RetrogeneDB ID:

retro_eeur_121

Retrocopy
location
Organism:Hedgehog (Erinaceus europaeus)
Coordinates:GeneScaffold_7473:9834..10395(-)
Located in intron of:ENSEEUG00000003624
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:CBX1
Ensembl ID:ENSEEUG00000004874
Aliases:None
Description:chromobox homolog 1 [Source:HGNC Symbol;Acc:1551]


Retrocopy-Parental alignment summary:






>retro_eeur_121
ATGGGAAAGAAAACCAAACAGACAGCTGATAGTTCTTCTTCTGAGGATGAAGAGGAATACGTCGTAGAGAAGGTGCTAGA
CAGACGTGTGGTGAAAGGGCAAGTGGAATATCTACTGAAGTGGAAAGGCTTTTCTGAGGAGCACAATACTTGGGAACCAG
AGAAAAATTTGGATTGTCCTGAACTAATTTCTGAGTTTATGAAAAAATATAAGAAGATGAAGGAGGGTGAAAATAACAAG
CCCAGAGAGAAGTCAGAAACTAACAAGAGGAAATCTAATTTCTCTAATAATGCTGATGATATCAAATCAAAAAAAGAGAG
AGAGCAGAGCAATGATATCGCTCGGGGATTTGAGAGAGGACTGGAACCAGAAAAGATTATTGGGGCGACAGATTCCTGTG
GCGATTTAATGTTCCTAATGAAATGGGAAGACACAGATGAAGCAGACTTGGTTCTGGCAAAAGAAGCTAATGTAAAGTGT
CCACAGATTGTGATAGCATTTTATGAAGAGAGACTGACGTGGCATGCGTATCCAGAGGACGTGGAAAACAAAGAGAAAGA
A

ORF - retro_eeur_121 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 59.57 %
Parental protein coverage: 98.92 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMGKKQNKKKVEEVLEEEEEEYVVEKVLDRRVVKGKVEYLLKWKGFSDEDNTWEPEENLDCPDLIAEFLQS
MGKK..K........E.EEEYVVEKVLDRRVVKG.VEYLLKWKGFS.E.NTWEPE.NLDCP.LI.EF...
RetrocopyMGKK-TKQTADSSSSEDEEEYVVEKVLDRRVVKGQVEYLLKWKGFSEEHNTWEPEKNLDCPELISEFMKK
ParentalQKTAHETDKSEGGKR----KADSDSEDKGEESKPKKKKEES-EKPRGFARGLEPERIIGATDSSGELMFL
.K...E.............K..S.........K.KK..E.S....RGF.RGLEPE.IIGATDS.G.LMFL
RetrocopyYKKMKEGENNKPREKSETNKRKSNFSNNADDIKSKKEREQSNDIARGFERGLEPEKIIGATDSCGDLMFL
ParentalMKWKNSDEADLVPAKEANVKCPQVVISFYEERLTWHSYLSEDDDKKDD
MKW...DEADLV.AKEANVKCPQ.VI.FYEERLTWH.Y......K...
RetrocopyMKWEDTDEADLVLAKEANVKCPQIVIAFYEERLTWHAYPEDVENKEKE

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 20 .14 RPM 21 .75 RPM
SRP017611_kidney 16 .69 RPM 30 .94 RPM
SRP017611_liver 6 .11 RPM 7 .72 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_121 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 17 parental genes, and 51 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000048902 retrocopies
Bos taurus ENSBTAG000000029499 retrocopies
Callithrix jacchus ENSCJAG000000075322 retrocopies
Dipodomys ordii ENSDORG000000007162 retrocopies
Erinaceus europaeus ENSEEUG00000004874 3 retrocopies
retro_eeur_121 , retro_eeur_228, retro_eeur_396,
Echinops telfairi ENSETEG000000002037 retrocopies
Felis catus ENSFCAG000000060561 retrocopy
Myotis lucifugus ENSMLUG000000050302 retrocopies
Mus musculus ENSMUSG000000186661 retrocopy
Oryctolagus cuniculus ENSOCUG000000080213 retrocopies
Otolemur garnettii ENSOGAG000000056589 retrocopies
Ochotona princeps ENSOPRG000000036991 retrocopy
Pongo abelii ENSPPYG000000088911 retrocopy
Rattus norvegicus ENSRNOG000000086892 retrocopies
Sarcophilus harrisii ENSSHAG000000081921 retrocopy
Ictidomys tridecemlineatus ENSSTOG000000239863 retrocopies
Tarsius syrichta ENSTSYG000000047692 retrocopies



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