RetrogeneDB ID:

retro_eeur_371

Retrocopy
location
Organism:Hedgehog (Erinaceus europaeus)
Coordinates:scaffold_272863:10259..12105(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:ABCB6
Ensembl ID:ENSEEUG00000007653
Aliases:None
Description:ATP-binding cassette, sub-family B (MDR/TAP), member 6 [Source:HGNC Symbol;Acc:47]


Retrocopy-Parental alignment summary:






>retro_eeur_371
CTGCCCGGGTACCTCCTGTCGGCCGCCTTCTTGGAGACATTGGCGGGCGCCTGCGGCCTGGGGCTGCTGATGGCGGAGCG
CAGGAGCGCGCTGCAGAAACTCGCCATGGGCGTGCGGGTGCGGTGCGGGCACAGCCCCGGGCTGCTGCTGCTCTGGACCG
TGATGTTCGCCGCCCAGAACTTGGCGCTGGTGTCCTGGAAGAGCCCGCAGTGGTGGTGAGCAAGGGCGGACCTGGGCCAG
CAGGTTCAGTTTGGCCTGTGGGCACTGCGGTATGTGGTGTCTGGGGGGCTTTTTCTCCTGGGGCTCTGGGCCCCTGGACT
GCGACCCCAGACATACACCTTGCGGGTCAATGAAGAGGATCAGGATGTAGAGAGAAGCCAGGTTCCCTCAACCCAGGGGT
CATCTCCATCTACCTGGGGTGACCTTGGCAGGAAGCTCCGCCTCCTAAGTGGCTATCTGTGGCCTCGGGGGAGCCCTGCC
CTGCAGCTAGTGGTGCTCTGCTGCCTGGGACTCATGGGGCTGGACCGGGGATTGAACGTGCTGGTCCCCATCTTCTACAG
AGACATAGTGAACTTGCTGACAGAGAAGGCCCCTTGGAACTCCCTGGCCTGGACCGTCACCACTTATGTCTTCCTCAAGT
TCCTGCAGGGGGGCGGCACTGGCAATACAGGCTTCGTGAGCAACCTTCCTCTGAATCCGGGTCCAGCAGTACACCTCTCG
CCGCGTGGAGCTGCGTCTCTTCTGCCACCTGCATGAGTTGTCACTGCGCTGGCACCTGGGTCGCCTCACAGGGGAAGTGC
TGCGGGTCGTGGACCGGGGCACATCCAGCGTCACTGGGCTGCTCAGTTACCTGGTATTCAACATCATCCCCACGCTGGCC
GACATCATCATTGGCATCATCTACTTCAGCATGTTCTTCAACGCCTGGTTTGGCCTCATCGTCTTCCTGTGCATGAGCCT
CTACCTCATCCTGACCATTGTGGTCACCGAGTGGAGAACTAAGTTCCGACGTGACATGAACATGCAGGAGAATGCTACCC
GGGCACGAGCCGTGGACTCCCTGTTGAACTTTGAGACGGTGAAGTATTACAATGCAGAAGGCTATGAAGTGGAGCGCTAC
CAAGAGGCCATCATCAAGTACCAGGGTTTGGAGTGGAAGTCAAGTGCTTCATTGGTTTTGCTGAATCAGACCCAGAACCT
GGTGATTGGCCTCGGGCTCCTGGCCGGCTCCCTGCTGTGTGCATTCTTTGTCAGCGAGCAGAAGCTGCAGCTCGGGGACT
TTGTGCTCTTTGGCACCTACATCATTCAGCTCTACATGCCCCTCAACTGGTTTGGCACCTACTACAGGATGATCCAGACT
AACTTCATCGACATGGAGAACATGTTTGATCTGCTCAAAGAGGAGGCAGAAGTGAAGGACCTCCCTGGCGCAGGGCCCCT
TCACTTCCAGAAGGGCCAGATCGAGTTTGAAAACGTGCACTTCAGCTATACAGATGGACGGGAGACCCTGCAAGACATGT
CCTTCACTGTGATGCCTGGCCAGACACTAGCCCTGGTGGGCCCGACCGGCGCAGGGAAGAGCACCATCCTGCGCCTGCTC
TTCCGCTTCTATGACATCAACAGTGGCTGTATCCGCATCGATGGGCAGGACATCTCCAAGGTAACCCAGACCTCCCTGCG
GTCCCACATTGGAGTTGTGCCACAGGACACCGTCCTCTTCAATGACACCATTGCCAACAACATCCGCTATGGCCGCATCA
CAGCTGATGCTGCTGAGGTGGAGGCAGCCGCCAAGGCTGCAGGCATCCATGAAGCCATCCTGGCTTTCCCCGAAGGCTAC
GAGACA

