RetrogeneDB ID:

retro_eeur_242

Retrocopy
location
Organism:Hedgehog (Erinaceus europaeus)
Coordinates:scaffold_22122:306..948(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:NACA
Ensembl ID:ENSEEUG00000010458
Aliases:None
Description:nascent polypeptide-associated complex alpha subunit [Source:HGNC Symbol;Acc:7629]


Retrocopy-Parental alignment summary:






>retro_eeur_242
ATGCCCAGTGAAGCCACAGAATCCGTCCCAGCTACAAAGCAGGAGTTGCCACAGCCACAGGCTGAGACAGGGTCTGGAAC
AGAATCTGATAGCGATGAGTCAGTACCAGAGCTTGAGGAACAGGATTCCACACAAGCAACCACACAAGCTCAGCTGGCAG
CAGCAGCTGAAATCGATGAAGAACCAGTCAGTAAAGCAAAACAGAGCCGGAGTGAAAAGAAGGCACGAAAGGCTATGTCC
AAAATGGGTCTTCAGCAGGTTACAGGGGTTATTAGAGTCACTACCCGAAAATCAAAGAATATCCTCTTTGTCATCACAAA
GCCAGACGTCTACAAATGCCCGGCATCAGATACCTACATAGTTTTTGGAGAAGCAAAGATTGAAGATTTGTCTCAGCAAG
CACAGCTAGCAGCTGATGAGAAATTCAAAGTTCAGGGTGAGGCGGTCTCAAACATCCAAGAAAACACGCAAACTCCAACT
GTACAAGAGGAGAGTAAAGAGGAAGAGGTTGACGAAACTGGTGTAGAAGTTAAAGACATAGAATTAGTCATGTCACAAGC
AAATGTCTCAAGAGCAAAGGCAGTTTGAGCCCTGAAGAACAACAGTAATGATATTGTAAACGCTATTATGGAACTAACAA
TG

ORF - retro_eeur_242 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 94.42 %
Parental protein coverage: 100. %
Number of stop codons detected: 1
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMPGEATETVPATEQELPQPQAETGSGTESDSDESVPELEEQDSTQATTQQAQLAAAAEIDEEPVSKAKQS
MP.EATE.VPAT.QELPQPQAETGSGTESDSDESVPELEEQDSTQATT.QAQLAAAAEIDEEPVSKAKQS
RetrocopyMPSEATESVPATKQELPQPQAETGSGTESDSDESVPELEEQDSTQATT-QAQLAAAAEIDEEPVSKAKQS
ParentalRSEKKARKAMSKLGLRQVTGVTRVTIRKSKNILFVITKPDVYKSPASDTYIVFGEAKIEDLSQQAQLAAA
RSEKKARKAMSK.GL.QVTGV.RVT.RKSKNILFVITKPDVYK.PASDTYIVFGEAKIEDLSQQAQLAA.
RetrocopyRSEKKARKAMSKMGLQQVTGVIRVTTRKSKNILFVITKPDVYKCPASDTYIVFGEAKIEDLSQQAQLAAD
ParentalEKFKVQGEAVSNIQENTQTPTVQEESEEEEVDETGVEVKDIELVMSQANVSRAKAVRALKNNSNDIVNAI
EKFKVQGEAVSNIQENTQTPTVQEES.EEEVDETGVEVKDIELVMSQANVSRAKAV.ALKNNSNDIVNAI
RetrocopyEKFKVQGEAVSNIQENTQTPTVQEESKEEEVDETGVEVKDIELVMSQANVSRAKAV*ALKNNSNDIVNAI
ParentalMELTM
MELTM
RetrocopyMELTM

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 7 .90 RPM 136 .49 RPM
SRP017611_kidney 14 .63 RPM 303 .06 RPM
SRP017611_liver 12 .06 RPM 208 .04 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_242 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 12 parental genes, and 65 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000041753 retrocopies
Bos taurus ENSBTAG000000107012 retrocopies
Canis familiaris ENSCAFG000000001418 retrocopies
Callithrix jacchus ENSCJAG000000107018 retrocopies
Erinaceus europaeus ENSEEUG00000010458 5 retrocopies
Loxodonta africana ENSLAFG000000045986 retrocopies
Myotis lucifugus ENSMLUG0000000116916 retrocopies
Nomascus leucogenys ENSNLEG000000174497 retrocopies
Pongo abelii ENSPPYG000000046706 retrocopies
Sarcophilus harrisii ENSSHAG000000021751 retrocopy
Ictidomys tridecemlineatus ENSSTOG000000090281 retrocopy
Vicugna pacos ENSVPAG000000040282 retrocopies



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