RetrogeneDB ID:

retro_eeur_531

Retrocopy
location
Organism:Hedgehog (Erinaceus europaeus)
Coordinates:scaffold_340459:576..870(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:RRAS2
Ensembl ID:ENSEEUG00000000240
Aliases:None
Description:related RAS viral (r-ras) oncogene homolog 2 [Source:HGNC Symbol;Acc:17271]


Retrocopy-Parental alignment summary:






>retro_eeur_531
TTTCAAAGACAAATTATCAGAGTGAAGGACCATGATGAGTTCCCAATGATTTTAATTGGTAATAAAGCAGATTTGGATCA
TCAAAGACAGGTAACACAGGGAGAAGGACAGCAGCTGGCACGGCAACTGAAAGTAACATACATGGAGGCCTCAGCAAAGA
TCAGGATGAATGCAGATCAGGCTTTCCATGATCTTGTCAAAGTTATCAGGAAATTTCAAGAGCAGGAATGTCCCCCTTCA
CCAGAGCCAACTAGGAAATAAAAAGATAAGAAAGGCTGCCATTGTGTCATTTTC

ORF - retro_eeur_531 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 92.86 %
Parental protein coverage: 58.33 %
Number of stop codons detected: 1
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalFQRQILRVKDRDEFPMILIGNKADLDHQRQVTQEEGQQLARQLKVTYMEASAKIRMNVDQAFHELVRVIR
FQRQI.RVKD.DEFPMILIGNKADLDHQRQVTQ.EGQQLARQLKVTYMEASAKIRMN.DQAFH.LV.VIR
RetrocopyFQRQIIRVKDHDEFPMILIGNKADLDHQRQVTQGEGQQLARQLKVTYMEASAKIRMNADQAFHDLVKVIR
ParentalKFQEQECPPSPEPTRKEKDKKGCHCVIF
KFQEQECPPSPEPTRK.KDKKGCHCVIF
RetrocopyKFQEQECPPSPEPTRK*KDKKGCHCVIF

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 0 .64 RPM 8 .38 RPM
SRP017611_kidney 1 .69 RPM 28 .32 RPM
SRP017611_liver 1 .13 RPM 17 .36 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_531 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 21 parental genes, and 35 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000023671 retrocopy
retro_amel_947,
Bos taurus ENSBTAG000000119051 retrocopy
retro_btau_1295,
Choloepus hoffmanni ENSCHOG000000031357 retrocopies
retro_chof_111, retro_chof_1639, retro_chof_2065, retro_chof_2644, retro_chof_2706, retro_chof_389, retro_chof_521,
Dasypus novemcinctus ENSDNOG000000118286 retrocopies
retro_dnov_124, retro_dnov_1458, retro_dnov_1708, retro_dnov_1779, retro_dnov_2331, retro_dnov_988,
Erinaceus europaeus ENSEEUG00000000240 1 retrocopy
retro_eeur_531 ,
Felis catus ENSFCAG000000095781 retrocopy
retro_fcat_386,
Homo sapiens ENSG000001338181 retrocopy
retro_hsap_390,
Gorilla gorilla ENSGGOG000000047591 retrocopy
retro_ggor_1813,
Myotis lucifugus ENSMLUG000000070051 retrocopy
retro_mluc_1264,
Macaca mulatta ENSMMUG000000006642 retrocopies
retro_mmul_1604, retro_mmul_965,
Monodelphis domestica ENSMODG000000283972 retrocopies
retro_mdom_1254, retro_mdom_577,
Oryctolagus cuniculus ENSOCUG000000113621 retrocopy
retro_ocun_1645,
Otolemur garnettii ENSOGAG000000276551 retrocopy
retro_ogar_1081,
Ochotona princeps ENSOPRG000000059671 retrocopy
retro_opri_2,
Pongo abelii ENSPPYG000000259121 retrocopy
retro_pabe_3043,
Pan troglodytes ENSPTRG000000033832 retrocopies
retro_ptro_1747, retro_ptro_301,
Rattus norvegicus ENSRNOG000000122581 retrocopy
retro_rnor_750,
Ictidomys tridecemlineatus ENSSTOG000000221691 retrocopy
retro_itri_1457,