RetrogeneDB ID:

retro_eeur_580

Retrocopy
location
Organism:Hedgehog (Erinaceus europaeus)
Coordinates:scaffold_348087:66612..67782(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:PDHA1
Ensembl ID:ENSEEUG00000005485
Aliases:None
Description:pyruvate dehydrogenase (lipoamide) alpha 1 [Source:HGNC Symbol;Acc:8806]


Retrocopy-Parental alignment summary:






>retro_eeur_580
ATGAGGAAGATGCTCAATGCGGTTTCGCGTGTGTTGTCGGGCGCCGCCCAGAAGCCGGCAAGCAGAGTGCTGGTTGCCTC
TCGTAATTTTGCGAATGATACTACATTGGAAATTAAGAAATGTGGTCTTCATCTGCTTGAAGAAGGTCCTCCTGTCACGA
CAGTGCTCACCAGGGAAGATGGGCTCAAGTACTACCGCATGATGCAGACTGTGCGCCGAATGGAGCTTAAGGCAGATCAG
CTCTACAAACAGAAGATTATCCGTGGCTTCTGTCACCTGTGTGATGGTCAGGAAGCTTGTTGTGTGGGTTTGGAGGCCGG
AATAAACCCCACAGACCATCTCATCACGTCCTACCGTGCTCATGGCTTTTGTTATACTCGCGGGCTATCTGTCCGAGAAA
TTCTTGCTGAACTTACAGGACGAAGAGGAGGTTGTGCTAAAGGAAAAGGAGGGTCGATGCATATGTATGCCAAAAACTTC
TATGGGGGCAATGGCATTGTGGGAGCACAGGTGCCTTTGGGAGCTGGGGTTGCTCTGGCCTGTAAGTATAATGGAAAAGA
TGAAGTGTGTTTAACTATATATGGCGATGGTGCTGCTAATCAGGGCCAGATATTTGAAACTTACAATATGGCAGCTTTGT
GGAAACTGCCTTGTATTTTCATCTGTGAGAATAACCGCTATGGAATGGGAACGTCTGTTGAGAGAGCAGCAGCCAGCACT
GATTACTACAAGAGAGGCAGCTTCATCCCTGGGCTGAGGGTAGATGGAATGGATGTCTTGTGTGTTCGGGAGGCAGCAAA
GTTTGCAGCGGCCTATTGTAGATCTGGAAAGGGGCCCATAGTAATGGAACTGCAGACTTACCGTTACCATGGGACACAGC
ATGAGTGATCCTGGAGTCAGCTACCGTTCAAGAGAAGAAATTCAGGAAGTAAGAGTAAGAGTGATCCTATTATGCTTCTC
AAGAGTAGAATGGTGAACAACAACCTTGCCAGTGTTGAAGAACTGAAGGAAATTGATGTTGAAGTAAAAAAAGAAATTGA
GGATGCTGCCCAGTTTGCCACTGCTGATCCTGAACCACCCCTGGAAGAGCTCGGCTACCACATCTATAGCAGTGAACCAC
CTTTTGAAGTCCGTGGTACCAATCAATGGATAAAGTTCAAGTCTATCAGT

