACAG
ATTGAATTTAGAATCTCCCAATTCAAAGTATTCCTTGAATACAGATTCCCCAGTGTCTTCTATTGATTCAGCTGTAATTT
CACGTGATACTGTCCAACTGGGAACAGGAACTTCCATATTATCAAACAGGTTCAAAATAAACCAAAAACTGGTCGAAGTT
TATTAAGAGGACCAGCAGCTCTTAGTCCATTAACCCCAAGTTTTGGGATTTTGCCATTAGAAACCCCAAGTCCTTGAGAT
GGATCCTATTTCCAAAACTACACTGATACACCTTTTGTAATTGATGTGCCATCCACCGGAGCCCCTTCAAAAAAGTCTGT
TGCCAGAATTGGCCAAACTGGAGCAAAATCTGTCTTCTCACGGAGTGGAAATAGCCGAGAGGTAACTCCAATTCTTTCAC
AAACGGGAAGTCCTGGTCCATAAACAAGTACAACACCTCAGGTATTGAGCCCCACTATGACATCTCCCCCAAATGCACTG
CATCAAAAAAGTTCACAAGTCTTTACTAGTGACAGTTCCACAACCAAGAAGAATAGGAAGAAATTAAAAATGAAGTTTCC
ACCTAAAATCCCAAACAGAAAAACAAAAAGTAAAACAAATAAAGGAGGAATAACTCAGCCTCATATAAATGACAGCCTGG
AAATTACAAAATTGGACTCTTCCATCAATTCAGAAGGGAAAATATCCACAATCACACCTGAGATTCAGGTATTAATCTAC
AAAAAGCAGCAGCAGAAGGCTTGATGAGGCTTCTTCCTGAAAAGGGGAAAGGTTATTTAGCTTTGTGTTCATACCACTGC
AAAGAAGCTATAAATATTTTGAGCCATCTACCTTCTCACCACTACAATTCTGGTTGGGTACTGTGCCAAATTGGAAGGGT
CTATTTTGAACTTTCAGAGTACATGCAAGCTGAAAGAATATTCTCAGAGGTTAGAAGGATTGAGGATTATAGAGTCAAAG
CCATGGAAATCTACTCTACAACACTTTGGCATCTTCAAAAACATGTTGCTCTTTCAGTTCTGTCAAAAGACTTAACAGAC
ATGGATAAAAATTCACCAGAGGCCTGGTGTGCTGCAGGGAACTGTTTTAGTCTGCAACAGGAACACGATATTGCAATTAA
ATTCCTCCAGAGAGCTATCCAAGTGGATCCAAATTATGCTTATGCCTATACTCTATTAGGGCATGAGTTTGTCTTAACTG
AAGAATGGACAAAGCATTAGCTTGTTTTTGAAATACTATCAGAGTCAATCCTAGACATTATAATGTATGG
ORF - retro_ptro_3294 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 85.05 % |
| Parental protein coverage: | 77.43 % |
| Number of stop codons detected: | 3 |
| Number of frameshifts detected: | 4 |
Retrocopy - Parental Gene Alignment:
| Parental | MTVLQEPVQAAIWQALNHYAYRDAVFLAERLYAEVHSEEALFLLATCYYRSGKAYKAYRLLKGHSCTTPQ |
| MTVLQEP.Q.A.WQALNHYAYRD.VF.AE.LYAEVHSEEALFLLATC.Y..GKAY..Y.L.K.HS..T.Q | |
| Retrocopy | MTVLQEPLQPATWQALNHYAYRDGVFPAECLYAEVHSEEALFLLATCSYYPGKAYNTYSLFKVHSFPTLQ |
| Parental | CKYLLAKCCVDLSKLAEGEQILSGGVFNKQKSHDDIVTEFGDSACFTLSLLGHVYCKTDRLAKGSECYQK |
| CKYLLAKCCVDLSKLAEGEQILSGGVF.KQKSHDDIVT.FGDSACF.L.LLGHVYCKTD.L.KGSE.YQK | |
| Retrocopy | CKYLLAKCCVDLSKLAEGEQILSGGVFHKQKSHDDIVTKFGDSACFPLPLLGHVYCKTDQLVKGSEYYQK |
| Parental | SLSLNPFLWSPF-ESLCEIGEKPDPDQTFKFTSLQNFSNCLPNSCTTQVPNHSLSHRQPETVLTETPQDT |
| .LSLNPFLW.P..ESLCEI.EKPDPDQTFKFTSLQNFSNCLPNSCTTQVPNHSL.H.Q.ET.LTETPQDT | |
| Retrocopy | CLSLNPFLWYPL<ESLCEIDEKPDPDQTFKFTSLQNFSNCLPNSCTTQVPNHSLCHKQSETFLTETPQDT |
| Parental | IELNRLNLESSNSKYSLNTDSSVSYIDSAVISPDTVPLGTGTSILS-KQVQNKPKTGRSLLGGPAALSPL |
| .ELNRLNLES.NSKYSLNTDS.VS.IDSAVIS.DTV.LGTGTSILS.KQVQNKPKTGRSLL.GPAALSPL | |
| Retrocopy | TELNRLNLESPNSKYSLNTDSPVSSIDSAVISRDTVQLGTGTSILS<KQVQNKPKTGRSLLRGPAALSPL |
| Parental | TPSFGILPLETPSPGDGSYLQNYTNTPSVIDVPSTGAPSKKSVARIGQTGTKSVFSQSGNSREVTPILAQ |
| TPSFGILPLETPSP.DGSY.QNYT.TP.VIDVPSTGAPSKKSVARIGQTG.KSVFS.SGNSREVTPIL.Q | |
