RetrogeneDB ID: | retro_eeur_70 | ||
Retrocopy location | Organism: | Hedgehog (Erinaceus europaeus) | |
| Coordinates: | GeneScaffold_4164:19006..19518(+) | ||
| Located in intron of: | ENSEEUG00000003713 | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | MS4A4A | ||
| Ensembl ID: | ENSEEUG00000003258 | ||
| Aliases: | None | ||
| Description: | membrane-spanning 4-domains, subfamily A, member 4A [Source:HGNC Symbol;Acc:13371] |
Retrocopy-Parental alignment summary:
>retro_eeur_70
GTTGTACAAATCATGATTGCCCTGATGAATTTCAGTTTTGGAGTCATAATTATGAGTGTCACAGTAACATATCATGGACA
GTATCCCTTCTCAGTATACACATGCTACACAATCTGGGGGTCAGTGATGTTTATTGTTTCAGGGTCATTATCAGTAGGAG
CAGGGAAAAGAACTACAAAGGGTATGGTCTGAGGTAGCCTAGAGTAAACACTACAAGCTCCATCTTTGCTGCAATAGGGA
TCATATTCATGGCAATCAGCTTGCACATTTATTCATTCCATCCTTACATCTGTTATGGCACTAAGATGCAAGAGGATTGT
GCCATGGTCATATCTATTATAACGGGTCTAGAATTCCTAGTGTTAATTTTAAGCATGCTGGAGTTCTGCATTGCTGTGTC
CCTATCTGCTTTTGGATGCAGAGTCACCTGTTGTAATCCTAGTGGGGTTGTACTCATTATGCCATCCAATTCTCACATGG
CAGAATCATCACCATCTGCACCATTTATGGAC
ORF - retro_eeur_70 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 88.95 % |
| Parental protein coverage: | 84.69 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | VVQIVIALMNFSFGVITMSVTITYHGSIP-SVYTCYTIWGSVMFIVSGSLSIGAGKRTTKGMVRGSLG-V |
| VVQI.IALMNFSFGVI.MSVT.TYHG..P.SVYTCYTIWGSVMFIVSGSLS.GAGKRTTKGMV.GSL..V | |
| Retrocopy | VVQIMIALMNFSFGVIIMSVTVTYHGQYPFSVYTCYTIWGSVMFIVSGSLSVGAGKRTTKGMV*GSLE<V |
| Parental | NITSSIFAAIGIIFMAISLHIYSFHPYICYG----DDCAMVVSIITGLEFLVLILSILEFCIAVSLSAFG |
| N.TSSIFAAIGIIFMAISLHIYSFHPYICYG.....DCAMV.SIITGLEFLVLILS.LEFCIAVSLSAFG | |
| Retrocopy | NTTSSIFAAIGIIFMAISLHIYSFHPYICYGTKMQEDCAMVISIITGLEFLVLILSMLEFCIAVSLSAFG |
| Parental | CRVTCCNPGGVVLIMPSNSHMAESSPSAPFMD |
| CRVTCCNP.GVVLIMPSNSHMAESSPSAPFMD | |
| Retrocopy | CRVTCCNPSGVVLIMPSNSHMAESSPSAPFMD |
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 .48 RPM | 1 .61 RPM |
| SRP017611_kidney | 0 .56 RPM | 1 .50 RPM |
| SRP017611_liver | 1 .77 RPM | 5 .95 RPM |
Erinaceus europaeus was not studied using ChIP-Seq data.
Erinaceus europaeus was not studied using EST data.
Erinaceus europaeus was not studied using FANTOM5 data.
retro_eeur_70 was not experimentally validated.
Retrocopy orthology:
Erinaceus europaeus 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 | |
|---|---|---|---|
| Erinaceus europaeus | ENSEEUG00000003258 | 1 retrocopy |
retro_eeur_70 ,
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