RetrogeneDB ID:

retro_eeur_427

Retrocopy
location
Organism:Hedgehog (Erinaceus europaeus)
Coordinates:scaffold_295917:3303..4302(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:GAPDH
Ensembl ID:ENSEEUG00000011444
Aliases:None
Description:glyceraldehyde-3-phosphate dehydrogenase [Source:HGNC Symbol;Acc:4141]


Retrocopy-Parental alignment summary:






>retro_eeur_427
ATGGTGAAGGTCGGCGTGAATGGATTTGGCCGCATCGGACGCCTGGTCACCTGGGTTGCATTTGACTCTGGAAAAGTGGA
AATCATTGCCATCAATGACCTCTTCATCAACCTCAACTACATGGTCTACATGTTCCAGTATGACTCCACTCACGGCAAGT
TCAAGGGCAGTGTCAAGGCAGAGAACGGGAAGCTTGTCATCAATGGAAAGCCCATCTCCATCTTCCAGGAGAGAGACCCC
ACCAACATCAAGTGGGATGATGCTGGTGCTGAGTATGTCCTGGAGTCTACTGGGGTCTTCACAACCATGGAGAAGGCTGG
GGCTCACCTGAAGGGTAGTGCCAAGCGGGTGATCATCTCTGCCCCATCCGCCGATGCCCCCATGTTTGTGATGGGTGTGA
ACCATGAGAAGTATGACAATTCCCTCAAGATTGTCAGCAACGCTTCCTGAACCACCAACTGCCTGGCTCCACTTTCCAAG
GTCATCCATGACAACTTTGGCATCGTCGAGGGACTCATGACCACAGTCCATGCCATCACTGCCACCCAGAAGACCATGGA
CAGCCCCTCTGGGAAGATGTGGCGTGACGGCCGAGGAGCTGCCCAGAACATCATCCCTGCCTCCACCGGCGCCGTCAAGG
CTGTGGGCAAGGTCATCCCTGAGCTTAATGGGAAGCTTACTGGCATGGCCTTCCGTGTGCCCACCCCCAACGTGTCTGTG
GTGGATCTGACCTGCCGCCTGGAGAAAGCGGCCAAGTATGACGAAATCAAGAAGGTGGTGAAGCAGGCTTCTGATGGTCC
CCTCAAGGGCATCCTAGGCTACACCGAGGACCAGGTCGTCTCCTGTGACTTCAATAGTGACACCCACTCCTCCACCTTTG
ACGCCGGTGCGGGCATTGCCCTCAACGACCACTTTGTCAAGCTCATCTCCTGGTATGACAATGAGTTTGGCTACAGCAAC
CGTGTGGTGGACCTGATGGCCTACATGGCCTCAAAGGAG

ORF - retro_eeur_427 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 90.09 %
Parental protein coverage: 100. %
Number of stop codons detected: 1
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMVKVGVNGFGRIGRLVTRAAFDSGKVEIVAINDPFIDLNYMVYMFQYDSTHGKFKGSVKAENGKLVINGK
MVKVGVNGFGRIGRLVT..AFDSGKVEI.AIND.FI.LNYMVYMFQYDSTHGKFKGSVKAENGKLVINGK
RetrocopyMVKVGVNGFGRIGRLVTWVAFDSGKVEIIAINDLFINLNYMVYMFQYDSTHGKFKGSVKAENGKLVINGK
ParentalPISIFQERDPANIKWGDAGAEYVVESTGVFTTMEKAGAHLKGGAKRVIISAPSADAPMFVMGVNHEKYDN
PISIFQERDP.NIKW.DAGAEYV.ESTGVFTTMEKAGAHLKG.AKRVIISAPSADAPMFVMGVNHEKYDN
RetrocopyPISIFQERDPTNIKWDDAGAEYVLESTGVFTTMEKAGAHLKGSAKRVIISAPSADAPMFVMGVNHEKYDN
ParentalSLKIVSNAS-CTNCLAPLAKVIHDNFGIV-GLMTTVHAITATQKTVDGPSGKMWRDGRGAAQNIIPASTG
SLKIVSNAS..TNCLAPL.KVIHDNFGIV.GLMTTVHAITATQKT.D.PSGKMWRDGRGAAQNIIPASTG
RetrocopySLKIVSNAS*TTNCLAPLSKVIHDNFGIVEGLMTTVHAITATQKTMDSPSGKMWRDGRGAAQNIIPASTG
ParentalAAKAVGKVIPELNRKLTGMAFRVPTPNVSVVDLTCRLEKPAKYDEIKKVVKQASDGPLKGILGYTEDQVV
A.KAVGKVIPELN.KLTGMAFRVPTPNVSVVDLTCRLEK.AKYDEIKKVVKQASDGPLKGILGYTEDQVV
RetrocopyAVKAVGKVIPELNGKLTGMAFRVPTPNVSVVDLTCRLEKAAKYDEIKKVVKQASDGPLKGILGYTEDQVV
ParentalSCDFNSDTHSSTLDACAGVALNDHFVKLISWYD-KFCYRNVGVELIAHLGLKE
SCDFNSDTHSST.DA.AG.ALNDHFVKLISWYD..F.Y.N..V.L.A....KE
RetrocopySCDFNSDTHSSTFDAGAGIALNDHFVKLISWYDNEFGYSNRVVDLMAYMASKE

