RetrogeneDB ID:

retro_btau_1287

Retrocopy
location
Organism:Cow (Bos taurus)
Coordinates:3:80749506..80750066(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:CYB5R3
Ensembl ID:ENSBTAG00000016516
Aliases:None
Description:NADH-cytochrome b5 reductase 3 [Source:RefSeq peptide;Acc:NP_001096720]


Retrocopy-Parental alignment summary:






>retro_btau_1287
AGCACTGCGCCCTAGCCATTTGAAATCCCAGATATCAAGTACTCACTGTGGCTTATTGATGAGGAGATTATCAGCCATAA
CACCAGTGGTTCTACTTCAACCTGCTATATCCCCATCACATCTTGGACCCCCTCATAAGTCATCACATCTAATTTTCAGT
TCAAATCCACCACAACCTAATCACTCAGCCCTACAGCATTTCCAGGCATGATGAAGGGGCTTGATGGGCCCAGTGATCAA
GGTTTACTTCAAAGATACCCATCCCATGTTTCCTATTGGAAGATGTTCCAGTACCTGGAAAACATGAAGACTGGAGACAT
CATTGAGTTTCAGCGCCCAATCTGGCTGCTAGCCTACCAGGGCAAAGAAAAGTTTGCCCTCTGTCCAGACCAGAAATTCA
AGCTCATTATCAAGAGGTGAAGTCTATTCATATGATCATGAGAGGAACAAGCATCACTTTGATGCTATGGGTGATCCACG
CCATCATGAGGGACCTGGATGACCACCCTGTGTGCCAACTGCTCTTTGCTGGTCAGAAAAAGAAGGACATTTTGTTGCAG

ORF - retro_btau_1287 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 50.52 %
Parental protein coverage: 62.91 %
Number of stop codons detected: 3
Number of frameshifts detected 4


Retrocopy - Parental Gene Alignment:

ParentalSTPAITLENPDIKYPLRLIDKEVISHDT-RRFRFALPSPEHILGLPVGQHIYLSARIDGNLVIRPYTPVS
ST.....E.PDIKY.L.LID.E.ISH.T...F.F.L..P.HIL......HI..S..I..NL...PY...S
RetrocopySTAP*PFEIPDIKYSLWLIDEEIISHNT<QWFYFNLLYPHHILDPLISHHI*FSVQIHHNLITQPYS-IS
ParentalSDDD-KGFVDLVIKVYFKDTHPKFPAGGKMSQYLESMKIGDTIEFRGPNG-LLVYQGKGKFAIRPDKKSD
..D...G....VIKVYFKDTHP.FP..G..S.............F....G.LL.YQGK.KFA..PD.K..
RetrocopyRHDE<RGLMGPVIKVYFKDTHPMFPI-GRCSSTWKT*RLETSLSFSAQSG<LLAYQGKEKFALCPDQKFK
ParentalPVIK-TVKSVGMIAGGTGITPMLQVIRAIMKDPDDHTVCHLLFANQTEKDILLR
..IK..VKS..MI..GT.IT.ML.VI.AIM.D.DDH.VC.LLFA.Q..KDILL.
RetrocopyLIIK<EVKSIHMIMRGTSITLMLWVIHAIMRDLDDHPVCQLLFAGQKKKDILLQ

Legend:
*Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide






(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 103 .89 RPM
ERP005899_muscle 0 .05 RPM 193 .16 RPM
SRP017611_brain 0 .00 RPM 102 .69 RPM
SRP017611_kidney 0 .00 RPM 247 .28 RPM
SRP017611_liver 0 .08 RPM 183 .41 RPM
SRP030211_testis 0 .39 RPM 96 .75 RPM
Bos taurus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_btau_1287 retrocopy.
Bos taurus was not studied using FANTOM5 data.
retro_btau_1287 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_btau_1287 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 4 parental genes, and 6 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000095491 retrocopy
Bos taurus ENSBTAG00000016516 2 retrocopies
retro_btau_1244, retro_btau_1287 ,
Pteropus vampyrus ENSPVAG000000141261 retrocopy
Tursiops truncatus ENSTTRG000000151432 retrocopies



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