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 symbol: CYB5R3
• Ensembl ID: ENSBTAG00000016516
• Aliases: None
• Description: NADH-cytochrome b5 reductase 3 [Source:RefSeq peptide;Acc:NP_001096720]

Sequence

>retro_btau_1287
AGCACTGCGCCCTAGCCATTTGAAATCCCAGATATCAAGTACTCACTGTGGCTTATTGATGAGGAGATTATCAGCCATAA
CACCAGTGGTTCTACTTCAACCTGCTATATCCCCATCACATCTTGGACCCCCTCATAAGTCATCACATCTAATTTTCAGT
TCAAATCCACCACAACCTAATCACTCAGCCCTACAGCATTTCCAGGCATGATGAAGGGGCTTGATGGGCCCAGTGATCAA
GGTTTACTTCAAAGATACCCATCCCATGTTTCCTATTGGAAGATGTTCCAGTACCTGGAAAACATGAAGACTGGAGACAT
CATTGAGTTTCAGCGCCCAATCTGGCTGCTAGCCTACCAGGGCAAAGAAAAGTTTGCCCTCTGTCCAGACCAGAAATTCA
AGCTCATTATCAAGAGGTGAAGTCTATTCATATGATCATGAGAGGAACAAGCATCACTTTGATGCTATGGGTGATCCACG
CCATCATGAGGGACCTGGATGACCACCCTGTGTGCCAACTGCTCTTTGCTGGTCAGAAAAAGAAGGACATTTTGTTGCAG

Alignment

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:

Parental  STPAITLENPDIKYPLRLIDKEVISHDT-RRFRFALPSPEHILGLPVGQHIYLSARIDGNLVIRPYTPVS
          ST.....E.PDIKY.L.LID.E.ISH.T...F.F.L..P.HIL......HI..S..I..NL...PY...S
Retrocopy STAP*PFEIPDIKYSLWLIDEEIISHNT<QWFYFNLLYPHHILDPLISHHI*FSVQIHHNLITQPYS-IS

Parental  SDDD-KGFVDLVIKVYFKDTHPKFPAGGKMSQYLESMKIGDTIEFRGPNG-LLVYQGKGKFAIRPDKKSD
          ..D...G....VIKVYFKDTHP.FP..G..S.............F....G.LL.YQGK.KFA..PD.K..
Retrocopy RHDE<RGLMGPVIKVYFKDTHPMFPI-GRCSSTWKT*RLETSLSFSAQSG<LLAYQGKEKFALCPDQKFK

Parental  PVIK-TVKSVGMIAGGTGITPMLQVIRAIMKDPDDHTVCHLLFANQTEKDILLR
          ..IK..VKS..MI..GT.IT.ML.VI.AIM.D.DDH.VC.LLFA.Q..KDILL.
Retrocopy LIIK<EVKSIHMIMRGTSITLMLWVIHAIMRDLDDHPVCQLLFAGQKKKDILLQ

Legend:

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

Expression

RNA-Seq

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

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1287 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1287 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1287 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000009549	1 retrocopy	retro_amel_1305,
Bos taurus	ENSBTAG00000016516	2 retrocopies	retro_btau_1244, retro_btau_1287 ,
Pteropus vampyrus	ENSPVAG00000014126	1 retrocopy	retro_pvam_310,
Tursiops truncatus	ENSTTRG00000015143	2 retrocopies	retro_ttru_408, retro_ttru_918,