RetrogeneDB ID: retro_btau_1506

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 6:98971201..98971548(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ATP5G1
• Ensembl ID: ENSBTAG00000018339
• Aliases: None
• Description: ATP synthase lipid-binding protein, mitochondrial [Source:UniProtKB/Swiss-Prot;Acc:P32876]

Sequence

>retro_btau_1506
ATCTACTCTTGTCCCAAGGGTCTGATCAGGCTTGTGTCTGCCTCCTTCCTGAGGAAGCCAGCGGTCCCATCTGAACAGCC
TTCCTACAGCAGTGTCCCACTCTAGGAGGCTAGGCGGGAGTCCCAGACCAGTGCTGATATTGACACAGCAGCCAAGTTTA
TTGGCGCTGGGGCTGCCACAGTTGGTGTGGCTGGTTCAGGAGCCAGCATTGGAACAGTCTTTGGCAGCTTGATCGCTGAC
TATGCCAGGAACCCGTCCCTGAAGCAGCGACTCTTCCCTGTGCCGTTCTGGGCTTTGCCGTGGCTGAGGCTAGGAGGCTC
TTCTGTCTGATGGCCCCCTTCCTCATC

Alignment

ORF - retro_btau_1506 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.33 %
• Parental protein coverage: 87.5 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  IRSCTRGLIRPVSASFLSRPEIQSVQPSYSSGPLQVARREFQTSVVSRDIDTAAKFIGAGAATVGVAGSG
          I.SC..GLIR.VSASFL..P...S.QPSYSS.PL..ARRE.QTS....DIDTAAKFIGAGAATVGVAGSG
Retrocopy IYSCPKGLIRLVSASFLRKPAVPSEQPSYSSVPL*EARRESQTSA---DIDTAAKFIGAGAATVGVAGSG

Parental  AGIGTVFGSLIIGYARNPSLKQQLFSY-AILGFALSEAMGLFCLMVAFLI
          A.IGTVFGSLI..YARNPSLKQ.LF...A.LGFA..EA..LFCLM..FLI
Retrocopy ASIGTVFGSLIADYARNPSLKQRLFPV<AVLGFAVAEARRLFCLMAPFLI

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	31.65 RPM
ERP005899_muscle	0.00 RPM	148.50 RPM
SRP017611_brain	0.00 RPM	42.66 RPM
SRP017611_kidney	0.06 RPM	160.21 RPM
SRP017611_liver	0.00 RPM	63.13 RPM
SRP030211_testis	0.03 RPM	22.09 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1506 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1506 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1506 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 41 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000006341	1 retrocopy	retro_acar_9,
Bos taurus	ENSBTAG00000002944	1 retrocopy	retro_btau_838,
Bos taurus	ENSBTAG00000005735	11 retrocopies	retro_btau_1405, retro_btau_1414, retro_btau_733, retro_btau_734, retro_btau_735, retro_btau_737, retro_btau_739, retro_btau_740, retro_btau_741, retro_btau_742, retro_btau_994,
Bos taurus	ENSBTAG00000018339	3 retrocopies	retro_btau_1506 , retro_btau_423, retro_btau_431,
Callithrix jacchus	ENSCJAG00000007352	7 retrocopies	retro_cjac_1190, retro_cjac_1549, retro_cjac_161, retro_cjac_1878, retro_cjac_289, retro_cjac_4060, retro_cjac_679,
Cavia porcellus	ENSCPOG00000009017	2 retrocopies	retro_cpor_43, retro_cpor_550,
Macropus eugenii	ENSMEUG00000005744	2 retrocopies	retro_meug_1650, retro_meug_1973,
Macaca mulatta	ENSMMUG00000013395	1 retrocopy	retro_mmul_173,
Oryctolagus cuniculus	ENSOCUG00000016225	2 retrocopies	retro_ocun_346, retro_ocun_375,
Otolemur garnettii	ENSOGAG00000011713	3 retrocopies	retro_ogar_1847, retro_ogar_2767, retro_ogar_531,
Rattus norvegicus	ENSRNOG00000007235	5 retrocopies	retro_rnor_1342, retro_rnor_2240, retro_rnor_529, retro_rnor_64, retro_rnor_880,
Sus scrofa	ENSSSCG00000017544	1 retrocopy	retro_sscr_348,
Tursiops truncatus	ENSTTRG00000008526	1 retrocopy	retro_ttru_279,
Vicugna pacos	ENSVPAG00000007653	1 retrocopy	retro_vpac_282,