RetrogeneDB ID: | retro_cpor_99 | ||
Retrocopy location | Organism: | Guinea Pig (Cavia porcellus) | |
| Coordinates: | scaffold_4:23333607..23334777(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSCPOG00000012343 | |
| Aliases: | None | ||
| Status: | KNOWN_PROTEIN_CODING | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | ZNF234 | ||
| Ensembl ID: | ENSCPOG00000004610 | ||
| Aliases: | None | ||
| Description: | zinc finger protein 234 [Source:HGNC Symbol;Acc:13027] |
Retrocopy-Parental alignment summary:
>retro_cpor_99
CCAGGAAAAGAGAAGTATGACAACCAAGAAGGAAATGTTCAGTCTGTTTCCCCTGAGAACACTCACTCTCAGGTGCTGTT
TCCTGGCCAGGCCAGAGGAGAGGTACCCTGGAGTCCTGAGCAGGGCCAGCCTCATGACAGGGCAGAAGGGCACTGGGAAC
CTCCTCCAGAAGATGAAATGGAGCAGTCCTTAACAGGAGCCACGGGTTGCAGAGAACTGGGGCCACCAAAGGAACTGCAG
CCAAAAAAACTTCATTTATGTCCCTTGTGTGGCAAAAATTTCTCTAATAACTCAAACCTAATTAGACATCAGAGAATACA
TGCAGCAGAAAGACTATGTATGGGTGTGGAGTGCAGTGAAATCTTTGGTGGGCATCCACATTTTCTCTCACTACATAAAG
CACACCTGGGAGAGGAGGCCCATAAGTGCCTAGAGTGTGGGAAATGCTTCAGTCAAAATACCCATCTGACTCGCCATCAG
CGAACCCACACAGGTGAGAAGCCTTATCAGTGCAATGTATGTGGAAAAAGCTTCTCTTGCAACTCCAACCTCCATAGGCA
CCAAAGGACACACACTGGAGAAAAACCCTACAAGTGCTCTGAGTGTGGGGAGATCTTTGCTCACAGCTCCAACCTTCTTA
GACACCAGAGGATCCACACAGGAGAGAGACCCTATAAGTGTGCTGAATGTGGGAAAAGTTTCTCTCGGAGTTCTCACCTT
GTCATTCATGAAAGAACTCATGAGAGAGAGAGACTTGACCCCTTCTCTGAGAATGGGGAGGCCATGAGTGATGGTACTCC
CTTTCTTCCAAGTCAGGGAACCCGCAGAGCAGAAAAGAAACTCTTTGAATGTTCAACTTGTGGTAAAAGCTTCCGGCAGG
GCATGCATCTTACTAGACACCAGAGAACGCACACAGGAGAGAAACCGTACAAATGTACCCTTTGTGGAGAAAATTTCTCT
CATAGATCCAACTTAATCCGGCACCAGAGAATTCACACAGGAGAAAAACCCTATACTTGTCATGAGTGCGGAGACAGTTT
CTCTCACAGCTCCAATCGGATTCGTCACCTGAGAACCCATACTGGAGAGAGGCCTTATAAATGTTCTGAATGTGGAGAAA
GCTTCTCTCGAAGTTCACGCCTTATGAGTCACCAGAGAACTCACACAGGT
ORF - retro_cpor_99 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 53.95 % |
| Parental protein coverage: | 66.3 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | CLQCSKAFNHRSYLRRHQRIHTGEKPYVCSECGKAFTHCSTFILHKRAHTGEKPFKCKECGKAFSNRKDL |
| C..C.K.F...S.L.RHQRIH..E......EC...F.....F.....AH.GE...KC.ECGK.FS....L | |
| Retrocopy | CPLCGKNFSNNSNLIRHQRIHAAERLCMGVECSEIFGGHPHFLSLHKAHLGEEAHKCLECGKCFSQNTHL |
| Parental | IRHFSIHTGEKPYECTECGKAFNRRSGLTRHQRIHSGEKPYECAECGKAFCWSTNLIRHAIIHTGEKPYK |
| .RH...HTGEKPY.C..CGK.F...S.L.RHQR.H.GEKPY.C.ECG..F..S.NL.RH..IHTGE.PYK | |
| Retrocopy | TRHQRTHTGEKPYQCNVCGKSFSCNSNLHRHQRTHTGEKPYKCSECGEIFAHSSNLLRHQRIHTGERPYK |
| Parental | CAECGKAFSRSSSLTQHQRMHAGERPYECSQCGKSFSRTSSLIHHRRLHTGERP-YECSKCGKSFKQGSS |
| CAECGK.FSRSS.L..H.R.H..ER....S..G...S..............E....ECS.CGKSF.QG.. | |
| Retrocopy | CAECGKSFSRSSHLVIHERTHERERLDPFSENGEAMSDGTPFLPSQGTRRAEKKLFECSTCGKSFRQGMH |
| Parental | FSSHRKVHTGERPYVCEECGKTFSHSSNLRNHERVHTGERPIKCKECEKSFSCKSNLIKHLRVHTGERPY |
| ...H...HTGE.PY.C..CG..FSH.SNL..H.R.HTGE.P..C.EC..SFS..SN.I.HLR.HTGERPY | |
| Retrocopy | LTRHQRTHTGEKPYKCTLCGENFSHRSNLIRHQRIHTGEKPYTCHECGDSFSHSSNRIRHLRTHTGERPY |
| Parental | ECSECGKSFSQSSSLIQHQRIHTG |
| .CSECG.SFS.SS.L..HQR.HTG | |
| Retrocopy | KCSECGESFSRSSRLMSHQRTHTG |
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 | 6 .21 RPM | 1 .44 RPM |
| SRP017611_kidney | 6 .49 RPM | 0 .84 RPM |
| SRP017611_liver | 3 .05 RPM | 0 .22 RPM |
| SRP040447_lung | 6 .78 RPM | 1 .44 RPM |
| SRP040447_skeletal_muscle | 3 .59 RPM | 0 .90 RPM |
Cavia porcellus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cpor_99 retrocopy.
Cavia porcellus was not studied using FANTOM5 data.
retro_cpor_99 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 | |
|---|---|---|---|
| Anolis carolinensis | ENSACAG00000026260 | 1 retrocopy | |
| Cavia porcellus | ENSCPOG00000004610 | 1 retrocopy |
retro_cpor_99 ,
|
| Monodelphis domestica | ENSMODG00000023632 | 1 retrocopy |