RetrogeneDB ID: | retro_cpor_227 | ||
Retrocopy location | Organism: | Guinea Pig (Cavia porcellus) | |
| Coordinates: | scaffold_101:4741287..4743057(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | DCP1A | ||
| Ensembl ID: | ENSCPOG00000000073 | ||
| Aliases: | None | ||
| Description: | decapping mRNA 1A [Source:HGNC Symbol;Acc:18714] |
Retrocopy-Parental alignment summary:
>retro_cpor_227
AGGGGCTCAGCTTCGAGATTCAAGATGGAGTCGTTGAGTCGAGCGGGGCAGGAGATGAGTCTGGCGGCTTTGAAGCAACA
CGACCCCTACATCACCAGCATCGCAGACCTCACGGGCCAGGTCGCTCTGTACACCTTCTGCCCCAAGGCCAACCAGTGGG
AGAAGACAGATATAGAAGGGACCTTATTTGTATATCGACGGTCAGCCTCACCCTACCATGGTTTTACCATTGTAAATCGA
CTGAATATGCACAATCTAGTTGAACCAGTGAATAAAGATTTGGAATTTCAACTCCATGAACCATTTCTTCTGTATAGAAA
TGCAAGCTTATCAATATACAGTATCTGGTTTTATGACAAGAACGACTGTCACCGCATAGCAAAACTCATGGCAGATGTGG
TAGAAGAGGAGACACGGTGATCCCAGCAAGCTGCTCGAGATAAACAGAGTCCCAGCCAGGCCAATGGCTGCAGTGACCAT
AGGCCTATTGACATCCTGGAAATGCTGAGTAGAGCCAAGGATGAGTACGAGAGGGCTCAGATGGGCGACTTAAATATCTC
CAGCCCTGGGTTACAGCCAAGCACTCAGCTTTTCAATCTAGGAAGCACTGAAACTCTAGAAGAGACATCCTCTGGATCAC
AAGATAAGTCTGCTCCATCTGGACATAAACATCTGACAGTGGAAGAATTGTTTGGAACTTCTTTGCCAAAAGAACAACCA
GCAGTTATGGGTCTGGATTCAGAAGAAGTAGAGAAGCTCGCAGGAGATGCCACCCAGAAAGAGCCCAGCTCGTTCCTACC
ATTTCCCTTTGAGCATTCTGGAGAAGCCGCTCAGTTGGAAAACCTAAGTGTCCATTCAGCTGCTCACCACACAGTCCAAC
CTGAAGTCTCCACTCCGGTGCTCATCACTCCAGCTTCAATCACACAGTCTAGTGAAAGGCATGCTCCAAGCTACACGAGC
CCATTGAGCCCCGTTCTCAGTCCCACTCTGCCACCTGAAGCTGCTACTACACAGGTTGCCCCTGCATTACCTCGAAATAG
CACTATGATGCCTGCAATGAAAACCACACCTAGGCAGAGGTCTCCACTGTTGAACCAGCCAATCCAGGAGCTAAGCCACA
GCAGTCTAATTGCCAGCCAGAGCCCCTTCAGGGCCCCACTGAGTATGACAAACACAGCTGGCACACCCCTCCCAAGTGTT
GATCTTCTGCAGAAACTCAGGTTGACTTCACAGCATGACCAAATACAGACACAGCCACTTGGGAAAGGTGCTGTAGCACC
CAGCTTTCCTCCAGCAGCTGGCCAGCTGGCCACACCCGAGAGCTTCATAGAGCCTCCCCCGAAGACAGCAGCCGCCAGAA
CAGTGGCCTCTGCCTCCCTGAGCAACATGGTGCTTGCTCCCCTTCAGTCTATGCAGCAAAACCAGGACCCTGAAGTATTT
GCCCAGCCTAAGATGCTATCCAGTGCCATCTCGGTTGCAGGCCCTCCATTGGTTACTGCGACAACCACAGCAGTATCTTC
AGTCCTGCTATCGCCAAGTGTTTTTCAGCAGACTGTTCCAAGGTCTGCCGACCTTGAGAGAAAAGCAAATTCTCCTTCTC
CCCTCACCATTGGCACACCAGAAAATCAGAGAAAGTCTTCCCTTATTCTCAGCAAGTCTCAGCTCCAGGATACATTGATA
CATCTGATTAAGAATGATTCCAGCTTCCTCAGTACACTTCATGAAGTTTACCTGCAGGTTCTGACCAAGAGCAAAGACAA
CCACAACCTA
ORF - retro_cpor_227 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 99.49 % |
| Parental protein coverage: | 98.33 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | RGSASRFKMESLSRAGQEMSLAALKQHDPYITSIADLTGQVALYTFCPKANQWEKTDIEGTLFVYRRSAS |
| RGSASRFKMESLSRAGQEMSLAALKQHDPYITSIADLTGQVALYTFCPKANQWEKTDIEGTLFVYRRSAS | |
| Retrocopy | RGSASRFKMESLSRAGQEMSLAALKQHDPYITSIADLTGQVALYTFCPKANQWEKTDIEGTLFVYRRSAS |
