RetrogeneDB ID:

retro_btau_258

Retrocopy
location
Organism:Cow (Bos taurus)
Coordinates:1:55264824..55266045(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:EIF4A2
Ensembl ID:ENSBTAG00000014724
Aliases:None
Description:Eukaryotic initiation factor 4A-II [Source:UniProtKB/Swiss-Prot;Acc:Q3SZ65]


Retrocopy-Parental alignment summary:






>retro_btau_258
ATGTCTGGTGGCTCTGCGGATTATAACAGAGAACATGGCGGCCCTGAGGGAATGGACCCCGATGGTGTCATCAAGAGCAA
CTGGAATGAGATTGTTGATAACTTTGATGATATAAACTTAAAGGAGTCTCTTCTTCGGGGCATCTATGCTTATGGTTTTG
AGAAGCCATCAGCTATTCAGCAGAGAGCTATTAGTCCATGTATTAAAGGGTATGATGTGATTGCTCAAGCTGAGTTAGGT
ACTGGCAAGACAGCCGCATTTGCTATTTCCATCCTGCAACAGTTGGAGATTGAGTTCAAGGAGACCCAAGCACTAGTACT
GGCCCCCACCAGAGAACTGGCTCAACAGATCCAAAAGGTAATTCTGGCACTTGGAGATTATATGGGAGCAACTTGTCATG
CCTGCATTGGTGGAACAAATGTTCGAAATGAAATGCAAAAACTGCAGGCTGAAGCACCACATATTGTTGTTGGAACACCA
GGGAGAGTGTTTGATATGTTAAACAGAAGATATCTCTCTCCAAAATGGATCAAAATGTTCGTTTTGGATGAAGCAGATGA
AATGCTGAGCCGAGGGTTTAAGGATCAAATCTATGAGATTTTCCAAAAATTAAATACTAGTATTCAGGTGGTGTTGCTTT
CTGCCATAATGCCAACGGATGTGTTGGAAGTGACCAAAAAATTCATGAGAGATCCAATTCGAATTTTGGTGAAAAAGGAA
GAATTGACCCTTGAAGGAATTAAACAGTTTTATATTAATGTTGAAAGAGAGGAATGGAAGTTGGATACACTTTGTGACTT
GTATGAGACACTGACAATTACACAGGCTGTTATTTTTCTCAATACAAGGCGCAAGGTGGACTGGCTCACAGAGAAAATGC
ATGCCAGGGACTTCACAGTTTCTGCCCTGCATGATGACATCGACCAGAAAGAAAGAGATGTTATCATGAGGGAATTTTGA
TCAGGGTCAAGCTGTGTTCTGATCACTACTGACTTGTTGGCTCGTGGAATTGATGTGCAACAAGGGTCATTGGTTATAAA
CTATGATCTACCTACCAATAGTGAAAATTATATTCACACAATTGGCAGAGGGGGTCGATTTGGGAGGAAAGGTGTGGCTA
TAAACTTTGTTACTGAAGAAGACAAGAGGATTCTTCTTGACATTGAGACTTTCTATAATACTACAGTGGAGAAAATGCCA
ATGAATGTGGCCGACCTTATT

ORF - retro_btau_258 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 96.07 %
Parental protein coverage: 100. %
Number of stop codons detected: 1
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMSGGSADYNREHGGPEGMDPDGVIESNWNEIVDNFDDMNLKESLLRGIYAYGFEKPSAIQQRAIIPCIKG
MSGGSADYNREHGGPEGMDPDGVI.SNWNEIVDNFDD.NLKESLLRGIYAYGFEKPSAIQQRAI.PCIKG
RetrocopyMSGGSADYNREHGGPEGMDPDGVIKSNWNEIVDNFDDINLKESLLRGIYAYGFEKPSAIQQRAISPCIKG
ParentalYDVIAQAQSGTGKTATFAISILQQLEIEFKETQALVLAPTRELAQQIQKVILALGDYMGATCHACIGGTN
YDVIAQA..GTGKTA.FAISILQQLEIEFKETQALVLAPTRELAQQIQKVILALGDYMGATCHACIGGTN
RetrocopyYDVIAQAELGTGKTAAFAISILQQLEIEFKETQALVLAPTRELAQQIQKVILALGDYMGATCHACIGGTN
ParentalVRNEMQKLQAEAPHIVVGTPGRVFDMLNRRYLSPKWIKMFVLDEADEMLSRGFKDQIYEIFQKLNTSIQV
VRNEMQKLQAEAPHIVVGTPGRVFDMLNRRYLSPKWIKMFVLDEADEMLSRGFKDQIYEIFQKLNTSIQV
RetrocopyVRNEMQKLQAEAPHIVVGTPGRVFDMLNRRYLSPKWIKMFVLDEADEMLSRGFKDQIYEIFQKLNTSIQV
ParentalVLLSATMPTDVLEVTKKFMRDPIRILVKKEELTLEGIKQFYINVEREEWKLDTLCDLYETLTITQAVIFL
VLLSA.MPTDVLEVTKKFMRDPIRILVKKEELTLEGIKQFYINVEREEWKLDTLCDLYETLTITQAVIFL
RetrocopyVLLSAIMPTDVLEVTKKFMRDPIRILVKKEELTLEGIKQFYINVEREEWKLDTLCDLYETLTITQAVIFL
ParentalNTRRKVDWLTEKMHARDFTVSALHGDMDQKERDVIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDL
NTRRKVDWLTEKMHARDFTVSALH.D.DQKERDVIMREF.SGSS.VLITTDLLARGIDVQQ.SLVINYDL
RetrocopyNTRRKVDWLTEKMHARDFTVSALHDDIDQKERDVIMREF*SGSSCVLITTDLLARGIDVQQGSLVINYDL
ParentalPTNRENYIHRIGRGGRFGRKGVAINFVTEEDKRILRDIETFYNTTVEEMPMNVADLI
PTN.ENYIH.IGRGGRFGRKGVAINFVTEEDKRIL.DIETFYNTTVE.MPMNVADLI
RetrocopyPTNSENYIHTIGRGGRFGRKGVAINFVTEEDKRILLDIETFYNTTVEKMPMNVADLI