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 422 .20 RPM 365 .96 RPM
SRP017611_kidney 898 .87 RPM 698 .96 RPM
SRP017611_liver 320 .91 RPM 231 .68 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_427 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 554 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000066755 retrocopies
Ailuropoda melanoleuca ENSAMEG0000001432935 retrocopies
Canis familiaris ENSCAFG000000150774 retrocopies
Callithrix jacchus ENSCJAG000000082341 retrocopy
Cavia porcellus ENSCPOG000000263501 retrocopy
Erinaceus europaeus ENSEEUG00000011444 3 retrocopies
retro_eeur_427 , retro_eeur_569, retro_eeur_677,
Homo sapiens ENSG0000011164042 retrocopies
Gorilla gorilla ENSGGOG0000000955330 retrocopies
Loxodonta africana ENSLAFG000000027803 retrocopies
Macropus eugenii ENSMEUG0000001527367 retrocopies
Microcebus murinus ENSMICG0000000654616 retrocopies
Macaca mulatta ENSMMUG0000001867933 retrocopies
Monodelphis domestica ENSMODG0000001806641 retrocopies
Mustela putorius furoENSMPUG0000001689128 retrocopies
Mus musculus ENSMUSG00000057666109 retrocopies
retro_mmus_1029, retro_mmus_1082, retro_mmus_1136, retro_mmus_1193, retro_mmus_1249, retro_mmus_1319, retro_mmus_1328, retro_mmus_136, retro_mmus_1365, retro_mmus_1371, retro_mmus_1467, retro_mmus_1474, retro_mmus_1480, retro_mmus_1615, retro_mmus_1692, retro_mmus_1721, retro_mmus_1728, retro_mmus_1886, retro_mmus_1922, retro_mmus_1957, retro_mmus_1983, retro_mmus_1985, retro_mmus_2009, retro_mmus_2020, retro_mmus_2030, retro_mmus_2100, retro_mmus_211, retro_mmus_2119, retro_mmus_2122, retro_mmus_2148, retro_mmus_2158, retro_mmus_2175, retro_mmus_2206, retro_mmus_2216, retro_mmus_2248, retro_mmus_2298, retro_mmus_2370, retro_mmus_2371, retro_mmus_2389, retro_mmus_2463, retro_mmus_2477, retro_mmus_2481, retro_mmus_2512, retro_mmus_2556, retro_mmus_2587, retro_mmus_2623, retro_mmus_2626, retro_mmus_2647, retro_mmus_2681, retro_mmus_2755, retro_mmus_2761, retro_mmus_2764, retro_mmus_2848, retro_mmus_2872, retro_mmus_2911, retro_mmus_2912, retro_mmus_2913, retro_mmus_2914, retro_mmus_2915, retro_mmus_2920, retro_mmus_2932, retro_mmus_2943, retro_mmus_300, retro_mmus_3036, retro_mmus_3064, retro_mmus_3120, retro_mmus_3137, retro_mmus_3140, retro_mmus_3148, retro_mmus_3151, retro_mmus_3188, retro_mmus_3193, retro_mmus_3197, retro_mmus_3216, retro_mmus_3228, retro_mmus_3306, retro_mmus_3335, retro_mmus_3336, retro_mmus_3357, retro_mmus_3377, retro_mmus_3445, retro_mmus_3514, retro_mmus_3575, retro_mmus_3650, retro_mmus_3658, retro_mmus_3693, retro_mmus_3716, retro_mmus_3814, retro_mmus_416, retro_mmus_437, retro_mmus_48, retro_mmus_553, retro_mmus_608, retro_mmus_619, retro_mmus_628, retro_mmus_635, retro_mmus_698, retro_mmus_745, retro_mmus_765, retro_mmus_766, retro_mmus_787, retro_mmus_811, retro_mmus_893, retro_mmus_914, retro_mmus_921, retro_mmus_946, retro_mmus_952, retro_mmus_976, retro_mmus_996,
Nomascus leucogenys ENSNLEG0000000382544 retrocopies
Pongo abelii ENSPPYG0000000418938 retrocopies
Pan troglodytes ENSPTRG0000000457743 retrocopies
Rattus norvegicus ENSRNOG000000186304 retrocopies
Rattus norvegicus ENSRNOG000000306382 retrocopies
Sarcophilus harrisii ENSSHAG000000149534 retrocopies
Xenopus tropicalis ENSXETG000000339751 retrocopy



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