RetrogeneDB ID:

retro_eeur_324

Retrocopy
location
Organism:Hedgehog (Erinaceus europaeus)
Coordinates:scaffold_254362:4330..4742(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:TPGS2
Ensembl ID:ENSEEUG00000005257
Aliases:None
Description:tubulin polyglutamylase complex subunit 2 [Source:HGNC Symbol;Acc:24561]


Retrocopy-Parental alignment summary:






>retro_eeur_324
AGTGGGAACCAGCCAGAGAAACCTCACTTTGATTCACACAGTGTGATATTTGAGTCGAATCCTTGCAAGGGCATGGGAAG
GTTTGTCTTCTCTACACAAGAGGGAAACCAAGACTGTGCAATCTGGTTCCTAGACAGAGCACCCTGCTGGCATTTTTCTC
ACAGACACTTTTACTTACTGCCTGTCATCGTCTGCTTGTCACCCACCTAGGTCTACTCCAGCGGCAATAGGTCTTCACCA
GTGATAGCATCGGCCCACAGGCTAAGCAATGTTTCAACATGTACAGATCCATAACATATAACACACACCTGCTAATGGAA
GGAAGTAACTCCTTTGTGAACAAGCTGGATCCCAGCCAAGTATTTAAGAGCAAGAGCAAGATCTTGGTCCCCATAAGAAA
GGGCCTGTTCAG

ORF - retro_eeur_324 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 63.89 %
Parental protein coverage: 53.03 %
Number of stop codons detected: 1
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalSENQPEKPHFDSRSVIFELDPCSGHGKVCLVYKRGKPGLAQDSEIWFLDRALYWH-FLTDTF--TAYYRL
S.NQPEKPHFDS.SVIFE..PC.G.G........G.....QD..IWFLDRA..WH.F...T...TA..RL
RetrocopySGNQPEKPHFDSHSVIFESNPCKGMGRFVFSTQEGN----QDCAIWFLDRAPCWH<FFSQTLLLTACHRL
ParentalLVTHLGLPQWQYAFTSYGVSPQAKQWFNMYKPITYNTNLLMEEADSFVNKLDPSKVFKSKNKTLV-PKKK
LVTHLGL.Q.Q..FTS....PQAKQ.FNMY..ITYNT.LLME...SFVNKLDPS.VFKSK.K.LV.P.KK
RetrocopyLVTHLGLLQRQ*VFTSDSIGPQAKQCFNMYRSITYNTHLLMEGSNSFVNKLDPSQVFKSKSKILV<PHKK
ParentalGPVQ
GPVQ
RetrocopyGPVQ

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 0 .32 RPM 52 .21 RPM
SRP017611_kidney 0 .00 RPM 16 .69 RPM
SRP017611_liver 0 .00 RPM 4 .02 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_324 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 11 parental genes, and 17 retrocopies.

Species Parental gene accession Retrocopies number
Canis familiaris ENSCAFG000000177663 retrocopies
Choloepus hoffmanni ENSCHOG000000079601 retrocopy
Erinaceus europaeus ENSEEUG00000005257 3 retrocopies
retro_eeur_208, retro_eeur_324 , retro_eeur_516,
Myotis lucifugus ENSMLUG000000017391 retrocopy
Mustela putorius furoENSMPUG000000010972 retrocopies
Mus musculus ENSMUSG000000242691 retrocopy
Otolemur garnettii ENSOGAG000000082181 retrocopy
Rattus norvegicus ENSRNOG000000149571 retrocopy
Sus scrofa ENSSSCG000000269531 retrocopy
Tarsius syrichta ENSTSYG000000052992 retrocopies
Tursiops truncatus ENSTTRG000000071531 retrocopy



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