RetrogeneDB ID: | retro_cpor_1153 | ||
Retrocopy location | Organism: | Guinea Pig (Cavia porcellus) | |
| Coordinates: | scaffold_50:702907..704319(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSCPOG00000026543 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | MAP4 | ||
| Ensembl ID: | ENSCPOG00000022345 | ||
| Aliases: | None | ||
| Description: | Microtubule-associated protein [Source:UniProtKB/TrEMBL;Acc:H0VUD6] |
Retrocopy-Parental alignment summary:
>retro_cpor_1153
TCCGGAAATGACATCTCTACCCCACCCAATAAGGAACTCCCACCCAGCCGAGAGACGAGAACCAAGCCTTTGGCCACCAC
TCAACCTGCAAAGACTTCAGCATTGAAAGCCAAAACACAGCTCACTCTTGTCCCTAAGCAGCCAGCTCCTACCACCTCTG
GTGGGGTGAATAAAAAACCCATGAGTCTTGCTTCAGGCTTAGTACCAGCTGCCCCACCCAAACGCCCTGCTGCTGCCACT
GCCAGGACTTCCACCTTTCCTTCAAGAGACCCCAAGCCAAAGCACATTACAGAGGCGAAGGTTCCTGAGAAGCAGGCCCT
ACCATCCAAGCCCGCCTCAGCCCTGGCTTTCCGCTCGGGGCCCAAGAGCATCTCAGCTGCTCTGAAGGTTGCACCAGCTG
CTGCCCCTGCTTCCACAGGGCCAAGCAGTAGAAGTCCTCCAGTGTCAGCATCCAAAAGGCCTGCTGCTCTTAAGATGGAG
GGCAGATCCGCAGACACTAAGAAGATGACGGTGAAGTCCGCACCAGCTGACTTGAGTCGCACCAAGGGTACCCCTACCAG
CTCTGGGAGGAAAGCCACCACTCCTACAGGGGCAGCTCCTCTGGCCACAGCGGCCCCCACTCGGGTCAAGCCTACCCCAC
TTTCCCGGCCCTCTGTGTCTCCTTCCGTGGACAAGAAACCCACTGTGGCCAAGCCCAGCTCTTCTGTCCCCAAGCTGAGC
CACCCAGCCACTGCAGTCCCTGCCCCCGATCTGAAGAACATCCGCTCCAAAGTTGGCTCCACAGAGAATATCAAGCACCA
GCCCGGAGGGGGCCAGGACAAAATAGAGAAAAAAACAGAGGCGTCACCACAGCTCGAAAGCCTGAACCTAATGTAGTCAC
TAAAACAGCTGGTCCTGTTGCGAGCACACAGAAATCGCCTGTTGGGAAAGTCCAGATAGTCTCTAAAAAAGTGAGCTACA
GCCATATTCAGTCCAAGTGTGGTTCCAAGGACAATACTAAGCATGTCCCTGGAGGTGGGAATGTCCAGATCCAGAGCCAG
AAGGTGGACATCTCCAAGGTCTCCTCCAAGTGTGGTTCCAAGGCAAACATCAAGCACAAGCCCGGTGAAGGAGATGTCAA
GATTGAGAGCCAGAAGATGAACTTGAGGGAGAAGGCCCAGGCCAAGGTGGGATCCCGGATAAGGTGGGTCACCTGCCTGC
AGGAGGCACCGTGAAGACTGAGGGATGTGGCAGCAAGGCCCCTCCGTGTCCAGGGCCCCCCAATGGGGAGGAGCTCTGAG
GCTGCGCCTGATGCGAGCCCCCCCCCCCCCCCCCCCGCTCCAGGTGGGGGGCTCAATGGCCTCATCACCCAGTCTGGGGG
GGGGGACCAAAGGGAGGGCCAAACCTTGGACAGCCAGATCCAGGAGAAAAGC
ORF - retro_cpor_1153 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 86.71 % |
| Parental protein coverage: | 95.92 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 3 |
Retrocopy - Parental Gene Alignment:
| Parental | TGNDISTPPNKELPPSPEKRTKPLATTQPAKTSASKAKTQLTPVPKQPAPTTSGGSNKKPMSLASGLVPA |
| .GNDISTPPNKELPPS.E.RTKPLATTQPAKTSA.KAKTQLT.VPKQPAPTTSGG.NKKPMSLASGLVPA | |
| Retrocopy | SGNDISTPPNKELPPSRETRTKPLATTQPAKTSALKAKTQLTLVPKQPAPTTSGGVNKKPMSLASGLVPA |
