RetrogeneDB ID: | retro_cpor_63 | ||
Retrocopy location | Organism: | Guinea Pig (Cavia porcellus) | |
| Coordinates: | scaffold_4:28332592..28333675(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSCPOG00000003132 | |
| Aliases: | None | ||
| Status: | KNOWN_PROTEIN_CODING | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | PCMTD1 | ||
| Ensembl ID: | ENSCPOG00000006593 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_cpor_63
ATGGGCGGTGCTGTGAGTGCTGGTGAGGACAATGACGAACTGATCGATAATTTGAAGGAAGCACAGTATATACGGACAGA
ATTGGTGGAACAGGCCTTCAGAGCTATTGATCGAGCAGATTACTACCTGGAGGAGTTTAAAGAAAATGCCTACAAAGACT
TGGCGTGGAAGCATGGAAACATTCACCTCTCAGCCCCGTGCATCTACTCAGAAGTGATGGAGGCCCTGGATTTGCAGCCA
GGGCTTTCGTTTCTGAACTTGGGCAGTGGTACTGGATACCTCAGCTCCATGGTTGGCCTCATTTTAGGTCCTTTTGGTGT
GAACCATGGAGTGGAGCTTCATTCTGATGTGATAGAGTACGCAAAACAGAAACTGGACTTCTTCATCAGAACAAGTGACA
GCTTTGACAAGTTTGACTTCTGTGAACCCTCTTTTGTTACTGGCAATTGCCTGGAGATTTCTCCAGATTGTTCTCAGTAT
GATCGAGTGTACTGTGGGGCTGGTGTGCAGAAGGAACATGAGGAATACATGAAAAATCTTCTTAAAGTTGGAGGAATCCT
TGTCATGCCTCTGGAAGAGAAGTTGACCAAGATAACGCGCACAGGCCCTTCTGCTTGGGAAACGAAAAAGATTTTGGCTG
TTTCCTTTGCCCCTCTGGTCCAGCCCTGTCACTCAGAGTCAGGAAAGTCCAGACTTGTCCAGCTTCCACCACTTGCTGTA
CGCAGCCTCCAGGACTTGGCCCGCATTGCCATCCGGGGTACCATTAAAAAGATCATTCATCAGGAAGCTTTGAGCAAAAG
TGGAAATGGACTGAAGAACACTCCCAGATTTAAACGAAGGAGGGTCCGCCGCCGTCAAATGGAAACAATAGTCTTTTTGG
ACAAAGAAGTCTTTGCCAGTCGTATTTCCAACCCCTCTGACGACAACAGCTGTGAAGACTTGGAAGAGGAACGGAGGGAA
GAAGATAAAACTTCACTAGAAGCCAAGCCAGATCCTCCCGTGAACTTCCTGCGTCAGAAGGTCCTGAGCCTCCCTCTGCC
AGACCCCCTGAAATACTACTTGCTTTATTACAGAGAAAAATAA
ORF - retro_cpor_63 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 66.39 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | MGGAVSAGEDNDDLIDNLKEAQYIRTERVEQAFRAIDRGDYYLEGYRDNAYKDLAWKHGNIHLSAPCIYS |
| MGGAVSAGEDND.LIDNLKEAQYIRTE.VEQAFRAIDR.DYYLE....NAYKDLAWKHGNIHLSAPCIYS | |
| Retrocopy | MGGAVSAGEDNDELIDNLKEAQYIRTELVEQAFRAIDRADYYLEEFKENAYKDLAWKHGNIHLSAPCIYS |
| Parental | EVMEALKLQPGLSFLNLGSGTGYLSTMVGLILGPFGINHGIELHSDVVEYAKEKLESFIKNSDSFDKFEF |
| EVMEAL.LQPGLSFLNLGSGTGYLS.MVGLILGPFG.NHG.ELHSDV.EYAK.KL..FI..SDSFDKF.F | |
| Retrocopy | EVMEALDLQPGLSFLNLGSGTGYLSSMVGLILGPFGVNHGVELHSDVIEYAKQKLDFFIRTSDSFDKFDF |
| Parental | CEPAFVVGNCLQIASDSHQYDRIYCGAGVQKDHENYMKILLKVGGILVMPIEDQLTQIMRTGQNTWESKN |
| CEP.FV.GNCL.I..D..QYDR.YCGAGVQK.HE.YMK.LLKVGGILVMP.E..LT.I.RTG...WE.K. | |
| Retrocopy | CEPSFVTGNCLEISPDCSQYDRVYCGAGVQKEHEEYMKNLLKVGGILVMPLEEKLTKITRTGPSAWETKK |
| Parental | ILAVSFAPLVQPSKNDNGKPDSVGLPPCAVRNLQDLARIYIRRTLRNFINDEMQAK-GIPQRAPPKRKRK |
| ILAVSFAPLVQP.....GK...V.LPP.AVR.LQDLARI.IR.T....I..E...K.G......P..KR. | |
| Retrocopy | ILAVSFAPLVQPCHSESGKSRLVQLPPLAVRSLQDLARIAIRGTIKKIIHQEALSKSGNGLKNTPRFKRR |
| Parental | RVKQR-INTYVFVGNQLIPQPLDSEEDEKMEEDNKEE-EEKDHSEAMKPEEPPQNLLREKIMKLPLPESL |
| RV..R...T.VF..............D....ED..EE..E.D.........PP.N.LR.K...LPLP..L | |
| Retrocopy | RVRRRQMETIVFLDKEVFASRISNPSDDNSCEDLEEERREEDKTSLEAKPDPPVNFLRQKVLSLPLPDPL |
| Parental | KAYLTYFRDK |
| K.YL.Y.R.K | |
| Retrocopy | KYYLLYYREK |
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 | 5 .35 RPM | 28 .18 RPM |
| SRP017611_kidney | 4 .71 RPM | 103 .85 RPM |
| SRP017611_liver | 2 .70 RPM | 103 .25 RPM |
| SRP040447_lung | 2 .75 RPM | 55 .28 RPM |
| SRP040447_skeletal_muscle | 4 .10 RPM | 30 .34 RPM |
Cavia porcellus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cpor_63 retrocopy.
Cavia porcellus was not studied using FANTOM5 data.
retro_cpor_63 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 3 parental genes, and 4 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Cavia porcellus | ENSCPOG00000006593 | 1 retrocopy |
retro_cpor_63 ,
|
| Monodelphis domestica | ENSMODG00000009645 | 1 retrocopy | |
| Oryctolagus cuniculus | ENSOCUG00000016958 | 2 retrocopies |