RetrogeneDB ID:

retro_btau_1

Retrocopy
location
Organism:Cow (Bos taurus)
Coordinates:2:72356581..72357634(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSBTAG00000026829
Aliases:TMEM185B, FAM11B
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:TMEM185A
Ensembl ID:ENSBTAG00000006818
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_btau_1
ATGAACCCCAGGGGCCTATTCCAGGACTTCAACCCGAGTAAGTTCCTCATCTACGCTTGCCTGCTGCTCTTCTCAGTGCT
GCTGCCCCTCCGACTGGACGGCGTCATCCAATGGAGCTACTGGGCCGTGTTCGCCCCCATCTGGTTGTGGAAGCTTCTGG
TCCTCGCGGGCGCCTCTGTTGGCGCGGGCGTTTGGGCGCGAAACCCGCGCTACCGCACAGAGGGAGAGGCCTGTGTGGAG
TTCAAGGCCATGCTGATCGCCGTGGGCATCCACCTGCTGCTGCTCATGTTCGAGGTCCTGGTCTGCGATCGGGTGGAGCG
CGGGACCCACTTCTGGCTGCTGGTCTTCATGCCGCTCTTCTTTGTGTCGCCCGTGTCCGTGGCCGCCTGCGTTTGGGGCT
TCCGACACGACCGGTCCCTGGAGCTGGAGATCCTGTGCTCCGTCAACATCCTGCAATTCATCTTCATCGCCCTGAGGCTG
GACCGGATCATCCACTGGCCTTGGCTGGTGGTGTTTGTGCCACTGTGGATCCTCATGTCATTCCTTTGCCTGGTAGTCCT
CTATTACATCGTTTGGTCCCTCCTGTTCCTGCGCTCCCTGGATGTGGTTGCTGAGCAGCGAAGAACCCACGTGACCATGG
CCATCTGCTGGATAACGATCGTGGTGCCGCTGCTCATTTTCGAGGTTCTGCTGGTGCACAGGCTGGATGGACACAACATG
TTTTCCTACATCTCCATATTCGTCCCCCTTTGGCTCTCATTAATCACATTAATGGCCACAACGTTTAGGCGAAAAGGGGG
CAACCATTGGTGGTTTGGTATTCGCAGAGATTTCTGTCAGTTTCTGCTTGAAATTTTCCCATTTTTAAGAGAATATGGAA
ACATTTCCTATGATCTACATCATGAAGATAGTGAAGATGCTGAAGAAACATCGGCTCCAGAAGCTCCTAAAATCGCTCCA
ATGTTTGGAAAGAAGGCCAGGGTGGTGATAACACAGAGCCCTGGGAAATATGTCCCCCCACCCCCCAAGTTAAATATTGA
CATGCCTGATTAA

ORF - retro_btau_1 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 87.54 %
Parental protein coverage: 98.57 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalLFVIFSPSKFLIYACLLLFSVLLALRLDGIIQWSYWAVFAPIWLWKLMVIVGASVGTGVWARNPQYRAEG
LF..F.PSKFLIYACLLLFSVLL.LRLDG.IQWSYWAVFAPIWLWKL.V..GASVG.GVWARNP.YR.EG
RetrocopyLFQDFNPSKFLIYACLLLFSVLLPLRLDGVIQWSYWAVFAPIWLWKLLVLAGASVGAGVWARNPRYRTEG
ParentalETCVEFKAMLIAVGIHLLLLMFEVLVCDRIERGSHFWLLVFMPLFFVSPVSVAACVWGFRHDRSLELEIL
E.CVEFKAMLIAVGIHLLLLMFEVLVCDR.ERG.HFWLLVFMPLFFVSPVSVAACVWGFRHDRSLELEIL
RetrocopyEACVEFKAMLIAVGIHLLLLMFEVLVCDRVERGTHFWLLVFMPLFFVSPVSVAACVWGFRHDRSLELEIL
ParentalCSVNILQFIFIALRLDKIIHWPWLVVCVPLWILMSFLCLVVLYYIVWSVLFLRSMDVIAEQRRTHITMAL
CSVNILQFIFIALRLD.IIHWPWLVV.VPLWILMSFLCLVVLYYIVWS.LFLRS.DV.AEQRRTH.TMA.
RetrocopyCSVNILQFIFIALRLDRIIHWPWLVVFVPLWILMSFLCLVVLYYIVWSLLFLRSLDVVAEQRRTHVTMAI
ParentalSWMTIVVPLLTFEILLVHKLDGHNAFSCIPIFVPLWLSLITLMATTFGQKGGNHWWFGIRKDFCQFLLEI
.W.TIVVPLL.FE.LLVH.LDGHN.FS.I.IFVPLWLSLITLMATTF..KGGNHWWFGIR.DFCQFLLEI
RetrocopyCWITIVVPLLIFEVLLVHRLDGHNMFSYISIFVPLWLSLITLMATTFRRKGGNHWWFGIRRDFCQFLLEI
ParentalCPFLREYGNISYDLHHEGSEETEETPVPEPPKIAPMFRKKTRVVITQSPGKYVLPPPKLNIEMPD
.PFLREYGNISYDLHHE.SE..EET..PE.PKIAPMF.KK.RVVITQSPGKYV.PPPKLNI.MPD
RetrocopyFPFLREYGNISYDLHHEDSEDAEETSAPEAPKIAPMFGKKARVVITQSPGKYVPPPPKLNIDMPD