| Retrocopy | TPSFGILPLETPSP*DGSYFQNYTDTPFVIDVPSTGAPSKKSVARIGQTGAKSVFSRSGNSREVTPILSQ |
| Parental | TQSSGPQTSTTPQVLSPTITSPPNALPRRSSRLFTSDSSTTKENSKKLKMKFPPKIPNRKTKSKTNKGGI |
| T.S.GP.TSTTPQVLSPT.TSPPNAL...SS..FTSDSSTTK.N.KKLKMKFP..............GGI | |
| Retrocopy | TGSPGP*TSTTPQVLSPTMTSPPNALHQKSSQVFTSDSSTTKKNRKKLKMKFPXXXXXXXXXXXXXXGGI |
| Parental | TQPNINDSLEITKLDSSIISEGKISTITPQIQAF-NLQKAAAEGLMSLLREMGKGYLALCSYNCKEAINI |
| TQP.INDSLEITKLDSSI.SEGKISTITP.IQ...NLQKAAAEGLM.LL.E.GKGYLALCSY.CKEAINI | |
| Retrocopy | TQPHINDSLEITKLDSSINSEGKISTITPEIQVL<NLQKAAAEGLMRLLPEKGKGYLALCSYHCKEAINI |
| Parental | LSHLPSHHYNTGWVLCQIGRAYFELSEYMQAERIFSEVRRIENYRVEGMEIYSTTLWHLQKDVALSVLSK |
| LSHLPSHHYN.GWVLCQIGR.YFELSEYMQAERIFSEVRRIE.YRV..MEIYSTTLWHLQK.VALSVLSK | |
| Retrocopy | LSHLPSHHYNSGWVLCQIGRVYFELSEYMQAERIFSEVRRIEDYRVKAMEIYSTTLWHLQKHVALSVLSK |
| Parental | DLTDMDKNSPEAWCAAGNCFSLQREHDIAIKFFQRAIQVDPNYAYAYTLLGHEFVLTEE-LDKALACFRN |
| DLTDMDKNSPEAWCAAGNCFSLQ.EHDIAIKF.QRAIQVDPNYAYAYTLLGHEFVLTEE..DKALACF.N | |
| Retrocopy | DLTDMDKNSPEAWCAAGNCFSLQQEHDIAIKFLQRAIQVDPNYAYAYTLLGHEFVLTEE<MDKALACF*N |
| Parental | AIRVNPRHYNAW |
| .IRVNPRHYN.W | |
| Retrocopy | TIRVNPRHYNVW |
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 | 31 .05 RPM |
| SRP007412_cerebellum | 0 .00 RPM | 34 .49 RPM |
| SRP007412_heart | 0 .00 RPM | 34 .54 RPM |
| SRP007412_kidney | 0 .00 RPM | 25 .21 RPM |
| SRP007412_liver | 0 .00 RPM | 17 .94 RPM |
| SRP007412_testis | 0 .00 RPM | 79 .56 RPM |
Pan troglodytes was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ptro_3294 retrocopy.
Pan troglodytes was not studied using FANTOM5 data.
retro_ptro_3294 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_ptro_3294 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 3 parental genes, and 47 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Homo sapiens | ENSG00000004897 | 3 retrocopies | |
| Pongo abelii | ENSPPYG00000008945 | 35 retrocopies |
retro_pabe_2094, retro_pabe_2169, retro_pabe_2170, retro_pabe_2172, retro_pabe_2178, retro_pabe_2182, retro_pabe_2183, retro_pabe_2184, retro_pabe_2185, retro_pabe_2186, retro_pabe_2190, retro_pabe_2192, retro_pabe_3526, retro_pabe_3545, retro_pabe_3547, retro_pabe_3550, retro_pabe_3551, retro_pabe_3553, retro_pabe_3556, retro_pabe_3582, retro_pabe_3583, retro_pabe_3589, retro_pabe_3592, retro_pabe_3598, retro_pabe_3599, retro_pabe_3603, retro_pabe_3605, retro_pabe_3606, retro_pabe_3607, retro_pabe_3609, retro_pabe_3610, retro_pabe_3827, retro_pabe_3828, retro_pabe_3833, retro_pabe_3834,
|
| Pan troglodytes | ENSPTRG00000009326 | 9 retrocopies |
retro_ptro_1644, retro_ptro_2972, retro_ptro_3053, retro_ptro_3071, retro_ptro_3072, retro_ptro_3288, retro_ptro_3294 , retro_ptro_3295, retro_ptro_3304,
|