RetrogeneDB ID: | retro_cpor_999 | ||
Retrocopy location | Organism: | Guinea Pig (Cavia porcellus) | |
| Coordinates: | scaffold_39:15914111..15914804(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | RCL1 | ||
| Ensembl ID: | ENSCPOG00000015354 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_cpor_999
AACAGGAACAACCTTATCCAGTACTATCAGCCTGGCTTCCTGAATTATGGATCTGTGAAACATGACACTAATGTCCTTTG
CAGCATTAGCTATAATGTGGAGGTTCTCTTTTGCCTGGCTCCATTTATGAAGCACCTATTAGAAATAGTTCTTCAAGGAA
TGACCGCTGACCACATTTATCCTTTGGTTGATGTTCGTAAGGCAACAGCACTCCTTCTATTGAAACAGTTTGGGATTGAT
GGTAAATTGCTCTAACAAAAGTTTATTCAACAAGGAATGCCTCCTGGAAAAGGAGGTGAAGTGGTTTTCTCCTGTCCTAT
CAGGAAGGTCCCGGAAGTCCATTCAGGTCAAGATTCCAGGAAAAATCAAATGTACAGAGGAATGGCATATTTAGTACATA
TGTCACCTTAGATAGCAAACTGGATTGTGGATTCTGCAAGGAGCATCCTCAATCAGCTCGTGCCCAGTCTCTGTACTTAC
ACAGACCACATGAGAGAAGCTGATGCTGCAAGTCTTCAGGCTTTGAGTTATCCCTGGTTTCTTAGACCACAGTGGCACTT
CCTTAGTGCTAACCTGACCTCCAATGCCCAGAGCCAAGGAGCAGCTGTGCTTTCAGAGGAGTTTGGGAGGAACTATGCCC
AGCTGCTGCTTGAAGAGATCCACAGAGGTGCATGTGTAGACTTAGGCAACCAA
ORF - retro_cpor_999 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 62.03 % |
| Parental protein coverage: | 62.2 % |
| Number of stop codons detected: | 3 |
| Number of frameshifts detected: | 5 |
Retrocopy - Parental Gene Alignment:
| Parental | NQTGTTLYYQPGLLYGGPVEHDCSVLRSIGYYLEGLLCLAPFMKHPLKIVLRGVTNDQIDPSVDVLKATA |
| N......YYQPG.L..G.V.HD..VL.SI.Y..E.L.CLAPFMKH.L.IVL.G.T.D.I.P.VDV.KATA | |
| Retrocopy | NRNNLIQYYQPGFLNYGSVKHDTNVLCSISYNVEVLFCLAPFMKHLLEIVLQGMTADHIYPLVDVRKATA |
| Parental | LPLLKQFGIDGESFELKIVRRGMPPGGGGEVFFSCPVRKV-LKPIQLTDPGKIK-RIRGMAYSVRVSPQM |
| L.LLKQFGIDG.....K....GMPPG.GGEV.FSCP.RKV..K.IQ...PGKIK...RGMAY.V..SP.. | |
| Retrocopy | LLLLKQFGIDGKLL*QKFIQQGMPPGKGGEVVFSCPIRKV>RKSIQVKIPGKIK<MYRGMAYLVHMSP*I |
| Parental | ANRIVDSARSILNKFIPDIYIYTDHMKGVNSG-KSPGFGLSLVAETT-NGT-FLSAELASNPQGQGTAVL |
| AN.IVDSARSILN...P....YTDHM.......KS.GF.LSLV..TT..GT.FLSA.L.SN.Q.QG.AVL | |
| Retrocopy | ANWIVDSARSILNQLVPSLCTYTDHMREADAA<KSSGFELSLVS*TT<SGT<FLSANLTSNAQSQGAAVL |
| Parental | PEDLGRNCARLLLEEIHRGGCVDSTNQ |
| .E..GRN.A.LLLEEIHRG.CVD..NQ | |
| Retrocopy | SEEFGRNYAQLLLEEIHRGACVDLGNQ |
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 .00 RPM | 5 .75 RPM |
| SRP017611_kidney | 0 .10 RPM | 13 .61 RPM |
| SRP017611_liver | 0 .04 RPM | 53 .41 RPM |
| SRP040447_lung | 0 .08 RPM | 12 .36 RPM |
| SRP040447_skeletal_muscle | 0 .01 RPM | 9 .22 RPM |
Cavia porcellus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cpor_999 retrocopy.
Cavia porcellus was not studied using FANTOM5 data.
retro_cpor_999 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 | ENSCPOG00000015354 | 1 retrocopy |
retro_cpor_999 ,
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