RetrogeneDB ID:

retro_btau_1610

Retrocopy
location
Organism:Cow (Bos taurus)
Coordinates:8:47218210..47219470(+)
Located in intron of:ENSBTAG00000007778
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:RBBP4
Ensembl ID:ENSBTAG00000005904
Aliases:None
Description:Histone-binding protein RBBP4 [Source:UniProtKB/Swiss-Prot;Acc:Q3MHL3]


Retrocopy-Parental alignment summary:






>retro_btau_1610
ATGGCCAACAAGGAAGCACCTTTGATGATGCAGTAGAAGAATGTGTGATCAACGAAGAATATAAAATATGGAAAAAGAAC
ACCCCTTTTCTTTACAACTTGGTGATGATCCATGCTCTGGAGTGGCCTAGCCTAACTGCACAGTGGCTTCCAAATGTAAC
CAGACCAGAAGGGAAAGAATTCAGTATTCACCGACTCGTCCTGGGGACACACTTGTCAGATGAACAAAACCACCTTGTGA
CAGTCAGCGTGCAGCTCCCTAATGATGATGCTCAGTTTGATGCTTCACACTACAACAGTGAAAAAGGAGAATTTGGAGGT
TTTGGCTCAGTTAGTGGAAAAATTGAAATAGAAATCAAGATCAGCCATGAAGGAGAGGTAAACAGTGCATGCTATATGCC
CCAGAACCCTTGCATTATTGCAACAAAGAATCCATCCAGTGATGTTCTTGCTTTTGACTATTCAAAATATCCTGCTAAAC
CAGACCCTTCTGGAGAGTGCAACCCAGACTTGTGCCTCCGTGGACATCAGAAGGAAGGCTATGGGCTTTCTTGGAACCCA
AATCTCAGTGGGCACTTACTGAGTGCTTCAGATGACCACACCATCTGCCTGTGGGACATAAGTGCTGTTCCAAAGGAAGG
GAAAGTGTGGATGTGAAGACCATCTTTACAGAGCACACAGCAGTAGTAGAGGTTATCTCCTGGCATCTGCTCCATGAGTC
CCTCTTTGGGTCAGTTGCTGATGATCAGAAACTCATGATCTGGGATACTCCTTCAAACAGTACTTCCAAACCAAGCCACT
CAGTTGATGCTCACATTGCTGAAGTGAACTGCCTTTCTTTCAGTCCTTATAGTGAGCTCATTCTTGCCACAGATCAGCTG
ACAAAACTGTTGCCCTGTGGGATCTGAGAAATCTGAAACTTAAGTTGGATTCCTTTGAATCACATAAGGATGAAATAGTC
CAGGTTCAGTGGTCGCCTCACAATGAGACTATTTTGGCTTCCAATGGTATTGATCAAAGACTGAATGTCTGGGATGTAAG
TAAAATTGGAGAGGAACAATCCCCAGAAGATGGGCCACCAGAGTTGTTGTTTATTCATGGTGGTCACACTGCCAAGATGT
CTGATTTCTTCTAGACTCCCAATGAACCTCGGGTGATTTGTTCTATATCAGAAGACAATATCATGCAAGTGTGGCAAATG
GCAGAGAACATTTATAATGATGAAGACCCTGAAGGAAGCATGGGTCCAGAAGGACAAGGA

ORF - retro_btau_1610 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 88.29 %
Parental protein coverage: 99.76 %
Number of stop codons detected: 1
Number of frameshifts detected: 3


Retrocopy - Parental Gene Alignment:

ParentalMADKEA-AFDDAVEERVINEEYKIWKKNTPFLYDLVMTHALEWPSLTAQWLPDVTRPEGKDFSIHRLVLG
MA.KEA..FDDAVEE.VINEEYKIWKKNTPFLY.LVM.HALEWPSLTAQWLP.VTRPEGK.FSIHRLVLG
RetrocopyMANKEA<TFDDAVEECVINEEYKIWKKNTPFLYNLVMIHALEWPSLTAQWLPNVTRPEGKEFSIHRLVLG
ParentalTHTSDEQNHLVIASVQLPNDDAQFDASHYDSEKGEFGGFGSVSGKIEIEIKINHEGEVNRARYMPQNPCI
TH.SDEQNHLV..SVQLPNDDAQFDASHY.SEKGEFGGFGSVSGKIEIEIKI.HEGEVN.A.YMPQNPCI
RetrocopyTHLSDEQNHLVTVSVQLPNDDAQFDASHYNSEKGEFGGFGSVSGKIEIEIKISHEGEVNSACYMPQNPCI
ParentalIATKTPSSDVLVFDYTKHPSKPDPSGECNPDLRLRGHQKEGYGLSWNPNLSGHLLSASDDHTICLWDISA
IATK.PSSDVL.FDY.K.P.KPDPSGECNPDL.LRGHQKEGYGLSWNPNLSGHLLSASDDHTICLWDISA
RetrocopyIATKNPSSDVLAFDYSKYPAKPDPSGECNPDLCLRGHQKEGYGLSWNPNLSGHLLSASDDHTICLWDISA
ParentalVPKEGKV-VDAKTIFTGHTAVVEDVSWHLLHESLFGSVADDQKLMIWDTRSNNTSKPSHSVDAHTAEVNC
VPKEGKV.VD.KTIFT.HTAVVE..SWHLLHESLFGSVADDQKLMIWDT.SN.TSKPSHSVDAH.AEVNC
RetrocopyVPKEGKV<VDVKTIFTEHTAVVEVISWHLLHESLFGSVADDQKLMIWDTPSNSTSKPSHSVDAHIAEVNC
ParentalLSFNPYSEFILATG-SADKTVALWDLRNLKLKLHSFESHKDEIFQVQWSPHNETILASSGTDRRLNVWDL
LSF.PYSE.ILAT..SADKTVALWDLRNLKLKL.SFESHKDEI.QVQWSPHNETILAS.G.D.RLNVWD.
RetrocopyLSFSPYSELILATD<SADKTVALWDLRNLKLKLDSFESHKDEIVQVQWSPHNETILASNGIDQRLNVWDV
ParentalSKIGEEQSPEDAEDGPPELLFIHGGHTAKISDFSWNPNEPWVICSVSEDNIMQVWQMAENIYNDEDPEGS
SKIGEEQSPED...GPPELLFIHGGHTAK.SDF...PNEP.VICS.SEDNIMQVWQMAENIYNDEDPEGS
RetrocopySKIGEEQSPED---GPPELLFIHGGHTAKMSDFF*TPNEPRVICSISEDNIMQVWQMAENIYNDEDPEGS
ParentalVDPEGQG
..PEGQG
RetrocopyMGPEGQG

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 77 .36 RPM
ERP005899_muscle 0 .00 RPM 96 .97 RPM
SRP017611_brain 0 .00 RPM 90 .45 RPM
SRP017611_kidney 0 .06 RPM 118 .01 RPM
SRP017611_liver 0 .08 RPM 62 .67 RPM
SRP030211_testis 0 .20 RPM 368 .11 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_1610 retrocopy.

TSS - click to see more details

Bos taurus was not studied using FANTOM5 data.

Lab - click to see more details

retro_btau_1610 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_btau_1610 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 22 parental genes, and 56 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000028201 retrocopy
retro_btau_1579,
Bos taurus ENSBTAG00000005904 2 retrocopies
retro_btau_1610 , retro_btau_630,
Canis familiaris ENSCAFG000000105271 retrocopy
retro_cfam_1550,
Choloepus hoffmanni ENSCHOG000000040666 retrocopies
retro_chof_1382, retro_chof_1649, retro_chof_1867, retro_chof_2116, retro_chof_2327, retro_chof_908,
Callithrix jacchus ENSCJAG000000010217 retrocopies
retro_cjac_1157, retro_cjac_1787, retro_cjac_1873, retro_cjac_244, retro_cjac_2557, retro_cjac_2719, retro_cjac_2939,
Cavia porcellus ENSCPOG000000153523 retrocopies
retro_cpor_154, retro_cpor_27, retro_cpor_899,
Equus caballus ENSECAG000000227841 retrocopy
retro_ecab_767,
Echinops telfairi ENSETEG000000200084 retrocopies
retro_etel_1088, retro_etel_1462, retro_etel_1877, retro_etel_676,
Felis catus ENSFCAG000000270171 retrocopy
retro_fcat_1507,
Homo sapiens ENSG000001625216 retrocopies
retro_hsap_1305, retro_hsap_2675, retro_hsap_2814, retro_hsap_3292, retro_hsap_3600, retro_hsap_3601,
Macropus eugenii ENSMEUG000000143791 retrocopy
retro_meug_1032,
Myotis lucifugus ENSMLUG000000007492 retrocopies
retro_mluc_2275, retro_mluc_892,
Macaca mulatta ENSMMUG000000099401 retrocopy
retro_mmul_75,
Mustela putorius furoENSMPUG000000152141 retrocopy
retro_mputfur_104,
Mus musculus ENSMUSG000000572361 retrocopy
retro_mmus_356,
Nomascus leucogenys ENSNLEG000000028056 retrocopies
retro_nleu_1061, retro_nleu_1179, retro_nleu_1194, retro_nleu_1356, retro_nleu_1379, retro_nleu_2982,
Petromyzon marinus ENSPMAG000000071891 retrocopy
retro_pmar_26,
Pongo abelii ENSPPYG000000015886 retrocopies
retro_pabe_1093, retro_pabe_2210, retro_pabe_2720, retro_pabe_2958, retro_pabe_3529, retro_pabe_3611,
Pteropus vampyrus ENSPVAG000000109812 retrocopies
retro_pvam_1094, retro_pvam_902,
Rattus norvegicus ENSRNOG000000214921 retrocopy
retro_rnor_1270,
Sarcophilus harrisii ENSSHAG000000109231 retrocopy
retro_shar_399,
Ictidomys tridecemlineatus ENSSTOG000000120111 retrocopy
retro_itri_1168,


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