RetrogeneDB ID:

retro_eeur_638

Retrocopy
location
Organism:Hedgehog (Erinaceus europaeus)
Coordinates:scaffold_372663:49707..50444(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:DNAJC8
Ensembl ID:ENSEEUG00000011136
Aliases:None
Description:DnaJ (Hsp40) homolog, subfamily C, member 8 [Source:HGNC Symbol;Acc:15470]


Retrocopy-Parental alignment summary:






>retro_eeur_638
TCTTCTGGAGGTGGTGGCAGTACAGAGAAAGCATTTATGACCTTCTATAGTGAGGTGAAATAAATAGAGAAGAGAGATTC
AGTTCTAACATCCAAAAATCAGATTGAAAGATTGACCCATCCTGGTTCTTACTGCTTCGATTTGAATCCATTTGAGGTTC
TTCAGGTAGATCCAGAAGTGACAGATGAAGAAATAAAAAAGAGGTTTCGGCAGTTATCCATATTGGTGCATCCTGACAAA
AATCAAGATGATGCTGACAGAGCACAAAAGGCTTTTGAAGCTGTGGACAAAGCTTACAAGTTGCTACAGGATCAAGAATA
AAAGAAGAGGGCCCTGGATGTAATTCAGGCAAGAAAAGAATATGTGGAACACACTGTAAAAGAGAGGAAAAAAACAGTTA
AAGAAGGAGGGCAAACCTACTAATGTGGAAGAGGATGATCCTTAGCTGTTCAAGCAAGCAGTATACAAACAGACCATAAA
ATTGTTTGCTGAGCTGGAAATTAAAAGGAAAGAGAGAGAAGCCAAAGAGATGCACGAAAGGAAACGACAAAGGGAAGAAG
AGATTGAAGCTCAAGAAAAAGCCAAAAATGAAAGCAAGTGGCAGAAAAACTTTGAGGAAAGTCGAGATGGCTGGGTGGAC
AGCTGGTGGATCTTCCAAGCAAATACCAAGGGGAAGAAAGAGAAGAAAAACCCGACCCTTCCTGAGACCACCAAAAGTAA
AAATGGAGCAGTGTGAG

ORF - retro_eeur_638 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 90.28 %
Parental protein coverage: 93.16 %
Number of stop codons detected: 3
Number of frameshifts detected: 2


Retrocopy - Parental Gene Alignment:

ParentalASGGGGSTEEAFMTFYSEVKQIEKRDSVLTSKNQIERLTRPGSSYFNLNPSEVLQIDPEVTDEEIKKRFR
.SGGGGSTE.AFMTFYSEVK.IEKRDSVLTSKNQIERLT.PGS..F.LNP.EVLQ.DPEVTDEEIKKRFR
RetrocopySSGGGGSTEKAFMTFYSEVK*IEKRDSVLTSKNQIERLTHPGSYCFDLNPFEVLQVDPEVTDEEIKKRFR
ParentalQLSILVHPDKNQDDADRAQKAFEAVDKAYKLLLDQEQKKRALDVIQAGKEYVEHTVKER-KKQLKKEGKP
QLSILVHPDKNQDDADRAQKAFEAVDKAYKLL.DQE.KKRALDVIQA.KEYVEHTVKER.KKQLKKEGKP
RetrocopyQLSILVHPDKNQDDADRAQKAFEAVDKAYKLLQDQE*KKRALDVIQARKEYVEHTVKER>KKQLKKEGKP
ParentalTNVEEDDPELFKQAVYKQTMKLFAELEIKRKEREAKEMHERKRQREEEIEAQEKAKREREWQKNFEESRD
TNVEEDDP.LFKQAVYKQT.KLFAELEIKRKEREAKEMHERKRQREEEIEAQEKAK.E..WQKNFEESRD
RetrocopyTNVEEDDP*LFKQAVYKQTIKLFAELEIKRKEREAKEMHERKRQREEEIEAQEKAKNESKWQKNFEESRD
ParentalGRVDSWRNFQANTKGKKEKKN-RTFLRPPKVKMEQRE
G.VDSW..FQANTKGKKEKKN.R.FLRPPKVKMEQ.E
RetrocopyGWVDSWWIFQANTKGKKEKKN>RPFLRPPKVKMEQCE

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 .97 RPM 41 .41 RPM
SRP017611_kidney 2 .44 RPM 61 .70 RPM
SRP017611_liver 0 .96 RPM 21 .22 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_638 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 23 parental genes, and 49 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000112311 retrocopy
retro_amel_703,
Bos taurus ENSBTAG000000183852 retrocopies
retro_btau_1332, retro_btau_794,
Canis familiaris ENSCAFG000000118852 retrocopies
retro_cfam_1506, retro_cfam_1663,
Choloepus hoffmanni ENSCHOG000000096491 retrocopy
retro_chof_1545,
Dasypus novemcinctus ENSDNOG000000154522 retrocopies
retro_dnov_133, retro_dnov_914,
Erinaceus europaeus ENSEEUG00000011136 2 retrocopies
retro_eeur_536, retro_eeur_638 ,
Echinops telfairi ENSETEG000000083484 retrocopies
retro_etel_374, retro_etel_502, retro_etel_745, retro_etel_846,
Felis catus ENSFCAG000000133931 retrocopy
retro_fcat_203,
Homo sapiens ENSG000001266983 retrocopies
retro_hsap_1319, retro_hsap_2840, retro_hsap_4119,
Gorilla gorilla ENSGGOG000000008212 retrocopies
retro_ggor_1030, retro_ggor_2766,
Microcebus murinus ENSMICG000000012225 retrocopies
retro_mmur_1152, retro_mmur_1355, retro_mmur_343, retro_mmur_601, retro_mmur_935,
Macaca mulatta ENSMMUG000000170804 retrocopies
retro_mmul_2004, retro_mmul_2078, retro_mmul_2168, retro_mmul_228,
Mustela putorius furoENSMPUG000000155401 retrocopy
retro_mputfur_202,
Mus musculus ENSMUSG000000544051 retrocopy
retro_mmus_916,
Nomascus leucogenys ENSNLEG000000097623 retrocopies
retro_nleu_1401, retro_nleu_1594, retro_nleu_2701,
Otolemur garnettii ENSOGAG000000155974 retrocopies
retro_ogar_2422, retro_ogar_2595, retro_ogar_3219, retro_ogar_84,
Pongo abelii ENSPPYG000000258332 retrocopies
retro_pabe_2351, retro_pabe_3382,
Pelodiscus sinensis ENSPSIG000000177211 retrocopy
retro_psin_34,
Pteropus vampyrus ENSPVAG000000176191 retrocopy
retro_pvam_1057,
Rattus norvegicus ENSRNOG000000132551 retrocopy
retro_rnor_488,
Ictidomys tridecemlineatus ENSSTOG000000128342 retrocopies
retro_itri_1361, retro_itri_1775,
Tarsius syrichta ENSTSYG000000070573 retrocopies
retro_tsyr_137, retro_tsyr_1389, retro_tsyr_885,
Tursiops truncatus ENSTTRG000000000471 retrocopy
retro_ttru_1430,


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