ORF - retro_eeur_580 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 93.37 %
Parental protein coverage: 100. %
Number of stop codons detected: 0
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalMRKMLAAISRVLSGAAQKPASRVLVASRNFANDATFEIKKCDLHRLEEGPPVTTVLTREDGLKYYRMMQT
MRKML.A.SRVLSGAAQKPASRVLVASRNFAND.T.EIKKC.LH.LEEGPPVTTVLTREDGLKYYRMMQT
RetrocopyMRKMLNAVSRVLSGAAQKPASRVLVASRNFANDTTLEIKKCGLHLLEEGPPVTTVLTREDGLKYYRMMQT
ParentalVRRMELKADQLYKQKIIRGFCHLCDGQEACCVGLEAGINPTDHLITSYRAHGFTFTRGMPVREILAELTG
VRRMELKADQLYKQKIIRGFCHLCDGQEACCVGLEAGINPTDHLITSYRAHGF..TRG..VREILAELTG
RetrocopyVRRMELKADQLYKQKIIRGFCHLCDGQEACCVGLEAGINPTDHLITSYRAHGFCYTRGLSVREILAELTG
ParentalRKGGCAKGKGGSMHMYAKNFYGGNGIVGAQVPLGAGVALACKYNGKDEVCLTLYGDGAANQGQIFEAYNM
R.GGCAKGKGGSMHMYAKNFYGGNGIVGAQVPLGAGVALACKYNGKDEVCLT.YGDGAANQGQIFE.YNM
RetrocopyRRGGCAKGKGGSMHMYAKNFYGGNGIVGAQVPLGAGVALACKYNGKDEVCLTIYGDGAANQGQIFETYNM
ParentalAALWKLPCIFICENNRYGMGTSVERAAASTDYYKRGDFIPGLRVDGMDILCVREATKFAADHCRSGKGPI
AALWKLPCIFICENNRYGMGTSVERAAASTDYYKRG.FIPGLRVDGMD.LCVREA.KFAA..CRSGKGPI
RetrocopyAALWKLPCIFICENNRYGMGTSVERAAASTDYYKRGSFIPGLRVDGMDVLCVREAAKFAAAYCRSGKGPI
ParentalLMELQTYRYH-GHSMSDPGVSYRTREEIQEVR-SKSDPIMLLKDRMVNNNLASVEELKEIDVEVRKEIED
.MELQTYRYH.GHSMSDPGVSYR.REEIQEVR.SKSDPIMLLK.RMVNNNLASVEELKEIDVEV.KEIED
RetrocopyVMELQTYRYH>GHSMSDPGVSYRSREEIQEVR<SKSDPIMLLKSRMVNNNLASVEELKEIDVEVKKEIED
ParentalAAQFATADPEPPLEELGYHIYSSDPPFEVRGANQWIKFKSIS
AAQFATADPEPPLEELGYHIYSS.PPFEVRG.NQWIKFKSIS
RetrocopyAAQFATADPEPPLEELGYHIYSSEPPFEVRGTNQWIKFKSIS

Legend:
*Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide






RNA-Seq - click to see more details

(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 .29 RPM 147 .93 RPM
SRP017611_kidney 1 .69 RPM 250 .36 RPM
SRP017611_liver 0 .32 RPM 60 .45 RPM

ChIP-Seq - click to see more details

Erinaceus europaeus was not studied using ChIP-Seq data.

EST - click to see more details

Erinaceus europaeus was not studied using EST data.

TSS - click to see more details

Erinaceus europaeus was not studied using FANTOM5 data.

Lab - click to see more details

retro_eeur_580 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 22 parental genes, and 27 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000167301 retrocopy
retro_amel_400,
Bos taurus ENSBTAG000000198522 retrocopies
retro_btau_100, retro_btau_1807,
Callithrix jacchus ENSCJAG000000054962 retrocopies
retro_cjac_2414, retro_cjac_27,
Dipodomys ordii ENSDORG000000118481 retrocopy
retro_dord_35,
Equus caballus ENSECAG000000019641 retrocopy
retro_ecab_21,
Erinaceus europaeus ENSEEUG00000005485 1 retrocopy
retro_eeur_580 ,
Homo sapiens ENSG000001318281 retrocopy
retro_hsap_41,
Gorilla gorilla ENSGGOG000000135741 retrocopy
retro_ggor_59,
Myotis lucifugus ENSMLUG000000129322 retrocopies
retro_mluc_2363, retro_mluc_323,
Macaca mulatta ENSMMUG000000173361 retrocopy
retro_mmul_123,
Mustela putorius furoENSMPUG000000032691 retrocopy
retro_mputfur_812,
Mus musculus ENSMUSG000000312992 retrocopies
retro_mmus_63, retro_mmus_631,
Nomascus leucogenys ENSNLEG000000098051 retrocopy
retro_nleu_74,
Oryctolagus cuniculus ENSOCUG000000147481 retrocopy
retro_ocun_264,
Pongo abelii ENSPPYG000000201711 retrocopy
retro_pabe_129,
Pan troglodytes ENSPTRG000000217171 retrocopy
retro_ptro_79,
Pteropus vampyrus ENSPVAG000000054201 retrocopy
retro_pvam_1306,
Sarcophilus harrisii ENSSHAG000000153751 retrocopy
retro_shar_84,
Sus scrofa ENSSSCG000000236432 retrocopies
retro_sscr_1015, retro_sscr_281,
Ictidomys tridecemlineatus ENSSTOG000000154331 retrocopy
retro_itri_1529,
Tupaia belangeri ENSTBEG000000143131 retrocopy
retro_tbel_3327,
Tursiops truncatus ENSTTRG000000006601 retrocopy
retro_ttru_1427,


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