RetrogeneDB ID: | retro_cpor_1173 | ||
Retrocopy location | Organism: | Guinea Pig (Cavia porcellus) | |
| Coordinates: | scaffold_52:8104575..8105163(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | INSIG1 | ||
| Ensembl ID: | ENSCPOG00000014739 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_cpor_1173
CCATATGTCTCATCTGTCACTAGCCAGAGTGTAAACTTGGTGATTCGAGGAGTAGTCTTGTTTTTTATTGGAGTATTTCT
TGCATTAGTGTTAAATTTGCTCCAGATTCAGAGAAATGTGACCTTATTTCCACCCGATGTAATTGCGAGCATCTTTTCTT
CTGCGTGGTGGGTACCACCATGCTGTGGCACAGCTTCAGCTGTGATTGGATTATTATACCCCTGCATTGACAGGCATCTA
GGAGAACCACATAAATTTAAAAGAGAGTGGTCCAGTGTAATGCGGTGTGTAGCTGTCTTTGTTGGTATAAATCATGCCAG
TGCTAAAGTGGATTTTGATAACATACAGTTGTCTGTCACACTGGCTGCACTCTCCATTGGACTGTGGTGGACTTTTGATA
GATCTAGAAGTGGTTTTGGCCTTGGAGTAGGAATCACTTTCTTGGCAACTGTGGTCACTCAACTGCTAGTTTATTATGGT
GTTTACCAGTATACATCTCTAGGTTTTTTCTATGTTCGCTCCTGGTTACCATGTATATTTTTTGCTGGAGGCATAACAAT
GGGAAACATTGGTTGACAATGGGCAATG
ORF - retro_cpor_1173 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 76.65 % |
| Parental protein coverage: | 77.56 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | PQSPRVSSWHHDLVQRSLVLFSVGVVLALVLNLLQIQRNVTLFPDEVIATIFSSAWWVPPCCGTAAAVVG |
| P....V.S....LV.R..VLF..GV.LALVLNLLQIQRNVTLFP..VIA.IFSSAWWVPPCCGTA.AV.G | |
| Retrocopy | PYVSSVTSQSVNLVIRGVVLFFIGVFLALVLNLLQIQRNVTLFPPDVIASIFSSAWWVPPCCGTASAVIG |
| Parental | LLYPCIDSHLGEPHKFKREWASVMRCIAVFVGINHASAKLDFANNVQLSLTLAALSLGLWWTFDRSRSGL |
| LLYPCID.HLGEPHKFKREW.SVMRC.AVFVGINHASAK.DF..N.QLS.TLAALS.GLWWTFDRSRSG. | |
| Retrocopy | LLYPCIDRHLGEPHKFKREWSSVMRCVAVFVGINHASAKVDF-DNIQLSVTLAALSIGLWWTFDRSRSGF |
| Parental | GLGITIAFLATLITQFLVYNGVYQYTSPDFLYIRSWLPCIFFSGGVTVGNIGRQLAM |
| GLG..I.FLAT..TQ.LVY.GVYQYTS..F.Y.RSWLPCIFF.GG.T.GNIG.Q.AM | |
| Retrocopy | GLGVGITFLATVVTQLLVYYGVYQYTSLGFFYVRSWLPCIFFAGGITMGNIG*QWAM |
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 .88 RPM | 15 .87 RPM |
| SRP017611_kidney | 3 .25 RPM | 26 .28 RPM |
| SRP017611_liver | 16 .84 RPM | 52 .89 RPM |
| SRP040447_lung | 2 .24 RPM | 70 .37 RPM |
| SRP040447_skeletal_muscle | 3 .68 RPM | 3 .74 RPM |
Cavia porcellus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cpor_1173 retrocopy.
Cavia porcellus was not studied using FANTOM5 data.
retro_cpor_1173 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 5 parental genes, and 5 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Choloepus hoffmanni | ENSCHOG00000001982 | 1 retrocopy | |
| Cavia porcellus | ENSCPOG00000014739 | 1 retrocopy |
retro_cpor_1173 ,
|
| Loxodonta africana | ENSLAFG00000028120 | 1 retrocopy | |
| Myotis lucifugus | ENSMLUG00000028113 | 1 retrocopy | |
| Rattus norvegicus | ENSRNOG00000006859 | 1 retrocopy |