RetrogeneDB ID: retro_btau_1222

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 3:42266720..42266928(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: ATP5I
• Ensembl ID: ENSBTAG00000017496
• Aliases: None
• Description: ATP synthase subunit e, mitochondrial [Source:UniProtKB/Swiss-Prot;Acc:Q00361]

Sequence

>retro_btau_1222
ATGGTGCTGCCAACGCATGTCTCTCCCTCATCAAGCTCGGCCACTACTCTGCTCTGTTCCTGGGCTTGACCTATGAAGCC
AAGTCTACAATTACCTGAAACACTGGGCAGGAGAGGAGAGGGTAGCAGCTGAGGAGAAAGAGAAGCAGGGTGAGCTGAAA
CGCATTCAGAGAGAATTGGCAGAAACCCAAGAGGACTGCATATTAAAG

Alignment

ORF - retro_btau_1222 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.86 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MVPPVQVSP-LIKLGRYSALFLGMAYGAKR-YNYLKPRAEEERRLAAEEKKKRDEQKRIERELAEAQEDT
          MV.P..VSP.LIKLG.YSALFLG..Y.AK..YNYLK..A.EE.R.AAEEK.K..E.KRI.RELAE.QED.
Retrocopy MVLPTHVSP<LIKLGHYSALFLGLTYEAKS<YNYLKHWAGEE-RVAAEEKEKQGELKRIQRELAETQEDC

Parental  ILK
          ILK
Retrocopy ILK

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	9.73 RPM
ERP005899_muscle	0.00 RPM	126.48 RPM
SRP017611_brain	0.00 RPM	27.77 RPM
SRP017611_kidney	0.00 RPM	55.30 RPM
SRP017611_liver	0.00 RPM	28.77 RPM
SRP030211_testis	0.00 RPM	53.90 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1222 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1222 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1222 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016722	2 retrocopies	retro_amel_1171, retro_amel_1761,
Bos taurus	ENSBTAG00000017496	2 retrocopies	retro_btau_1222 , retro_btau_219,
Canis familiaris	ENSCAFG00000023527	1 retrocopy	retro_cfam_62,
Callithrix jacchus	ENSCJAG00000001989	1 retrocopy	retro_cjac_352,
Cavia porcellus	ENSCPOG00000008678	1 retrocopy	retro_cpor_98,
Felis catus	ENSFCAG00000029708	1 retrocopy	retro_fcat_268,
Mustela putorius furo	ENSMPUG00000011414	1 retrocopy	retro_mputfur_494,
Mus musculus	ENSMUSG00000050856	1 retrocopy	retro_mmus_3152,
Otolemur garnettii	ENSOGAG00000012271	1 retrocopy	retro_ogar_1292,
Rattus norvegicus	ENSRNOG00000000064	1 retrocopy	retro_rnor_697,
Tursiops truncatus	ENSTTRG00000002962	1 retrocopy	retro_ttru_1938,