ORF - retro_eeur_371 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 96.77 %
Parental protein coverage: 69.67 %
Number of stop codons detected: 3
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalLPGYLLSAAFLETLAGACGLGLLLAERRSALQKLAMGVRVRCGHSPGLLLLWTVTFAAQNLVLVSWKSPQ
LPGYLLSAAFLETLAGACGLGLL.AERRSALQKLAMGVRVRCGHSPGLLLLWTV.FAAQNL.LVSWKSPQ
RetrocopyLPGYLLSAAFLETLAGACGLGLLMAERRSALQKLAMGVRVRCGHSPGLLLLWTVMFAAQNLALVSWKSPQ
ParentalWWWARADLGQQVQFGLWALRYVVSGGLFLLGLWAPGLRPQTYTLRVNEEDQDVERSQVPSTQGSSRSTWG
WW.ARADLGQQVQFGLWALRYVVSGGLFLLGLWAPGLRPQTYTLRVNEEDQDVERSQVPSTQGSS.STWG
RetrocopyWW*ARADLGQQVQFGLWALRYVVSGGLFLLGLWAPGLRPQTYTLRVNEEDQDVERSQVPSTQGSSPSTWG
ParentalDLGRKLRLLSGYLWPRGSPALQLVVLCCLGLMGLDRGLNVLVPIFYRDIVNLLTEKAPWNSLAWTVTTYV
DLGRKLRLLSGYLWPRGSPALQLVVLCCLGLMGLDRGLNVLVPIFYRDIVNLLTEKAPWNSLAWTVTTYV
RetrocopyDLGRKLRLLSGYLWPRGSPALQLVVLCCLGLMGLDRGLNVLVPIFYRDIVNLLTEKAPWNSLAWTVTTYV
ParentalFLKFLQGGGTGSTG-FVSNLRTFLWIRVQQYTSRRVELRLFCHLHELSLRWHLGRRTGEVLRVVDRGTSS
FLKFLQG...G.TG.......TFL.IRVQQYTSRRVELRLFCHLHELSLRWHLGR.TGEVLRVVDRGTSS
RetrocopyFLKFLQG---GGTG>IQAS*ATFL*IRVQQYTSRRVELRLFCHLHELSLRWHLGRLTGEVLRVVDRGTSS
ParentalVTGLLSYLVFNIIPTLADIIIGIIYFSMFFNAWFGLIVFLCMSLYLILTIVVTEWRTKFRRDMNMQENAT
VTGLLSYLVFNIIPTLADIIIGIIYFSMFFNAWFGLIVFLCMSLYLILTIVVTEWRTKFRRDMNMQENAT
RetrocopyVTGLLSYLVFNIIPTLADIIIGIIYFSMFFNAWFGLIVFLCMSLYLILTIVVTEWRTKFRRDMNMQENAT
ParentalRARAVDSLLNFETVKYYNAEGYEVERYQEAIIKYQGLEWKSSASLVLLNQTQNLVIGLGLLAGSLLCAFF
RARAVDSLLNFETVKYYNAEGYEVERYQEAIIKYQGLEWKSSASLVLLNQTQNLVIGLGLLAGSLLCAFF
RetrocopyRARAVDSLLNFETVKYYNAEGYEVERYQEAIIKYQGLEWKSSASLVLLNQTQNLVIGLGLLAGSLLCAFF
ParentalVSEQKLQVGDFVLFGTYIIQLYMPLNWFGTYYRMIQTNFIDMENMFDLLKEEAEVKDLPGAGPLHFQKGQ
VSEQKLQ.GDFVLFGTYIIQLYMPLNWFGTYYRMIQTNFIDMENMFDLLKEEAEVKDLPGAGPLHFQKGQ
RetrocopyVSEQKLQLGDFVLFGTYIIQLYMPLNWFGTYYRMIQTNFIDMENMFDLLKEEAEVKDLPGAGPLHFQKGQ
ParentalIEFENVHFSYTDGRETLQDMSFTVMPGQTLALVGPSGAGKSTILRLLFRFYDINSGCIRIDGQDISKVTQ
IEFENVHFSYTDGRETLQDMSFTVMPGQTLALVGP.GAGKSTILRLLFRFYDINSGCIRIDGQDISKVTQ
RetrocopyIEFENVHFSYTDGRETLQDMSFTVMPGQTLALVGPTGAGKSTILRLLFRFYDINSGCIRIDGQDISKVTQ
ParentalTSLRSHIGVVPQDTVLFNDTIANNIRYGRITADAAEVEAAAKAAGIHEAILAFPEGYET
TSLRSHIGVVPQDTVLFNDTIANNIRYGRITADAAEVEAAAKAAGIHEAILAFPEGYET
RetrocopyTSLRSHIGVVPQDTVLFNDTIANNIRYGRITADAAEVEAAAKAAGIHEAILAFPEGYET

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 6 .28 RPM 29 .81 RPM
SRP017611_kidney 12 .00 RPM 49 .89 RPM
SRP017611_liver 3 .54 RPM 12 .54 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_371 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 1 parental gene, and 1 retrocopy.

Species Parental gene accession Retrocopies number
Erinaceus europaeus ENSEEUG00000007653 1 retrocopy
retro_eeur_371 ,


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