RetrogeneDB ID: | retro_eeur_320 | ||
Retrocopy location | Organism: | Hedgehog (Erinaceus europaeus) | |
| Coordinates: | scaffold_252947:3334..4465(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | ABCG2 | ||
| Ensembl ID: | ENSEEUG00000011333 | ||
| Aliases: | None | ||
| Description: | ATP-binding cassette, sub-family G (WHITE), member 2 [Source:HGNC Symbol;Acc:74] |
Retrocopy-Parental alignment summary:
>retro_eeur_320
ATGTCTTCCAGTAGTGACCAAGTTGTTATCACAATGCCACAAAGCAACGGCCTCCCCACGGTGACTCTCAACAACCTTAA
TACTTTTACTAAGGGGTCTATGCTAAGTTTTCATAACATATGCTACAGGGTGAAAGTGAAGTGCGGCTCTCTCCTTGATG
GAAGCACATGGGAGAAAGAAATACTCAAGAATGTCAATGGGATCATGGGACCTGGCCTCAATGCCATTCTGGGACCCACA
GGTGGAGGCAAATCTTCCTTGTTGGATGTTCTAGCTGCAAGGAAAGATCCACAGGGATTATCTGGGGATGTTTTGATAAA
TGGAAAACCTCGCCCTGCCAATTTCAAATGCATTTCCGGTTATGTGGTACAGGATGACGTGGTGATGGGAACGCTGACCG
TGAGAGAAAACCTACAGTTCTCAGCAGCGCTGCGGCTCCCTGAGACCATGACCATGGGCGAAAAAAATCAAAGGGTCTGC
CAGATCCTTCAAGAGTTGGGTCTGGATAACGTGGCAGATTCCAAAGTTGGGACTCAGTTTACCCGTGGTGTGTCTGGAGG
AGAGAGAAAAAGGACTAGCATTGGGATGGAGCTTATTACTGACCCATCCATCTTGTTCCTTGATGAGCCCACCACTGGCT
TAGATTCAAGCACAGCAAATGCTGTCCTTTTGCTCCTGAAGAGGATGTCGAAGCAAGGGAGGACCATCATCTTCTCTATC
CATCAGCCTCGCTATTCCATCTTCCGGCTGTTTGATAGCCTCACCTTATTGGCCTCTGGAAGACTGGTGTTCCATGGGCC
GGCTCAGGAGGCCTTGGGGTACTTTGAATCTGCTGGTTACCAGTGTGAGGCCTATAATAACCCTGCAGACTTCTTCCTGG
ACGTCATCAATGGAGACTCCTCTGCTGTGATATTAAACAGAGACAATGAAAGTGATGAAACCAGGGGCATCATGGAGCCC
ACCCAAATAGAGACTCTATGCATAGAAAAATTAGCTGAGTTGTATGTCAACTCCACCTTTTTCAGAGAGACGAACATTGT
ATTAAGTCATCTCTCAGTCGTCCTAAGACAGAAAGAGCCCCACTTTCTGAAGAGGATCACCTATGCCACCTCCTTCTGTC
ACCAACTTAAG
ORF - retro_eeur_320 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 74.41 % |
| Parental protein coverage: | 57.71 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | MSCRTEQVFITMSERNVNGLPGATRNNLKTCSEGSVLSFHNICYRVKVKSGFLFCGKTVEKEILSGINGI |
| MS....QV.ITM...N..GLP..T.NNL.T...GS.LSFHNICYRVKVK.G.L..G.T.EKEIL...NGI | |
| Retrocopy | MSSSSDQVVITMPQSN--GLPTVTLNNLNTFTKGSMLSFHNICYRVKVKCGSLLDGSTWEKEILKNVNGI |
| Parental | MRPGLNAILGPTGGGKSSLLDILAARKDPRGLSGDVLINGGPRPANFKCISGYVVQDDVVMGTLTVRENL |
| M.PGLNAILGPTGGGKSSLLD.LAARKDP.GLSGDVLING.PRPANFKCISGYVVQDDVVMGTLTVRENL | |
| Retrocopy | MGPGLNAILGPTGGGKSSLLDVLAARKDPQGLSGDVLINGKPRPANFKCISGYVVQDDVVMGTLTVRENL |
| Parental | QFSAALRLPTMMDSREKNERIDKIIKELGLDKVADSKVGTQFIRGVSGGERKRTSIGMELITDPSILFLD |
| QFSAALRLP..M...EKN.R...I..ELGLD.VADSKVGTQF.RGVSGGERKRTSIGMELITDPSILFLD | |
| Retrocopy | QFSAALRLPETMTMGEKNQRVCQILQELGLDNVADSKVGTQFTRGVSGGERKRTSIGMELITDPSILFLD |
| Parental | EPTTGLDSSTASAVLLLLKRMSRQGRTIIFSIHQPRYSIFKLFDSLTLLASGRLMFHGPAQEALGYFETA |
| EPTTGLDSSTA.AVLLLLKRMS.QGRTIIFSIHQPRYSIF.LFDSLTLLASGRL.FHGPAQEALGYFE.A | |
| Retrocopy | EPTTGLDSSTANAVLLLLKRMSKQGRTIIFSIHQPRYSIFRLFDSLTLLASGRLVFHGPAQEALGYFESA |
| Parental | GYHCEAYNNPADFFLDVINGDSTAVALNQEEEADAAKDLAEAPKRDTSVVKRLAEFYISSSFFRDSQAEL |
| GY.CEAYNNPADFFLDVINGDS.AV.LN...E.D......E.....T.....LAE.Y..S.FFR.....L | |
| Retrocopy | GYQCEAYNNPADFFLDVINGDSSAVILNRDNESDETRGIMEPTQIETLCIEKLAELYVNSTFFRETNIVL |
| Parental | DQLLEVPQKKNTAF-NEVTYATSFFHQLR |
| ..L..V...K...F....TYATSF.HQL. | |
| Retrocopy | SHLSVVLRQKEPHFLKRITYATSFCHQLK |
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 | 18 .21 RPM |
| SRP017611_kidney | 0 .00 RPM | 9 .75 RPM |
| SRP017611_liver | 0 .00 RPM | 109 .01 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_320 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 3 parental genes, and 3 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Erinaceus europaeus | ENSEEUG00000011333 | 1 retrocopy |
retro_eeur_320 ,
|
| Tupaia belangeri | ENSTBEG00000004706 | 1 retrocopy | |
| Tursiops truncatus | ENSTTRG00000015227 | 1 retrocopy |