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 1 .37 RPM 6 .42 RPM
ERP005899_muscle 9 .03 RPM 10 .19 RPM
SRP017611_brain 11 .65 RPM 18 .00 RPM
SRP017611_kidney 8 .77 RPM 15 .88 RPM
SRP017611_liver 4 .23 RPM 12 .91 RPM
SRP030211_testis 14 .67 RPM 6 .41 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_1 retrocopy.

TSS - click to see more details

Bos taurus was not studied using FANTOM5 data.

Lab - click to see more details

retro_btau_1 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_btau_1 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Sus scrofa retro_sscr_494
Equus caballus retro_ecab_426
Parental genes homology:
Parental genes homology involve 22 parental genes, and 22 retrocopies.

Species Parental gene accession Retrocopies number
Anolis carolinensis ENSACAG000000086371 retrocopy
retro_acar_65,
Ailuropoda melanoleuca ENSAMEG000000093511 retrocopy
retro_amel_8,
Bos taurus ENSBTAG00000006818 1 retrocopy
retro_btau_1 ,
Canis familiaris ENSCAFG000000191031 retrocopy
retro_cfam_159,
Dasypus novemcinctus ENSDNOG000000118641 retrocopy
retro_dnov_2451,
Dipodomys ordii ENSDORG000000150271 retrocopy
retro_dord_67,
Equus caballus ENSECAG000000093991 retrocopy
retro_ecab_426,
Felis catus ENSFCAG000000244831 retrocopy
retro_fcat_1116,
Homo sapiens ENSG000001559841 retrocopy
retro_hsap_104,
Gorilla gorilla ENSGGOG000000242681 retrocopy
retro_ggor_189,
Loxodonta africana ENSLAFG000000030441 retrocopy
retro_lafr_898,
Microcebus murinus ENSMICG000000046391 retrocopy
retro_mmur_106,
Macaca mulatta ENSMMUG000000028881 retrocopy
retro_mmul_310,
Mustela putorius furoENSMPUG000000118961 retrocopy
retro_mputfur_46,
Mus musculus ENSMUSG000000731391 retrocopy
retro_mmus_358,
Nomascus leucogenys ENSNLEG000000134871 retrocopy
retro_nleu_2723,
Otolemur garnettii ENSOGAG000000164141 retrocopy
retro_ogar_88,
Procavia capensis ENSPCAG000000091601 retrocopy
retro_pcap_260,
Pongo abelii ENSPPYG000000208091 retrocopy
retro_pabe_118,
Pteropus vampyrus ENSPVAG000000138221 retrocopy
retro_pvam_30,
Rattus norvegicus ENSRNOG000000110471 retrocopy
retro_rnor_6,
Tursiops truncatus ENSTTRG000000006431 retrocopy
retro_ttru_868,


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