RetrogeneDB ID: | retro_ptro_2972 | ||
Retrocopy location | Organism: | Chimpanzee (Pan troglodytes) | |
| Coordinates: | GL389469.1:1448..3107(+) | ||
| Located in intron of: | None | ||
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_2972
CTTGCAGAAGGGGAACAAATCTTACCTTTTGGAGTGTTTCATAAGCAGAAAAGCCATGATGATATTGTTACTGAGTTTGG
TGATTCAGCTTGCTTTACTCTTTCATTGCTGGGACATGCATATTGCAAGACAGATCGGCTTGCCAAAGGATCAGAGTATG
ACCAAAACAGCCTTAGTTTAAAGCCTTTCCTCTGGTATCCCTTTGAATCATTATGTGAAATAGATGAAAAGCCAGATCCT
GACCAAACATTTAAATTTGCATCTTTACAGAACTTTAGCAACTGTCTGCCCAACTCTTGCACAACACAAGTACCTAATCA
TAGTTTATGTCACAGACAGCCTGAGACCGTTCTTACGGAAACACCCCAGGACACCACTGAATTAAATAGATTGAATTTAG
AAACTTCCAATTCAAAGTATTCCTTGAATACAGATTCCCCAGTGTCTTCTATTGATTCAGCTGTAATTTCACCTGATACT
GTCCCACTGGGAACAGGAACTTCCATATTATCTAAACAGGTTCAAAATAAACCAAAAACTTGTTGAAGTTTGTCAGGAGG
ACCAGCAGCTCTTAGTCCATTCACCCCAAGCTTTGGGATTTTGCCATTAGAAACCCCAAGTCCTGGAAATGGATCCTATT
TACAAATCTACACTAATACACCTCTGAAATTGATGTGCCATCCACTGGAGCCCCTTCAGAAAAGTCTGTCATCAGAAACA
GCCAAACTGGAGCAAAGTCTGTCTTCTCGCAGAGTGGAAATAGCCGAGAGGTAACTCCAATTATTGCACAAACAGAAAGT
TCTGGTCCATAAATAAGTACAACACCTCAGGTATTGAGCCCCACTATGACATCTCCCCCAAATGCACTCCATTGAAGAAG
TTCATGACTCTTTACTAGTGACAGTTCCACAACCAAGGTGAATAGGAAGAAATTAAAAATGAAGTTTCCACCTAAAATCC
CGAACAGAAAAACAAAAAGTAAAACTAATAAGGGAGGAATAACTCAACCTAACATAAATGATAGCCTGGAAATTACAAAA
TTGGACTCTTTCATGATTTCAGAAGGGAAAAAAGCCACAATCACACCTCAGATTCAGGCATTAATCTAAAAGAAGCAGCA
ACAGAAGGCTTGATGAGCTTTCTTCATGAAAGGGGAAAGGTTATTTAGCTTTGTGTTCATACCACTGCAAAGAAGCTATA
AATATTTTGAGCCATCTACTTTCTCACCACTACAATTCTGGTTGGGTACTGTGCCACATTGGAAGGGTCTATTTTGAACT
TTCAGAGTACATGCAAGCTGAAAGAATATTCTCAGAGGTTAGAAGGATTGAGAATTATAGAGTCGAAGGCATGGAAATCT
ACTCTACAACACTTTGGCATCTTCAAAAAGATGTTGCTCTTTCAGTTCTGTCAAAAGACTTAACAGACATAGATAAAAAT
TTACCAGAGGCCTGGTGTGCTGCAGGGAACTGTTTCAGTCTGCAACAGGAACACGATATTGCAATTAAATTCTTCCAGAG
AGCTATCAAAATGGATCCAAATTATGCTTATGCCTATACTCTATCAGGGCGAGAGTTTGTCTTAACTGAAGAATTGGACA
AAGCATTAGCTTGTTTTTGAAATGCTATCAGAGTCAATCCTAGACATTATAATGCATGG
ORF - retro_ptro_2972 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 88.33 % |
| Parental protein coverage: | 67.23 % |
| Number of stop codons detected: | 5 |
| Number of frameshifts detected: | 3 |
Retrocopy - Parental Gene Alignment:
| Parental | LAEGEQILSGGVFNKQKSHDDIVTEFGDSACFTLSLLGHVYCKTDRLAKGSECYQKSLSLNPFLWSPFES |
