RetrogeneDB ID: | retro_cjac_4189 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | X:73521000..73522542(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | GPR176 | ||
| Ensembl ID: | ENSCJAG00000020926 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_cjac_4189
ATGGGACATAACGGGAGCTGGATCTCTCTAAACGCCAGCGAGCCGAGCAAGGCGTCGGGCGTCGAGACTGCAAGCGCAAA
CCGCGGCGCACTCAGGGAGTTCGTCGAGGCGCAGCTGTACCGCCAGTTCACCACCACCTTGCTGGTCGTCATCTTCATAG
GCTCGTTGCTCGGAAACTTCATGGTGTTATGGTTAACTTGCTGCACAACCGTGTTCAAATCTGTCACCAACGGGTTCATT
AAAAACCTGGCCTGCTCGGGATTTGTGCCAGCCTGGACTGTGTGCCCTTTGACATCATCCTCAGCACCAGTCCTCACTGT
TGCTGGTGGATCTACACCATGCTCTTCTGCAAGGTCGTCAAATTTTTTTCACAAAGTATTCTGCTCTGTGACCATCCTCA
GCTTCACTGCTATTGCTTTGGACAGATACTACTCAGTCTTCTATCCGCTGGAGAGGAAAATATCTGATGCCAAGTTCCAT
GAACTGGTGATGTACATCTGGGCCCATGCAGTGGTGGCCAGTGTTCCTGTGTTTGCAGTGACCAATGTGGCCAATATCTA
TGCCACATCCACCTGCACGGAAGTCTGGAGCAACTCCTTGGGCCACCTGGTGTATGTTCTGGTGTAAAACATCACCACAG
TCATTGTGCCTGTGGCGGTGGTGTTCCTCTTCTTGATACTGATCCGAAGGGCCCTGACTGCCAGCCAGAAAAAGAAGGTC
ATTATAGCAGTGCTCTGGACCCCACAGAACACCATCTCCATCCCCTATGCCTCCCAGAGGGAGGCAGAGCTGCACACCAC
TCTGCTCTCCATGGTGATGGTCTTCATCTTGTGTAGCATGCCCTATGCCAGCCTGGTCATCTACCAGACCATGTTCAATG
TCCATGACATTTCCATCTTCTTGCTGCTCACTGCCATTTGGCTGCACAAAGTCTCCCTGCTGGCAAACCCTGTTCTCTTT
CTTACTGTGAACAAATCTTGCCACAAGTGCTTGATAGGGACCCTGGTGCAACTACACCACCAGTACAGTCGCCATAATGT
GATCAGTACCGGGAGCATCCTGGCTGAGGCTAGCCCGGAACCCAGCATACATTGGGGCAGCCAGCTCCTGGAGATCTTCC
ACATTGGGCAGCAACATATCTTTAAGCCCACAGAGGATAAGGAAGAGAGTGAGGCCAAGTACATTGGCTCAGCTGACTTC
CAGGCCAAGGAGATATTTAGCATCTGCCTGGAGGGAGAGCAGGGGCCACAGTTTGCACCCTCTGCCCCACCCCTGGGCAC
AGTGGACTCTGTATCCCAGGTAGCACCAGCAGCTCCTGTGGAATCTGAAACATTCTCTGATACGTATTGCCTGCAGTTTG
GCTTTGGGCCTTTTGAGTTGCCTCCTCTGTGGCTCTCAGAAACCTGAAACAGAAGAAGCGGCTGCTTCCCCCCTTTGGTA
ACACCCCAGAAGAGCTGATCCAGACAAGATTCCCAAGGTAGGCAGGGTGGAGTGGAAGATGAGTAGAAAGAATAAAGTGA
GCATTTTCCAAAGGTGGATTCC
ORF - retro_cjac_4189 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 87.31 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 2 |
| Number of frameshifts detected: | 5 |
Retrocopy - Parental Gene Alignment:
| Parental | MGHNGSWISQNASEPRNASGAETAGVNRSALGEFGEAQLYRQFTTTVQVVIFIGSLLGNFMVLWSTCRTT |
| MGHNGSWIS.NASEP..ASG.ETA..NR.AL.EF.EAQLYRQFTTT..VVIFIGSLLGNFMVLW.TC.TT | |
| Retrocopy | MGHNGSWISLNASEPSKASGVETASANRGALREFVEAQLYRQFTTTLLVVIFIGSLLGNFMVLWLTCCTT |
| Parental | VFKSVTNRFIKNLACS-GICASLVCVPFDIALSTSPHCCWWIYSMLFCKVVK-FLHKVFCSVTILSFPAI |
