RetrogeneDB ID:

retro_btau_168

Retrocopy
location
Organism:Cow (Bos taurus)
Coordinates:15:84007597..84008311(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSBTAG00000001432
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:ZCCHC17
Ensembl ID:ENSBTAG00000016818
Aliases:None
Description:nucleolar protein of 40 kDa [Source:RefSeq peptide;Acc:NP_001029824]


Retrocopy-Parental alignment summary:






>retro_btau_168
ATGAATTCAGGAAGACCCGAGACCATGGAGAACTTGCCTGCTCTCTACACTATTTTCCAAGGAGAGGTTGCTATGGTCAC
AGACTATGGAGCCTTTATCAAAATCCCAGGCTGTCGGAAGCAAGGTCTGGTCCATCGAACTCACATGTCATCCTGTCGCG
TGGATAAGCCCTCTGAGATAGTAGATGTTGGCGACAAAGTGTGCGTGAAACTTATTGGCCGAGAGATGAAAGATGATAGG
ATAAAAGTATCCCTCTCCATGAAGGTTGTCGACCAAGGGACTGTGAAGGACCTTGATCCCAACAACGTTATCATTGAGCA
GGAAGAGAGGCGGAGGTGGTCCTTCCAGGATTACACAGGGCAGAGGATCACCCTCGAGGCTGTTCTGAACGCCACCTGCA
AGAAGTGTGGCTGTAAAGGCCACTTTGCAAAGGATTGTTTCATGCAACCAGGTGGGGCCAAGTATTCTCTGATACCTGAT
GAGGAAGAGGAGAAAGAAGAGCCAAAGTCAGCAGAGTTTGAAAAGCCTGACACCACAAGAAATTCTTCTAGAAAAAGAAA
GAAAGAAAAGAAGAAAAAGAAACATAGAGACAGGAAGTCATCTGACTCTGACAGCTCAGACTCTGAGAGTGATACAGGCA
AGAGGGCAAGGCACACGTCAAAGGACAGCAAGGCAGCAAAGAAGAAGAAAAAGAAGAAGAAGCACAAGGAGTGA

ORF - retro_btau_168 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 95.78 %
Parental protein coverage: 98.34 %
Number of stop codons detected: 0
Number of frameshifts detected: 0


Retrocopy - Parental Gene Alignment:

ParentalMNSGRPETMENLPALYTIFQGEVAMVTDYGAFIKIPGCRKQGLVHRTHMSSCRVDKPSEIVDVGDKVWVK
MNSGRPETMENLPALYTIFQGEVAMVTDYGAFIKIPGCRKQGLVHRTHMSSCRVDKPSEIVDVGDKV.VK
RetrocopyMNSGRPETMENLPALYTIFQGEVAMVTDYGAFIKIPGCRKQGLVHRTHMSSCRVDKPSEIVDVGDKVCVK
ParentalLIGREMKNDRIKVSLSMKVVNQGTGKDLDPNNVIIEQEERRRRSFQDYTGQKITLEAVLNTTCKKCGCKG
LIGREMK.DRIKVSLSMKVV.QGT.KDLDPNNVIIEQEERRR.SFQDYTGQ.ITLEAVLN.TCKKCGCKG
RetrocopyLIGREMKDDRIKVSLSMKVVDQGTVKDLDPNNVIIEQEERRRWSFQDYTGQRITLEAVLNATCKKCGCKG
ParentalHFAKDCFMQPGGTKYSLIPDEEEEKEEAKSAEFEKPDTTRNSSRKRKKEKKKKKHRDRKSSDSDSSDSES
HFAKDCFMQPGG.KYSLIPDEEEEKEE.KSAEFEKPDTTRNSSRKRKKEKKKKKHRDRKSSDSDSSDSES
RetrocopyHFAKDCFMQPGGAKYSLIPDEEEEKEEPKSAEFEKPDTTRNSSRKRKKEKKKKKHRDRKSSDSDSSDSES
ParentalDTGKRARHTSKDSKAAKKKKKKKKHKK
DTGKRARHTSKDSKAAKKKKKKKKHK.
RetrocopyDTGKRARHTSKDSKAAKKKKKKKKHKE

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
ERP005899_liver 0 .94 RPM 18 .74 RPM
ERP005899_muscle 0 .00 RPM 34 .21 RPM
SRP017611_brain 1 .42 RPM 49 .88 RPM
SRP017611_kidney 0 .30 RPM 17 .13 RPM
SRP017611_liver 0 .23 RPM 9 .44 RPM
SRP030211_testis 0 .31 RPM 58 .50 RPM

ChIP-Seq - click to see more details

Bos taurus was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_btau_168 retrocopy.

TSS - click to see more details

Bos taurus was not studied using FANTOM5 data.

Lab - click to see more details

retro_btau_168 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_btau_168 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 16 parental genes, and 19 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000177101 retrocopy
retro_amel_1501,
Bos taurus ENSBTAG00000016818 2 retrocopies
retro_btau_168 , retro_btau_273,
Canis familiaris ENSCAFG000000111312 retrocopies
retro_cfam_485, retro_cfam_835,
Callithrix jacchus ENSCJAG000000062591 retrocopy
retro_cjac_4218,
Dasypus novemcinctus ENSDNOG000000005091 retrocopy
retro_dnov_2548,
Dipodomys ordii ENSDORG000000041281 retrocopy
retro_dord_200,
Echinops telfairi ENSETEG000000074211 retrocopy
retro_etel_1280,
Loxodonta africana ENSLAFG000000153641 retrocopy
retro_lafr_534,
Myotis lucifugus ENSMLUG000000005941 retrocopy
retro_mluc_2176,
Monodelphis domestica ENSMODG000000170821 retrocopy
retro_mdom_252,
Mustela putorius furoENSMPUG000000154421 retrocopy
retro_mputfur_680,
Mus musculus ENSMUSG000000287721 retrocopy
retro_mmus_2150,
Otolemur garnettii ENSOGAG000000137491 retrocopy
retro_ogar_1225,
Sorex araneus ENSSARG000000079441 retrocopy
retro_sara_691,
Ictidomys tridecemlineatus ENSSTOG000000038251 retrocopy
retro_itri_405,
Tursiops truncatus ENSTTRG000000148702 retrocopies
retro_ttru_1383, retro_ttru_1613,


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