RetrogeneDB ID:

retro_eeur_368

Retrocopy
location
Organism:Hedgehog (Erinaceus europaeus)
Coordinates:scaffold_272620:196..1152(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSEEUG00000007246
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:GNB2L1
Ensembl ID:ENSEEUG00000008729
Aliases:None
Description:guanine nucleotide binding protein (G protein), beta polypeptide 2-like 1 [Source:HGNC Symbol;Acc:4399]


Retrocopy-Parental alignment summary:






>retro_eeur_368
ATGACTGAGCAGATGACCCTTCGGGGAACCCTCAAGGGCCACAATGGCTGGGTAACTCAGATCGCCACCACCCCGCAGTT
CCCGGACATGATTTTGTCAGCCTCTCGAGATAAAACAAAACAATCATCATGTGGAAGCTGACCAGGGATGAGACCAACTA
TGGTATCCCACAGCGTGCTCTCCGGGGTCACTCACACTTTGTTAGTGATGTGGTCATCTCCTCAGACGGCCAGTTTGCCC
TCTCAGGCTCCTGGGATGGAACTCTGCGCCTTTGGGATCTCACAACGGGCACCACCACACACCGGTTTGTGGGTCATACC
AAGGATGTGCTGAGTGTAGCCTCCTCCTCTGACAACTGGCAAATTGTCTTTGGCTCCCGAGATAAAACCATCAAGCTCTG
GAATACACTGGGAGTGTGCAAATACACTGTGCAGGACGAGAGCCACTCAGAGTGGGTATCTTGTGTGCGCTTCTCGCCCA
ACAGCAGCAATCTCATCATTGTTTCCTGTGGCTGGGACAAGTTGGTCAAGGTGTGGAACCTGGCAAACTGCAAACTAAAG
ACAAACCACATTGGCCACACAGGCTATCTGAACACAGTGACTGTCTCTCCTGATGGGTCCCTGTGTGCTTCTGGAGGCAA
AGATGGCCAGGCTATGCTGTGGGACCTCAATGAAGGAAAGCATCTTTACACGCTGGATGGTGGGGACATCATCAACGTCC
TGTGCTTCAGCCCCAATCGCTACTGGCTCTGTGCTGCCACTGGCCCCAGCATCAAGATCTGGGACTTGGAGGGCAAGATC
ATTGTGGATGAACTGAAGCAAGAAGTCATCAGCACCAGCAGCAAGGCGGAGCCACCACAGTGCACCTCTCTGGCCTGGTC
TGCTGATGGCCAGACTCTGTTCACTGGCTATATTGACAACCTAGTGCGGGTGTGGCAGGTGACCATTGGCACACGT

ORF - retro_eeur_368 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 88.44 %
Parental protein coverage: 100. %
Number of stop codons detected: 1
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalMTEQMTLRGTLKGHNGWVTQIATT-PQFP--DMILSASRDKTIIMWKLTRDETNYGIPQRALRGHSHFVS
MTEQMTLRGTLKGHNGWVTQIATT.P..P..D........KTIIMWKLTRDETNYGIPQRALRGHSHFVS
RetrocopyMTEQMTLRGTLKGHNGWVTQIATT<PAVPGHDFVSLSR*NKTIIMWKLTRDETNYGIPQRALRGHSHFVS
ParentalDVVISSDGQFALSGSWDGTLRLWDLTTGTTTRRFVGHTKDVLSVAFSSDNRQIVSGSRDKTIKLWNTLGV
DVVISSDGQFALSGSWDGTLRLWDLTTGTTT.RFVGHTKDVLSVA.SSDN.QIV.GSRDKTIKLWNTLGV
RetrocopyDVVISSDGQFALSGSWDGTLRLWDLTTGTTTHRFVGHTKDVLSVASSSDNWQIVFGSRDKTIKLWNTLGV
ParentalCKYTVQEESHSEWGSCVRFSPNSXXXXXXXXXXXXXXXVWNLANCKLKTNHIGHTGYLNTVTVSPDGSLC
CKYTVQ.ESHSEW.SCVRFSPNS...............VWNLANCKLKTNHIGHTGYLNTVTVSPDGSLC
RetrocopyCKYTVQDESHSEWVSCVRFSPNSSNLIIVSCGWDKLVKVWNLANCKLKTNHIGHTGYLNTVTVSPDGSLC
ParentalASGGKDGQAMLWDLNEGKHLYTLDGGDIINALCFSPNRYWLCAATGPSIKIWDLEGKIIVDELKQEVIST
ASGGKDGQAMLWDLNEGKHLYTLDGGDIIN.LCFSPNRYWLCAATGPSIKIWDLEGKIIVDELKQEVIST
RetrocopyASGGKDGQAMLWDLNEGKHLYTLDGGDIINVLCFSPNRYWLCAATGPSIKIWDLEGKIIVDELKQEVIST
ParentalSSKAEPPQCTSLAWSADGQTLFAGYTDNLVRVWQVTIGTR
SSKAEPPQCTSLAWSADGQTLF.GY.DNLVRVWQVTIGTR
RetrocopySSKAEPPQCTSLAWSADGQTLFTGYIDNLVRVWQVTIGTR

