RetrogeneDB ID:

retro_eeur_167

Retrocopy
location
Organism:Hedgehog (Erinaceus europaeus)
Coordinates:scaffold_133780:626..1198(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:CAPZA2
Ensembl ID:ENSEEUG00000009063
Aliases:None
Description:capping protein (actin filament) muscle Z-line, alpha 2 [Source:HGNC Symbol;Acc:1490]


Retrocopy-Parental alignment summary:






>retro_eeur_167
ATGGCCGACTTCGAGCATTGGGTGTCGGATGAGGAGAAGGTAGCATAGCTGCTAAATTCATCACCCATGCACCCCCAGGG
GAATTTAATGAAGTATTCAACGATGTCCGGCTGCTACTTAATAATGACAATCTCCTCAGGGAAGGGGCAGCACATGCATT
TGCCCAGTATAACATGGATCAGCTCACACCAGTGAAGATAGAAGGATATGAAGAACAGGTCTTAATTACAAAACATGGTG
ACCTGGGCAATAGCAGATTTTTAGATCCAAAAAACAAAATTTCCTTTAAATTTGATCATTTACAGAAAGAAGCAAGTGAC
CCTCATCCAGAAGAAGCAGATGGAGGTCTGAAATCTTGGAAAGAATCCTGTGACAGTGCTTTAAGAGCCTATGTGAAAGA
CCATTATTCCAATGGCTTCTGTACTGTTTATGCTAAAACTATAGATGGACAGCAGACCATTATTGCATGTATTGAAAGTT
ACCAGTTTCAGCCTAAAAACTTCTGGAATGGTCATTGGAGATCAGAGTGGAAGTTCACCATCACACCACCTACAGCTCAA
GTGGTTGAGGTT

ORF - retro_eeur_167 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 75.52 %
Parental protein coverage: 66.55 %
Number of stop codons detected: 0
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalMADLEEQLSDEEKVR-IAAKFIIHAPPGEFNEVFNDVRLLLNNDNLLREGAAQALAQYNLD--TPVKIEA
MAD.E...SDEEKV..IAAKFI.HAPPGEFNEVFNDVRLLLNNDNLLREGAA.A.AQYN.D..TPVKIE.
RetrocopyMADFEHWVSDEEKVA<IAAKFITHAPPGEFNEVFNDVRLLLNNDNLLREGAAHAFAQYNMDQLTPVKIEG
ParentalYEDQVLITEHGDLGNGKFLDPKNRICFKFDHLRKEATDPRPYEAENAVESWRTSVETALRAYVKEHYPNG
YE.QVLIT.HGDLGN..FLDPKN.I.FKFDHL.KEA.DP.P.EA.....SW..S...ALRAYVK.HY.NG
RetrocopyYEEQVLITKHGDLGNSRFLDPKNKISFKFDHLQKEASDPHPEEADGGLKSWKESCDSALRAYVKDHYSNG
ParentalVCTVYGKKIDGQQTIIACIESHQFQAKNFWNGRWRSEWKFTISPSSTQVVGI
.CTVY.K.IDGQQTIIACIES.QFQ.KNFWNG.WRSEWKFTI.P...QVV..
RetrocopyFCTVYAKTIDGQQTIIACIESYQFQPKNFWNGHWRSEWKFTITPPTAQVVEV

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 .16 RPM 101 .68 RPM
SRP017611_kidney 0 .38 RPM 92 .27 RPM
SRP017611_liver 0 .16 RPM 43 .73 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_167 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 14 parental genes, and 24 retrocopies.

Species Parental gene accession Retrocopies number
Choloepus hoffmanni ENSCHOG000000049252 retrocopies
Cavia porcellus ENSCPOG000000076771 retrocopy
Dasypus novemcinctus ENSDNOG000000057711 retrocopy
Dipodomys ordii ENSDORG000000162261 retrocopy
Erinaceus europaeus ENSEEUG00000009063 5 retrocopies
Echinops telfairi ENSETEG000000197113 retrocopies
Gorilla gorilla ENSGGOG000000121581 retrocopy
Microcebus murinus ENSMICG000000007071 retrocopy
Myotis lucifugus ENSMLUG000000079101 retrocopy
Oryctolagus cuniculus ENSOCUG000000035912 retrocopies
Pongo abelii ENSPPYG000000179331 retrocopy
Sus scrofa ENSSSCG000000269422 retrocopies
Ictidomys tridecemlineatus ENSSTOG000000248281 retrocopy
Tupaia belangeri ENSTBEG000000126572 retrocopies



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