RetrogeneDB ID: retro_btau_1264

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 3:27978007..27978841(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSBTAG00000027923
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: ATP5B
• Ensembl ID: ENSBTAG00000013315
• Aliases: None
• Description: ATP synthase subunit beta, mitochondrial [Source:UniProtKB/Swiss-Prot;Acc:P00829]

Sequence

>retro_btau_1264
CTGCTGGGACTCAAGGGTTGTGTGGCTGCTACCTGGGCCTCAGGGTCCTTTTGGGGATTCAGCCCTTCAGCACGGCTACC
ACAAGCCCAGCTCTTTCTGAGGATCACCTCAGTAGTGCTCCAGGCTGCCAGAGACTATGCTGACCAAACACTTCCATTGC
CAAAGGCATGTGCCACCACTGGGCAATGGTGGCTGTCATTGGTGCAGTGGTAGATGTCCAATTTGGTGAGGAGCTGCCAC
CCATCCTAAATGCCCTGGAAGTGCAAGGCAGGGAGACCAAGCTGGTTTTGGAGATGGCCCAGTCTTTGAGTGAGAGAACA
ATAAGGACCATTGCCATGGATGGTATGGAAAGCATGGTTAGAGGCCAGAATGTCCTGGATTCTGGTACATCAATCAAAAT
TCCTGTTGGCCCTGAGACCTTGGGTAGATTTGTGAATGTCACTGGAGAATCTTTGATGACCGGGGTCCCATAAAAACCAA
ACAATTTGTAGCTATTCGTGCTGAAGCTCCTGAATTCATAGAGATGAGTGTTGAGCAGCAAATTCTGGTTACTGGTATAA
AGATTGTGGATCTGCTGGCTCCCTATGCCAAAGGTGGCAAAATTGAGCACTTTGTTGGTGCTGGAATTGGCAAGACAGTA
CTTATCATAGTGTTAATCAACAATGTTGTTAAGCCTGTGGTGGGTACTCTGTGTTTGCTGGTGTTGGTGAGAGGATGCAA
GAGGATAATGACTTCTACCATGAAATGACTGAGTCTGGTGATGCCAACTTAAAAAATTCTACCTCCAAGGTAGCACTGAT
ATGTGATCAAATGAATGAACTGCCTGGTGCTCGA

Alignment

ORF - retro_btau_1264 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.4 %
• Parental protein coverage: 52.84 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MLGLVGRVVAASASGALRGLSPSAPLPQAQLLLRAAPAALQPARDYAAQASPSPKAGATTGR-IVAVIGA
          .LGL.G.V.A..ASG...G.SPSA.LPQAQL.LR.....LQ.ARDYA.Q..P.PKA.ATTG...VAVIGA
Retrocopy LLGLKGCVAATWASGSFWGFSPSARLPQAQLFLRITSVVLQAARDYADQTLPLPKACATTGQ<MVAVIGA

Parental  VVDVQFDEGLPPILNALEVQGRETRLVLEVAQHLGESTVRTIAMDGTEGLVRGQKVLDSGAPIRIPVGPE
          VVDVQF.E.LPPILNALEVQGRET.LVLE.AQ.L.E.T.RTIAMDG.E..VRGQ.VLDSG..I.IPVGPE
Retrocopy VVDVQFGEELPPILNALEVQGRETKLVLEMAQSLSERTIRTIAMDGMESMVRGQNVLDSGTSIKIPVGPE

Parental  TLGRIMNVIGEPI-DERGPIKTKQFAAIHAEAPEFVEMSVEQEILVTGIKVVDLLAPYAKGGKIGLFGGA
          TLGR..NV.GE...D.RGPIKTKQF.AI.AEAPEF.EMSVEQ.ILVTGIK.VDLLAPYAKGGKI..F.GA
Retrocopy TLGRFVNVTGESL<DDRGPIKTKQFVAIRAEAPEFIEMSVEQQILVTGIKIVDLLAPYAKGGKIEHFVGA

Parental  GVGKTVLIMELINNVAK-AHGGYSVFAGVGERTREGNDLYHEMIESGVINLKDATSKVALVYGQMNEPPG
          G.GKTVLI..LINNV.K.A.GGYSVFAGVGER..E.ND.YHEM.ESG..NLK..TSKVAL...QMNE.PG
Retrocopy GIGKTVLIIVLINNVVK<ACGGYSVFAGVGERMQEDNDFYHEMTESGDANLKNSTSKVALICDQMNELPG

Parental  AR
          AR
Retrocopy AR

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	212.11 RPM
ERP005899_muscle	0.00 RPM	863.05 RPM
SRP017611_brain	0.00 RPM	424.41 RPM
SRP017611_kidney	0.00 RPM	1353.35 RPM
SRP017611_liver	0.00 RPM	289.73 RPM
SRP030211_testis	0.00 RPM	249.61 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1264 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1264 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1264 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 17 parental genes, and 25 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000016752	1 retrocopy	retro_acar_181,
Bos taurus	ENSBTAG00000013315	1 retrocopy	retro_btau_1264 ,
Choloepus hoffmanni	ENSCHOG00000005350	1 retrocopy	retro_chof_1544,
Callithrix jacchus	ENSCJAG00000033571	2 retrocopies	retro_cjac_1488, retro_cjac_928,
Dasypus novemcinctus	ENSDNOG00000011289	1 retrocopy	retro_dnov_361,
Echinops telfairi	ENSETEG00000010208	1 retrocopy	retro_etel_2162,
Homo sapiens	ENSG00000110955	1 retrocopy	retro_hsap_2128,
Gorilla gorilla	ENSGGOG00000011596	1 retrocopy	retro_ggor_1648,
Macropus eugenii	ENSMEUG00000002875	6 retrocopies	retro_meug_1416, retro_meug_1608, retro_meug_411, retro_meug_430, retro_meug_685, retro_meug_908,
Microcebus murinus	ENSMICG00000001084	1 retrocopy	retro_mmur_495,
Macaca mulatta	ENSMMUG00000001027	1 retrocopy	retro_mmul_103,
Pongo abelii	ENSPPYG00000004668	2 retrocopies	retro_pabe_1921, retro_pabe_2032,
Pan troglodytes	ENSPTRG00000005107	1 retrocopy	retro_ptro_1557,
Sus scrofa	ENSSSCG00000000405	1 retrocopy	retro_sscr_453,
Tarsius syrichta	ENSTSYG00000009962	1 retrocopy	retro_tsyr_644,
Tursiops truncatus	ENSTTRG00000002144	1 retrocopy	retro_ttru_371,
Vicugna pacos	ENSVPAG00000004025	2 retrocopies	retro_vpac_405, retro_vpac_562,