RetrogeneDB ID: | retro_cpor_151 | ||
Retrocopy location | Organism: | Guinea Pig (Cavia porcellus) | |
| Coordinates: | scaffold_0:31888981..31889610(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSCPOG00000025760 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | NAA60 | ||
| Ensembl ID: | ENSCPOG00000005731 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_cpor_151
ATGAAGGACGTGGTGCCTTCTCGTGCCCTCAGCGAGGTCTGCCTGTGCCTTCTCTGCCGTGATGACACAGACACCGTAAA
GCACCTGTGCAGGGACTGGCTCCCCACCGAGTACCCAGACTCATGGTACCGTGATATCACATCCAACAAGAAGTTCGTCT
CTCTGGCTGCCACTGTGTGGTACCAGGGGTACCATTATGGGGATGATGGCAGCTGAAATTAAGAGCAGGACTAAAACACA
TGAAGAGGATGGAGATATCCTAGCCTCCAACTTCTCTGTGGACACACAGAATGTGTACATTCTAAGTCTGGGAGTAGTGA
AGGGATTCAGAAAGTATGGTTCCCTTTCACTTGGAAGTTTAAAGAATCACATATCAACCACTGTCCATGATCACAGCAAA
GCCATCTACCTACACATCCTCACCACCAACAACGTGGCAATAAACTACAAAAACAGAGGCTTTAGGCAGCATCACTCTGC
CTGATTACTACTCCATCCAAGGGGTTCTCAAAGATGGCTTCACTTATGTCCTTTATATCAATACTGGCCACCCTCTCTGG
ACTATCTTAGAATACGTCCAGCATCTGGACTCAGCAGTCACCAACCTGAGCCCCTGCTCCATCTCACAC
ORF - retro_cpor_151 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 75.81 % |
| Parental protein coverage: | 87.19 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 2 |
Retrocopy - Parental Gene Alignment:
| Parental | MTEVVPSSALSEVSLRLLCHDDIDTVKHLCSDWFPIEYPDSWYRDITSNKKFFSLAAT--YRG-AIVGMI |
| M..VVPS.ALSEV.L.LLC.DD.DTVKHLC.DW.P.EYPDSWYRDITSNKKF.SLAAT..Y.G..I.GM. | |
| Retrocopy | MKDVVPSRALSEVCLCLLCRDDTDTVKHLCRDWLPTEYPDSWYRDITSNKKFVSLAATVWYQG>TIMGMM |
| Parental | VAEIKSRTKIHKEDGDILASNFSVDTQVAYILSLGVVKEFRKHGIGSLLLESLKDHISTTAQDHCKAIYL |
| .AEIKSRTK.H.EDGDILASNFSVDTQ..YILSLGVVK.FRK...GSL.L.SLK.HISTT..DH.KAIYL | |
| Retrocopy | AAEIKSRTKTHEEDGDILASNFSVDTQNVYILSLGVVKGFRKY--GSLSLGSLKNHISTTVHDHSKAIYL |
| Parental | HVLTTNNTAINFYENRDFRQHHYL-PYYYSIRGVLKDGFTYVLYINGGHPPWTILDYIQHLGSALANLSP |
| H.LTTNN.AIN.Y.NR.FRQHH....YY.SI.GVLKDGFTYVLYIN.GHP.WTIL.Y.QHL.SA..NLSP | |
| Retrocopy | HILTTNNVAIN-YKNRGFRQHHSA>DYY-SIQGVLKDGFTYVLYINTGHPLWTILEYVQHLDSAVTNLSP |
| Parental | CSIPH |
| CSI.H | |
| Retrocopy | CSISH |
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 | 37 .27 RPM |
| SRP017611_kidney | 0 .00 RPM | 50 .25 RPM |
| SRP017611_liver | 0 .00 RPM | 23 .29 RPM |
| SRP040447_lung | 0 .00 RPM | 33 .59 RPM |
| SRP040447_skeletal_muscle | 0 .00 RPM | 23 .08 RPM |
Cavia porcellus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cpor_151 retrocopy.
Cavia porcellus was not studied using FANTOM5 data.
retro_cpor_151 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 3 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Cavia porcellus | ENSCPOG00000005731 | 1 retrocopy |
retro_cpor_151 ,
|
| Echinops telfairi | ENSETEG00000014209 | 1 retrocopy | |
| Myotis lucifugus | ENSMLUG00000017721 | 1 retrocopy |