RetrogeneDB ID:

retro_eeur_18

Retrocopy
location
Organism:Hedgehog (Erinaceus europaeus)
Coordinates:GeneScaffold_7910:16226..17021(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSEEUG00000003092
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:TAF9B
Ensembl ID:ENSEEUG00000010916
Aliases:None
Description:TAF9B RNA polymerase II, TATA box binding protein (TBP)-associated factor, 31kDa [Source:HGNC Symbol;Acc:17306]


Retrocopy-Parental alignment summary:






>retro_eeur_18
ATGGAGTCTGGCAAGATGGCTTCTCCCAAGAGCATGCCGAAAGATGCACAGATGATGGCACAAATCCTGAAGGATATGGG
GATTACAGAATATGAGCCAAGAGTTATAAATCAGATGTTGGAGTTTGCCTTCCGATATGTGACCACTATTTTAGATGATG
CGAAAATTTATTCAAGTCATGCTAAGAAAAGTACTGTTGACGCAGATGATGTGAGATTAGCAATTCAGTGTCGTGCAGAT
CAGTCTTTCACTTCTCCTCCCCCAAGAGATTTTTTACTGGATATCGCAAGGCAAAGAAATCAAACCCCTTTGCCATTAAT
CAAGCCATATTCAGGCCCTCGGTTGCCACCTGACAGATACTGCTTGACTGCTCCAAACTATAAACTTAAGTCTTTACAAA
AAAAGGCATCTACTTCTGCGGGAAGAATAACAGTTCCAAGGTTGAGTGTTGGTTCAGTTACTAGCAGACCAACTACCCCT
ACACTTGGCACACCAACGCCACAAACCATGTCTGTTTCAACTAAAGCAGGGACTCCAATGTCCCTTACAGGGCAGAGGTT
TACAGTGCAGATGCCCACTGCACAGGCCCCAGCTGTAAAGGCAGCAATTCCTGCAACATCAGCAGTTCAGAATGTTCTTA
TTAATCCATCATTAATTGGGTCCAAAAATATCCTTATTACCACAAATATGGTGTCATCACAAAATGCTGCCAGTGAATCA
TCCAATGCCATGAAAAGAAAGCGTGAAGATGATGATGATGACGATGATGATGATGATGACTATGATAATGTGTAG

ORF - retro_eeur_18 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 85.8 %
Parental protein coverage: 100. %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMESGKMAPPKNAPRDALVMAQILKDMGITEYEPRVINQMLEFAFRYVTTILDDAKIYSSHAKKPHIDADD
MESGKMA.PK..P.DA..MAQILKDMGITEYEPRVINQMLEFAFRYVTTILDDAKIYSSHAKK...DADD
RetrocopyMESGKMASPKSMPKDAQMMAQILKDMGITEYEPRVINQMLEFAFRYVTTILDDAKIYSSHAKKSTVDADD
ParentalVRLAIQCRADQSFTSPPPRDFLLDIARQRNQTPLPLIKPYAGHRLPPDRYCLTAPNYRLKSLVKK-GPNQ
VRLAIQCRADQSFTSPPPRDFLLDIARQRNQTPLPLIKPY.G.RLPPDRYCLTAPNY.LKSL.KK.....
RetrocopyVRLAIQCRADQSFTSPPPRDFLLDIARQRNQTPLPLIKPYSGPRLPPDRYCLTAPNYKLKSLQKKASTSA
ParentalGRL-VPRLSVGAVSSRPTTPTI
GR..VPRLSVG.V.SRPTTPT.
RetrocopyGRITVPRLSVGSVTSRPTTPTL

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 17 .56 RPM 3 .71 RPM
SRP017611_kidney 17 .63 RPM 9 .94 RPM
SRP017611_liver 11 .09 RPM 3 .38 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_18 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 28 parental genes, and 46 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000176131 retrocopy
retro_amel_449,
Bos taurus ENSBTAG000000008951 retrocopy
retro_btau_196,
Canis familiaris ENSCAFG000000172781 retrocopy
retro_cfam_192,
Callithrix jacchus ENSCJAG000000195201 retrocopy
retro_cjac_246,
Cavia porcellus ENSCPOG000000020982 retrocopies
retro_cpor_906, retro_cpor_967,
Equus caballus ENSECAG000000101891 retrocopy
retro_ecab_303,
Erinaceus europaeus ENSEEUG00000010916 1 retrocopy
retro_eeur_18 ,
Felis catus ENSFCAG000000254932 retrocopies
retro_fcat_1036, retro_fcat_260,
Homo sapiens ENSG000001873251 retrocopy
retro_hsap_2619,
Gorilla gorilla ENSGGOG000000024702 retrocopies
retro_ggor_1833, retro_ggor_45,
Macropus eugenii ENSMEUG000000096971 retrocopy
retro_meug_140,
Myotis lucifugus ENSMLUG000000145811 retrocopy
retro_mluc_519,
Macaca mulatta ENSMMUG000000128751 retrocopy
retro_mmul_1480,
Monodelphis domestica ENSMODG000000040771 retrocopy
retro_mdom_850,
Mustela putorius furoENSMPUG000000000841 retrocopy
retro_mputfur_63,
Mus musculus ENSMUSG000000472421 retrocopy
retro_mmus_161,
Nomascus leucogenys ENSNLEG000000013785 retrocopies
retro_nleu_1677, retro_nleu_2566, retro_nleu_637, retro_nleu_920, retro_nleu_932,
Oryctolagus cuniculus ENSOCUG000000147171 retrocopy
retro_ocun_490,
Otolemur garnettii ENSOGAG000000111073 retrocopies
retro_ogar_1128, retro_ogar_3100, retro_ogar_679,
Pongo abelii ENSPPYG000000204974 retrocopies
retro_pabe_1634, retro_pabe_2341, retro_pabe_2748, retro_pabe_941,
Pan troglodytes ENSPTRG000000220534 retrocopies
retro_ptro_1329, retro_ptro_1765, retro_ptro_2145, retro_ptro_772,
Pteropus vampyrus ENSPVAG000000174081 retrocopy
retro_pvam_6,
Rattus norvegicus ENSRNOG000000024531 retrocopy
retro_rnor_1492,
Sus scrofa ENSSSCG000000267142 retrocopies
retro_sscr_1080, retro_sscr_525,
Ictidomys tridecemlineatus ENSSTOG000000019823 retrocopies
retro_itri_1640, retro_itri_411, retro_itri_763,
Tarsius syrichta ENSTSYG000000079681 retrocopy
retro_tsyr_3,
Tursiops truncatus ENSTTRG000000159641 retrocopy
retro_ttru_572,
Vicugna pacos ENSVPAG000000012101 retrocopy
retro_vpac_16,


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