RetrogeneDB ID: | retro_eeur_450 | ||
Retrocopy location | Organism: | Hedgehog (Erinaceus europaeus) | |
| Coordinates: | scaffold_308367:2532..3345(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | NOB1 | ||
| Ensembl ID: | ENSEEUG00000014384 | ||
| Aliases: | None | ||
| Description: | NIN1/RPN12 binding protein 1 homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:29540] |
Retrocopy-Parental alignment summary:
>retro_eeur_450
GGAAGAACATCTACACCATCCTCGATGTGGGGGGCGAGATCCGGGACAAGGCCACGCACAGGCGCCTCGCGGTCCTGCCC
TATGAGCTGCGCTTTCTGGCAGCCTGGCGCGGAGGCCGTGCGGCGCGTGGCTGAGTTTTCAAAGAAAACTGGAGACTAAC
CCCAGCCTCTCTGCTACCGATATTCAAGTTCTGGCCCTCACCTACCAAATGGAAGCAGAATTTGTTGGTATTTCTCACCT
AAAATAAGAACCAGAGAAGGTTAAAGTGAAGCTCGTTGATTCAGCATCCAGAAACTCCTCTACATATTTCTGGCTTCCAC
TTGCCCTCAAAGCCACAACACTCACAAGAACCCATAGAAAATGGGTACCCCACCAGTGAACCTGAGGATCTGGAATACAA
TTCCTTCACGTTCTGGAGAAACCCTCTGCCTAATATTGATCATGAGTTGCAAGAGCTGCTGGTTGACAAAGGTGAAGATG
TTCCAAGTGAAGAGGGGAAGAGAATGAAGAAAAAGACAGTGAAGATAGTGACAGTGATGGGGGTGGATGGAGAACCCCCA
GCAACATCAAGCAGGTCCAGCAGGAGCTGGGGCAGTGCACCATCCCAAAGGACATGCAGGTGCGCTGTGTGACCACGCAC
TTTGCCACGCAGAATGTTCGGCTCCAGATGGGGCTGCACGTGCTGGCTGTGAAAGGCAGGCTGATCCTGAGGCACCGAGT
TACAAGTTGCGCTGCCACAGCTGTTTCAAGACAACATCCGACAGGAGCCGCGTGTTCTGTTCACATTGCGGAAACAAGAC
TGAAGAAAGAGTC
ORF - retro_eeur_450 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 75.64 % |
| Parental protein coverage: | 63.79 % |
| Number of stop codons detected: | 2 |
| Number of frameshifts detected: | 4 |
Retrocopy - Parental Gene Alignment:
| Parental | GRISTPSAMWWARSGTRPRAGASRSCPTSCA-SGSPAPRPCGAVXXFQRKLET-TPASLLQIFKFWPLPT |
| GR.STPS.MW.ARSGTRPR.GASRSCP.SCA.SGS.A.RPCGA...FQRKLET.TPASLL.IFKFWP.PT | |
| Retrocopy | GRTSTPSSMWGARSGTRPRTGASRSCPMSCA>SGSLARRPCGAWLSFQRKLET>TPASLLPIFKFWPSPT |
| Parental | NWKQNLGVSHL-KQEPEKVKVSSSIQHPETPLHISGFHLPSKPQHWQEPVENGHPTSEPEDLEYNSFMFW |
| .WKQNL.V...........K.SS.IQHPETPLHISGFHLPSKPQH.QEP.ENG.PTSEPEDLEYNSF.FW | |
| Retrocopy | KWKQNLLVFLT*NKNQRRLK*SSLIQHPETPLHISGFHLPSKPQHSQEPIENGYPTSEPEDLEYNSFTFW |
| Parental | RNPLPNIDHELQELLVDKGEDVPSEQ-EENEE-RDSEDSDNYGGG--TPS-IQQGQQELEQCTIPKDIRV |
| RNPLPNIDHELQELLVDKGEDVPSE...E..E..DSEDSD..GGG..TPS.I.Q.QQEL.QCTIPKD..V | |
| Retrocopy | RNPLPNIDHELQELLVDKGEDVPSEE<GEENEEKDSEDSDSDGGGWRTPSNIKQVQQELGQCTIPKDMQV |
| Parental | GCVTTDFGMQNVLLQMGLHVLAVNGMLI-REARSYILRCHGCFKTTSDMNRVFCSHCGNKTLKKV |
| .CVTT.F..QNV.LQMGLHVLAV.G.LI..EA.SY.LRCH.CFKTTSD..RVFCSHCGNKT...V | |
| Retrocopy | RCVTTHFATQNVRLQMGLHVLAVKGRLI<PEAPSYKLRCHSCFKTTSDRSRVFCSHCGNKTEERV |
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 | 1 .61 RPM | 54 .95 RPM |
| SRP017611_kidney | 1 .50 RPM | 56 .26 RPM |
| SRP017611_liver | 0 .48 RPM | 26 .37 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_450 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 4 parental genes, and 4 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Erinaceus europaeus | ENSEEUG00000014384 | 1 retrocopy |
retro_eeur_450 ,
|
| Homo sapiens | ENSG00000141101 | 1 retrocopy | |
| Gorilla gorilla | ENSGGOG00000025456 | 1 retrocopy | |
| Pan troglodytes | ENSPTRG00000008285 | 1 retrocopy |