RetrogeneDB ID: retro_btau_1244

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 3:107670232..107670968(+)
• Located in intron of: ENSBTAG00000008023

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_1244
CTGGGCCACAGGGTCCTGTCCCCAGTCTGGCTCCTGTGCAGCCTCCTCGGGAAGCTGTTTCAGCGCTCCACCCCGGCCAT
CATGCTCCAGAGTTGGGACATCAAGTACCCGCTGTGGCTCATCAACAAGAAGGTCATCAGCCAGGATACCCGGCGGTTCT
GCTTTGCTCTGCCGTCACCCCAGCACATCCTGGGCCTCCCCGTTGGCCAGCACATCTACCTCTCTGCTTGAATCAATAGG
AACCTGGTCCTTTGGCCCTACACGCGTGTTTCCAGTGATGATGACCAGGGCTTTGTGGACCTGGTCGTCAAGGTTTACTT
TAAAGACACCCATCCCACATTTCCCTCTGGAGGAAAGATGCCCCAGTACGTGGAAAGCACAAAGACTGGAGACACCATTT
GAGTGCTGGGGCTCCAATGGGCTGCTGGTCTACCAGGGCAAAGTGAAGTTTGCCATCTCTCTGGACAAGAAATCCAACCC
GGTCTTCAAGACGCTGAAGTCTGTGGGCATGATTGCTGGAGGGACCGGCACCACTTCAATGCTGCAGGTGATCCATGCCA
TCATGAAGGACCCCAGCGATCGCACCGTGTGTCACCTGCTGCTTGCCAACCAGACCGAGAAGGACATCGTGCTGCAGCCT
GAGCTGGAGAAACTGAGGAATGAGCATTCTGCATGCTTCAAGCTCTGGTACACGGTGGACAGAGCCCCTGAAGCCTAGAA
ATACAGCCAGGGCTTC

Alignment

ORF - retro_btau_1244 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.86 %
• Parental protein coverage: 81.13 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LGHVVLSPVWFLYSLIMKLFQRSTPAITLENPDIKYPLRLIDKEVISHDTRRFRFALPSPEHILGLPVGQ
          LGH.VLSPVW.L.SL..KLFQRSTPAI.L...DIKYPL.LI.K.VIS.DTRRF.FALPSP.HILGLPVGQ
Retrocopy LGHRVLSPVWLLCSLLGKLFQRSTPAIMLQSWDIKYPLWLINKKVISQDTRRFCFALPSPQHILGLPVGQ

Parental  HIYLSARIDGNLVIRPYTPVSSDDDKGFVDLVIKVYFKDTHPKFPAGGKMSQYLESMKIGDTI-EFRGPN
          HIYLSA.I..NLV..PYT.VSSDDD.GFVDLV.KVYFKDTHP.FP.GGKM.QY.ES.K.GDTI.E..G.N
Retrocopy HIYLSA*INRNLVLWPYTRVSSDDDQGFVDLVVKVYFKDTHPTFPSGGKMPQYVESTKTGDTI>ECWGSN

Parental  GLLVYQGKGKFAIRPDKKSDPVIKTVKSVGMIAGGTGITPMLQVIRAIMKDPDDHTVCHLLFANQTEKDI
          GLLVYQGK.KFAI..DKKS.PV.KT.KSVGMIAGGTG.T.MLQVI.AIMKDP.D.TVCHLL.ANQTEKDI
Retrocopy GLLVYQGKVKFAISLDKKSNPVFKTLKSVGMIAGGTGTTSMLQVIHAIMKDPSDRTVCHLLLANQTEKDI

Parental  LLRPELEELRNEHSARFKLWYTVDKAPEAWDYSQGF
          .L.PELE.LRNEHSA.FKLWYTVD.APEA..YSQGF
Retrocopy VLQPELEKLRNEHSACFKLWYTVDRAPEA*KYSQGF

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	0.48 RPM	193.16 RPM
SRP017611_brain	0.46 RPM	102.69 RPM
SRP017611_kidney	0.00 RPM	247.28 RPM
SRP017611_liver	0.00 RPM	183.41 RPM
SRP030211_testis	0.48 RPM	96.75 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1244 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1244 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1244 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,