| LAEGEQIL..GVF.KQKSHDDIVTEFGDSACFTLSLLGH.YCKTDRLAKGSE..Q.SLSL.PFLW.PFES | |
| Retrocopy | LAEGEQILPFGVFHKQKSHDDIVTEFGDSACFTLSLLGHAYCKTDRLAKGSEYDQNSLSLKPFLWYPFES |
| Parental | LCEIGEKPDPDQTFKFTSLQNFSNCLPNSCTTQVPNHSLSHRQPETVLTETPQDTIELNRLNLESSNSKY |
| LCEI.EKPDPDQTFKF.SLQNFSNCLPNSCTTQVPNHSL.HRQPETVLTETPQDT.ELNRLNLE.SNSKY | |
| Retrocopy | LCEIDEKPDPDQTFKFASLQNFSNCLPNSCTTQVPNHSLCHRQPETVLTETPQDTTELNRLNLETSNSKY |
| Parental | SLNTDSSVSYIDSAVISPDTVPLGTGTSILSKQVQNKPKTGRSLLGGPAALSPLTPSFGILPLETPSPGD |
| SLNTDS.VS.IDSAVISPDTVPLGTGTSILSKQVQNKPKT..SL.GGPAALSP.TPSFGILPLETPSPG. | |
| Retrocopy | SLNTDSPVSSIDSAVISPDTVPLGTGTSILSKQVQNKPKTC*SLSGGPAALSPFTPSFGILPLETPSPGN |
| Parental | GSYLQNYTNTP-SVIDVPSTGAPSKKSVARIGQTGTKSVFSQSGNSREVTPILAQTQSSGPQTSTTPQVL |
| GSYLQ.YTNTP.S.IDVPSTGAPS.KSV.R..QTG.KSVFSQSGNSREVTPI.AQT.SSGP..STTPQVL | |
| Retrocopy | GSYLQIYTNTP<SEIDVPSTGAPSEKSVIRNSQTGAKSVFSQSGNSREVTPIIAQTESSGP*ISTTPQVL |
| Parental | SPTITSPPNALPRRSSRLFTSDSSTTKENSKKLKMKFPPKIPNRKTKSKTNKGGITQPNINDSLEITKLD |
| SPT.TSPPNAL..RSS.LFTSDSSTTK.N.KKLKMKFPPKIPNRKTKSKTNKGGITQPNINDSLEITKLD | |
| Retrocopy | SPTMTSPPNALH*RSS*LFTSDSSTTKVNRKKLKMKFPPKIPNRKTKSKTNKGGITQPNINDSLEITKLD |
| Parental | SSIISEGKISTITPQIQA-FNLQKAAAEGLMSLLRE-MGKGYLALCSYNCKEAINILSHLPSHHYNTGWV |
| S..ISEGK..TITPQIQA..NL..AA.EGLMS.L.E..GKGYLALCSY.CKEAINILSHL.SHHYN.GWV | |
| Retrocopy | SFMISEGKKATITPQIQA<INLKEAATEGLMSFLHE<KGKGYLALCSYHCKEAINILSHLLSHHYNSGWV |
| Parental | LCQIGRAYFELSEYMQAERIFSEVRRIENYRVEGMEIYSTTLWHLQKDVALSVLSKDLTDMDKNSPEAWC |
| LC.IGR.YFELSEYMQAERIFSEVRRIENYRVEGMEIYSTTLWHLQKDVALSVLSKDLTD.DKN.PEAWC | |
| Retrocopy | LCHIGRVYFELSEYMQAERIFSEVRRIENYRVEGMEIYSTTLWHLQKDVALSVLSKDLTDIDKNLPEAWC |
| Parental | AAGNCFSLQREHDIAIKFFQRAIQVDPNYAYAYTLLGHEFVLTEELDKALACFRNAIRVNPRHYNAW |
| AAGNCFSLQ.EHDIAIKFFQRAI..DPNYAYAYTL.G.EFVLTEELDKALACF.NAIRVNPRHYNAW | |
| Retrocopy | AAGNCFSLQQEHDIAIKFFQRAIKMDPNYAYAYTLSGREFVLTEELDKALACF*NAIRVNPRHYNAW |
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 .02 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_2972 retrocopy.
Pan troglodytes was not studied using FANTOM5 data.
retro_ptro_2972 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_ptro_2972 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,
|