| Parental | APPKRPAAATARTSTFPSRDTNIQHITEAKVPEKQALPSKHASALAFRSGPKSISTAPKVASAAAPASTG |
| APPKRPAAATARTSTFPSRD....HITEAKVPEKQALPSK.ASALAFRSGPKSIS.A.KVA.AAAPASTG | |
| Retrocopy | APPKRPAAATARTSTFPSRDPKPKHITEAKVPEKQALPSKPASALAFRSGPKSISAALKVAPAAAPASTG |
| Parental | PSSRSPPVSAPKRPAALKTEGRPADTKKMTVKSAPADLSRTKGTPTSSGRKATTPTGAAPLATVAPTRVK |
| PSSRSPPVSA.KRPAALK.EGR.ADTKKMTVKSAPADLSRTKGTPTSSGRKATTPTGAAPLAT.APTRVK | |
| Retrocopy | PSSRSPPVSASKRPAALKMEGRSADTKKMTVKSAPADLSRTKGTPTSSGRKATTPTGAAPLATAAPTRVK |
| Parental | PTPLSRPSVSPSVDKKPTAAKPSSSVPKLSRPATAAPAPDLKNIRSKVGSTENIKHQPGGGRAKIEKKTE |
| PTPLSRPSVSPSVDKKPT.AKPSSSVPKLS.PATA.PAPDLKNIRSKVGSTENIKHQPGGG..KIEKKTE | |
| Retrocopy | PTPLSRPSVSPSVDKKPTVAKPSSSVPKLSHPATAVPAPDLKNIRSKVGSTENIKHQPGGGQDKIEKKTE |
| Parental | AAP-TARKPEPNAVTKTAGPIASTQKSPAGKVQIVSKKVSYSHIQSKCGSKDNIKHVPGGGNVQIQSQKV |
| A.P.TARKPEPN.VTKTAGP.ASTQKSP.GKVQIVSKKVSYSHIQSKCGSKDN.KHVPGGGNVQIQSQKV | |
| Retrocopy | ASP<TARKPEPNVVTKTAGPVASTQKSPVGKVQIVSKKVSYSHIQSKCGSKDNTKHVPGGGNVQIQSQKV |
| Parental | DISKVSSKCGSKANIKHKPGGGDVKIESQKLNFKEKAQAKVGSL-DNVGHLPAGGTVKTEGGGSEAPPCP |
| DISKVSSKCGSKANIKHKPG.GDVKIESQK.N..EKAQAKVGS..D.VGHLPAGGTVKTEG.GS.APPCP | |
| Retrocopy | DISKVSSKCGSKANIKHKPGEGDVKIESQKMNLREKAQAKVGSR<DKVGHLPAGGTVKTEGCGSKAPPCP |
| Parental | GP-PIGEEP-AASEAAPDAGAPAPAGGLSGLITLSGGGDQREAQTLDSQIQETS |
| GP.P.G....AA..A........P.GGL.GLIT.S....QRE.QTLDSQIQE.S | |
| Retrocopy | GP>PMGRSSEAAPDAXXXXXXXXPGGGLNGLITQSXXXXQREGQTLDSQIQEKS |
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 |
|---|---|---|
| SRP017611_brain | 2 .01 RPM | 96 .28 RPM |
| SRP017611_kidney | 1 .88 RPM | 67 .00 RPM |
| SRP017611_liver | 1 .00 RPM | 30 .51 RPM |
| SRP040447_lung | 1 .03 RPM | 123 .13 RPM |
| SRP040447_skeletal_muscle | 1 .43 RPM | 143 .07 RPM |
Cavia porcellus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cpor_1153 retrocopy.
Cavia porcellus was not studied using FANTOM5 data.
retro_cpor_1153 was not experimentally validated.
Retrocopy orthology:
Cavia porcellus does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.Parental genes homology:
Parental genes homology involve 1 parental gene, and 1 retrocopy.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Cavia porcellus | ENSCPOG00000022345 | 1 retrocopy |
retro_cpor_1153 ,
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