| Parental | PYHGFTIVNRLNMHNLVEPVNKDLEFQLHEPFLLYRNASLSIYSIWFYDKNDCHRIAKLMADVVEEETRR |
| PYHGFTIVNRLNMHNLVEPVNKDLEFQLHEPFLLYRNASLSIYSIWFYDKNDCHRIAKLMADVVEEETR. | |
| Retrocopy | PYHGFTIVNRLNMHNLVEPVNKDLEFQLHEPFLLYRNASLSIYSIWFYDKNDCHRIAKLMADVVEEETR* |
| Parental | SQQAARDKQSPSQANGCSDHRPIDILEMLSRAKDEYERAQMGDSNISSPGLQPSTQLFNLGSTETLEETS |
| SQQAARDKQSPSQANGCSDHRPIDILEMLSRAKDEYERAQMGD.NISSPGLQPSTQLFNLGSTETLEETS | |
| Retrocopy | SQQAARDKQSPSQANGCSDHRPIDILEMLSRAKDEYERAQMGDLNISSPGLQPSTQLFNLGSTETLEETS |
| Parental | SGSQDKSAPSGHKHLTVEELFGTSLPKEQPAVMGLDSEEVEKLAGDATQKEPSSFLPFPFEHSGEAAQLE |
| SGSQDKSAPSGHKHLTVEELFGTSLPKEQPAVMGLDSEEVEKLAGDATQKEPSSFLPFPFEHSGEAAQLE | |
| Retrocopy | SGSQDKSAPSGHKHLTVEELFGTSLPKEQPAVMGLDSEEVEKLAGDATQKEPSSFLPFPFEHSGEAAQLE |
| Parental | NLSVHSAAHHTVQPEVSTPVLITPASITQSSERHAPSYTSPLSPVLSPTLPPEAATTQVAPALPRNSTMM |
| NLSVHSAAHHTVQPEVSTPVLITPASITQSSERHAPSYTSPLSPVLSPTLPPEAATTQVAPALPRNSTMM | |
| Retrocopy | NLSVHSAAHHTVQPEVSTPVLITPASITQSSERHAPSYTSPLSPVLSPTLPPEAATTQVAPALPRNSTMM |
| Parental | PAMKTTPRQRSPLLNQPIQELSHSSLIASQSPFRAPLSMTNTAGTPLPSVDLLQKLRLTSQHDQIQTQPL |
| PAMKTTPRQRSPLLNQPIQELSHSSLIASQSPFRAPLSMTNTAGTPLPSVDLLQKLRLTSQHDQIQTQPL | |
| Retrocopy | PAMKTTPRQRSPLLNQPIQELSHSSLIASQSPFRAPLSMTNTAGTPLPSVDLLQKLRLTSQHDQIQTQPL |
| Parental | GKGAVAPSFPPAAGQLATPESFIEPPPKTAAARTVASASLSNMVLAPLQSMQQNQDPEVFAQPKMLSSAI |
| GKGAVAPSFPPAAGQLATPESFIEPPPKTAAARTVASASLSNMVLAPLQSMQQNQDPEVFAQPKMLSSAI | |
| Retrocopy | GKGAVAPSFPPAAGQLATPESFIEPPPKTAAARTVASASLSNMVLAPLQSMQQNQDPEVFAQPKMLSSAI |
| Parental | SVAGPPLVTATTTAVSSVLLSPSVFQQTVPRSADLERKANSPSPLTIGTPENQRKSSLILSKSQLQDTLI |
| SVAGPPLVTATTTAVSSVLLSPSVFQQTVPRSADLERKANSPSPLTIGTPENQRKSSLILSKSQLQDTLI | |
| Retrocopy | SVAGPPLVTATTTAVSSVLLSPSVFQQTVPRSADLERKANSPSPLTIGTPENQRKSSLILSKSQLQDTLI |
| Parental | HLIKNDSSFLSTLHEVYLQVLTKSKDNYNL |
| HLIKNDSSFLSTLHEVYLQVLTKSKDN.NL | |
| Retrocopy | HLIKNDSSFLSTLHEVYLQVLTKSKDNHNL |
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 | 0 .06 RPM | 3 .91 RPM |
| SRP017611_kidney | 0 .31 RPM | 2 .93 RPM |
| SRP017611_liver | 0 .00 RPM | 2 .09 RPM |
| SRP040447_lung | 0 .03 RPM | 7 .69 RPM |
| SRP040447_skeletal_muscle | 0 .08 RPM | 4 .33 RPM |
Cavia porcellus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cpor_227 retrocopy.
Cavia porcellus was not studied using FANTOM5 data.
retro_cpor_227 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 2 parental genes, and 2 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Choloepus hoffmanni | ENSCHOG00000006436 | 1 retrocopy | |
| Cavia porcellus | ENSCPOG00000000073 | 1 retrocopy |
retro_cpor_227 ,
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