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 35 .94 RPM 133 .91 RPM
SRP017611_kidney 94 .71 RPM 382 .95 RPM
SRP017611_liver 95 .34 RPM 360 .14 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_368 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 26 parental genes, and 37 retrocopies.

Species Parental gene accession Retrocopies number
Anolis carolinensis ENSACAG000000120081 retrocopy
retro_acar_185,
Ailuropoda melanoleuca ENSAMEG000000000041 retrocopy
retro_amel_1627,
Bos taurus ENSBTAG000000196481 retrocopy
retro_btau_1461,
Canis familiaris ENSCAFG000000248181 retrocopy
retro_cfam_1824,
Callithrix jacchus ENSCJAG000000187521 retrocopy
retro_cjac_2876,
Cavia porcellus ENSCPOG000000087241 retrocopy
retro_cpor_687,
Dipodomys ordii ENSDORG000000107351 retrocopy
retro_dord_117,
Equus caballus ENSECAG000000225673 retrocopies
retro_ecab_172, retro_ecab_218, retro_ecab_986,
Erinaceus europaeus ENSEEUG00000008729 1 retrocopy
retro_eeur_368 ,
Echinops telfairi ENSETEG000000160243 retrocopies
retro_etel_1135, retro_etel_114, retro_etel_2086,
Homo sapiens ENSG000002046281 retrocopy
retro_hsap_3226,
Gorilla gorilla ENSGGOG000000253671 retrocopy
retro_ggor_2194,
Macropus eugenii ENSMEUG000000110553 retrocopies
retro_meug_1095, retro_meug_1109, retro_meug_1532,
Myotis lucifugus ENSMLUG000000155071 retrocopy
retro_mluc_811,
Macaca mulatta ENSMMUG000000036041 retrocopy
retro_mmul_1956,
Monodelphis domestica ENSMODG000000040911 retrocopy
retro_mdom_1426,
Mustela putorius furoENSMPUG000000011482 retrocopies
retro_mputfur_1103, retro_mputfur_1111,
Mus musculus ENSMUSG000000203721 retrocopy
retro_mmus_3282,
Nomascus leucogenys ENSNLEG000000026041 retrocopy
retro_nleu_729,
Ornithorhynchus anatinus ENSOANG000000026001 retrocopy
retro_oana_127,
Otolemur garnettii ENSOGAG000000149242 retrocopies
retro_ogar_1257, retro_ogar_1591,
Pongo abelii ENSPPYG000000199391 retrocopy
retro_pabe_149,
Pan troglodytes ENSPTRG000000227341 retrocopy
retro_ptro_2178,
Rattus norvegicus ENSRNOG000000023903 retrocopies
retro_rnor_1831, retro_rnor_2130, retro_rnor_895,
Ictidomys tridecemlineatus ENSSTOG000000070631 retrocopy
retro_itri_1752,
Tupaia belangeri ENSTBEG000000146612 retrocopies
retro_tbel_3897, retro_tbel_3899,




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