RetrogeneDB ID:

retro_btau_1403

Retrocopy
location
Organism:Cow (Bos taurus)
Coordinates:5:103703794..103704540(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:NDUFV2
Ensembl ID:ENSBTAG00000004871
Aliases:None
Description:NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial [Source:UniProtKB/Swiss-Prot;Acc:P04394]


Retrocopy-Parental alignment summary:






>retro_btau_1403
ATGTTCCTCTCCGCAGTGCTACAGGCCCGCGTGGCCGGCCTCGCCACCCACTGGGGAAAACATATAAGAAATCTGCATAA
GACAGCTGTTCAGAATGGAGCTGGAGGAGCCTTATTTGTGCACAGAGATACTCCTGGAATAACCCAGAAACTCCATTTGA
TTTCACACCAGAAAACTATAAGAGGATAGAGGCCGTTGTGAAAAACTAGCCAGAAGGGGATAAGGCAGCAGCTGTGCTTC
CAGTTCTGGATTTAGCCCAGAGACAGAATGGATGGCTGCCCATCTCTGCTATGAACAAGGTTGCAGAAATTTTACAAGTA
CCTCCAATGAGAGTGTATGAAGTAGCAACTTTTTACGCAATGTATAAGTGAAAGCCTGTTGGAAAGTATCACATTCAAGT
CCGCACTACCACACCTTGCATGCTCCAAAACTCCGACAGCATACTGGAAGCCATTCAGAAAAAACTTGGAATAAAGGTTG
GAGAGACTACACCTGACAAACTTTTCACTCTTATAGAAGTCGAATGTTTAGGGGCCTGTGTAAATGCACCAATGGTTCAA
ATAAATGACAACTACTATGAGGATCTGACACCTAAAGATATTGAAGAAATTATTGATGAACTGAAGGCTGGCAAAATCCC
AAAACCTGGGCCAAGGAGTGGACGCTTCTCCTGTGAGCCAGCTGGAGGTCTTACCTCTTTGACTGAACCACTAAAAGGAC
CTAGGTTTGGTGTGCAAGCAGGCCTT

ORF - retro_btau_1403 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 93.6 %
Parental protein coverage: 100. %
Number of stop codons detected: 2
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalMFLSAALRARAAGLAAHWGKHIRNLHKTAVQNGAGGALFVHRDTPE-NNPETPFDFTPENYKRIEAIVKN
MFLSA.L.AR.AGLA.HWGKHIRNLHKTAVQNGAGGALFVHRDTP..NNPETPFDFTPENYKRIEA.VKN
RetrocopyMFLSAVLQARVAGLATHWGKHIRNLHKTAVQNGAGGALFVHRDTPG<NNPETPFDFTPENYKRIEAVVKN
ParentalYPEGHKAAAVLPVLDLAQRQNGWLPISAMNKVAEILQVPPMRVYEVATFYTMYNRKPVGKYHIQVCTTTP
.PEG.KAAAVLPVLDLAQRQNGWLPISAMNKVAEILQVPPMRVYEVATFY.MY..KPVGKYHIQV.TTTP
Retrocopy*PEGDKAAAVLPVLDLAQRQNGWLPISAMNKVAEILQVPPMRVYEVATFYAMYK*KPVGKYHIQVRTTTP
ParentalCMLRNSDSILEAIQKKLGIKVGETTPDKLFTLIEVECLGACVNAPMVQINDNYYEDLTPKDIEEIIDELK
CML.NSDSILEAIQKKLGIKVGETTPDKLFTLIEVECLGACVNAPMVQINDNYYEDLTPKDIEEIIDELK
RetrocopyCMLQNSDSILEAIQKKLGIKVGETTPDKLFTLIEVECLGACVNAPMVQINDNYYEDLTPKDIEEIIDELK
ParentalAGKIPKPGPRSGRFSCEPAGGLTSLTEPPKGPGFGVQAGL
AGKIPKPGPRSGRFSCEPAGGLTSLTEP.KGP.FGVQAGL
RetrocopyAGKIPKPGPRSGRFSCEPAGGLTSLTEPLKGPRFGVQAGL

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 .14 RPM 45 .64 RPM
ERP005899_muscle 0 .11 RPM 73 .27 RPM
SRP017611_brain 0 .09 RPM 22 .84 RPM
SRP017611_kidney 0 .12 RPM 68 .10 RPM
SRP017611_liver 0 .08 RPM 23 .63 RPM
SRP030211_testis 0 .09 RPM 150 .68 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_1403 retrocopy.

TSS - click to see more details

Bos taurus was not studied using FANTOM5 data.

Lab - click to see more details

retro_btau_1403 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_btau_1403 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 21 parental genes, and 46 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000074151 retrocopy
retro_amel_810,
Bos taurus ENSBTAG00000004871 2 retrocopies
retro_btau_1403 , retro_btau_1831,
Choloepus hoffmanni ENSCHOG000000137141 retrocopy
retro_chof_1621,
Cavia porcellus ENSCPOG000000084794 retrocopies
retro_cpor_1500, retro_cpor_389, retro_cpor_401, retro_cpor_689,
Dasypus novemcinctus ENSDNOG000000170361 retrocopy
retro_dnov_254,
Dipodomys ordii ENSDORG000000081795 retrocopies
retro_dord_161, retro_dord_233, retro_dord_327, retro_dord_503, retro_dord_750,
Erinaceus europaeus ENSEEUG000000068181 retrocopy
retro_eeur_286,
Homo sapiens ENSG000001781271 retrocopy
retro_hsap_2068,
Loxodonta africana ENSLAFG000000105202 retrocopies
retro_lafr_133, retro_lafr_872,
Macaca mulatta ENSMMUG000000220951 retrocopy
retro_mmul_188,
Mustela putorius furoENSMPUG000000047102 retrocopies
retro_mputfur_1106, retro_mputfur_1623,
Oryctolagus cuniculus ENSOCUG000000098993 retrocopies
retro_ocun_1083, retro_ocun_1381, retro_ocun_678,
Otolemur garnettii ENSOGAG000000101182 retrocopies
retro_ogar_2531, retro_ogar_3030,
Ochotona princeps ENSOPRG000000127882 retrocopies
retro_opri_307, retro_opri_660,
Procavia capensis ENSPCAG000000062842 retrocopies
retro_pcap_109, retro_pcap_405,
Rattus norvegicus ENSRNOG000000425031 retrocopy
retro_rnor_2993,
Sorex araneus ENSSARG000000118762 retrocopies
retro_sara_543, retro_sara_625,
Sus scrofa ENSSSCG000000036831 retrocopy
retro_sscr_424,
Ictidomys tridecemlineatus ENSSTOG000000162591 retrocopy
retro_itri_1510,
Tupaia belangeri ENSTBEG000000154268 retrocopies
retro_tbel_1013, retro_tbel_1522, retro_tbel_2199, retro_tbel_2667, retro_tbel_3333, retro_tbel_3587, retro_tbel_455, retro_tbel_468,
Tursiops truncatus ENSTTRG000000024263 retrocopies
retro_ttru_1543, retro_ttru_435, retro_ttru_486,


Copyright © RetrogeneDB 2014-2017