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 .00 RPM 180 .60 RPM
ERP005899_muscle 0 .48 RPM 260 .83 RPM
SRP017611_brain 0 .46 RPM 287 .78 RPM
SRP017611_kidney 0 .36 RPM 227 .01 RPM
SRP017611_liver 0 .08 RPM 105 .94 RPM
SRP030211_testis 0 .22 RPM 125 .70 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_258 retrocopy.

TSS - click to see more details

Bos taurus was not studied using FANTOM5 data.

Lab - click to see more details

retro_btau_258 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_btau_258 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 22 parental genes, and 50 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000001321 retrocopy
retro_btau_1207,
Bos taurus ENSBTAG00000014724 2 retrocopies
retro_btau_258 , retro_btau_522,
Canis familiaris ENSCAFG000000136591 retrocopy
retro_cfam_378,
Cavia porcellus ENSCPOG000000111831 retrocopy
retro_cpor_639,
Dasypus novemcinctus ENSDNOG000000115025 retrocopies
retro_dnov_1264, retro_dnov_2018, retro_dnov_2066, retro_dnov_648, retro_dnov_869,
Echinops telfairi ENSETEG000000185653 retrocopies
retro_etel_1174, retro_etel_2164, retro_etel_451,
Homo sapiens ENSG000001569762 retrocopies
retro_hsap_593, retro_hsap_878,
Gorilla gorilla ENSGGOG000000058672 retrocopies
retro_ggor_525, retro_ggor_712,
Macropus eugenii ENSMEUG000000117371 retrocopy
retro_meug_237,
Microcebus murinus ENSMICG000000073771 retrocopy
retro_mmur_525,
Macaca mulatta ENSMMUG000000037022 retrocopies
retro_mmul_1055, retro_mmul_2450,
Nomascus leucogenys ENSNLEG000000066331 retrocopy
retro_nleu_2589,
Oryctolagus cuniculus ENSOCUG000000050113 retrocopies
retro_ocun_392, retro_ocun_696, retro_ocun_763,
Otolemur garnettii ENSOGAG000000107292 retrocopies
retro_ogar_2830, retro_ogar_943,
Ochotona princeps ENSOPRG000000041701 retrocopy
retro_opri_498,
Pongo abelii ENSPPYG000000143842 retrocopies
retro_pabe_596, retro_pabe_677,
Pan troglodytes ENSPTRG000000157181 retrocopy
retro_ptro_437,
Rattus norvegicus ENSRNOG000000018152 retrocopies
retro_rnor_1163, retro_rnor_2340,
Ictidomys tridecemlineatus ENSSTOG000000126011 retrocopy
retro_itri_858,
Tupaia belangeri ENSTBEG0000000226811 retrocopies
retro_tbel_114, retro_tbel_1488, retro_tbel_1500, retro_tbel_2048, retro_tbel_2524, retro_tbel_2729, retro_tbel_2733, retro_tbel_3159, retro_tbel_3793, retro_tbel_4599, retro_tbel_841,
Takifugu rubripes ENSTRUG000000056602 retrocopies
retro_trub_14, retro_trub_6,
Tarsius syrichta ENSTSYG000000130503 retrocopies
retro_tsyr_1905, retro_tsyr_903, retro_tsyr_935,


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