| VFKSVTN.FIKNLACS.GICASL.CVPFDI.LSTSPHCCWWIY.MLFCKVVK.F.HKVFCSVTILSF.AI | |
| Retrocopy | VFKSVTNGFIKNLACS<GICASLDCVPFDIILSTSPHCCWWIYTMLFCKVVK>FFHKVFCSVTILSFTAI |
| Parental | ALDRYYSVLYPLERKISDAKSRELVMYIWAHAVVASVPVFAVTNVADIYATSTCTEVWSNSLGHLVYVLV |
| ALDRYYSV.YPLERKISDAK..ELVMYIWAHAVVASVPVFAVTNVA.IYATSTCTEVWSNSLGHLVYVLV | |
| Retrocopy | ALDRYYSVFYPLERKISDAKFHELVMYIWAHAVVASVPVFAVTNVANIYATSTCTEVWSNSLGHLVYVLV |
| Parental | YNITTIIVPVVVVFLFLILIRRALSASQKKKVIIAALRTPQNTISIPYASQREAELHATLLSMVMVFILC |
| .NITT.IVPV.VVFLFLILIRRAL.ASQKKKVIIA.L.TPQNTISIPYASQREAELH.TLLSMVMVFILC | |
| Retrocopy | *NITTVIVPVAVVFLFLILIRRALTASQKKKVIIAVLWTPQNTISIPYASQREAELHTTLLSMVMVFILC |
| Parental | SVPYATLVIYQTVLNVPDTSVFLLLTAIWLPKVSLLANPVLFLTVNKSVRKCLIGTLVQLHHRYSRRNVV |
| S.PYA.LVIYQT..NV.D.S.FLLLTAIWL.KVSLLANPVLFLTVNKS..KCLIGTLVQLHH.YSR.NV. | |
| Retrocopy | SMPYASLVIYQTMFNVHDISIFLLLTAIWLHKVSLLANPVLFLTVNKSCHKCLIGTLVQLHHQYSRHNVI |
| Parental | STGSGLAEASLEPSIRSGSQLLEMFHIGQQQIFKPTEDEEESEAKYIGSADFQAKEIFSTCLEGEQGPQF |
| STGS.LAEAS.EPSI..GSQLLE.FHIGQQ.IFKPTED.EESEAKYIGSADFQAKEIFS.CLEGEQGPQF | |
| Retrocopy | STGSILAEASPEPSIHWGSQLLEIFHIGQQHIFKPTEDKEESEAKYIGSADFQAKEIFSICLEGEQGPQF |
| Parental | APSAPPLGTVDSVSQVAPAAPVESETFSDKYSLQFGFGPFELPPQWLSETRN-SKKRLLPPLGNTPEELI |
| APSAPPLGTVDSVSQVAPAAPVESETFSD.Y.LQFGFGPFELPP.WLSET.N..KKRLLPP.GNTPEELI | |
| Retrocopy | APSAPPLGTVDSVSQVAPAAPVESETFSDTYCLQFGFGPFELPPLWLSET*N<QKKRLLPPFGNTPEELI |
| Parental | QT-KVPKVGRGERKMSRNNKVSI-FPKVDS |
| QT.K.PKVGR.E.KMSR.NKVSI.FPKVDS | |
| Retrocopy | QT<KIPKVGRVEWKMSRKNKVSI<FPKVDS |
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 |
|---|---|---|
| SRP051959_colon | 0 .00 RPM | 1 .60 RPM |
| SRP051959_heart | 0 .00 RPM | 2 .37 RPM |
| SRP051959_kidney | 0 .00 RPM | 0 .64 RPM |
| SRP051959_liver | 0 .00 RPM | 0 .17 RPM |
| SRP051959_lung | 0 .00 RPM | 0 .26 RPM |
| SRP051959_lymph_node | 0 .00 RPM | 2 .10 RPM |
| SRP051959_skeletal_muscle | 0 .00 RPM | 0 .41 RPM |
| SRP051959_spleen | 0 .00 RPM | 5 .97 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_4189 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_4189 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_4189 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 | |
|---|---|---|---|
| Callithrix jacchus | ENSCJAG00000020926 | 1 retrocopy |
retro_cjac_4189 ,
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