RetrogeneDB ID: retro_btau_810

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 2:14600499..14600748(+)
• Located in intron of: ENSBTAG00000044009

Retrocopy information

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

Parental gene information

• Parental gene symbol: PLP2
• Ensembl ID: ENSBTAG00000016093
• Aliases: None
• Description: Proteolipid protein 2 [Source:UniProtKB/Swiss-Prot;Acc:Q6Y1E2]

Sequence

>retro_btau_810
ACTGACTTCTCACTCACCAGAAAGGGATTTCTCCTGTTTGCTGAGAATATATTGTGCCTGGTGATTCTGATCTGCTTTCG
TGCCTCGACAGCAGGGTACTCCTTTTCAGTGACAGAGATGATCTTTGCCACTATCTTTGTTGTCTACATGTGTGACCTGC
ACACCAAGATACAGATCATCAACCAGCCTTGGAGTGATTGCTTCTGAACCCTTGTAGTGATCATCCTCTACCTGATCACC
TCCATTGTG

Alignment

ORF - retro_btau_810 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.35 %
• Parental protein coverage: 55.92 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  TSFSRTRKGFLLFAEIILCLVILICFSTSTSGYSFLSVIEMIFAAIFFVVYMCDLHTKIQIINWPWSDFF
          T.FS.TRKGFLLFAE.ILCLVILICF..ST.GYSF.SV.EMIFA.I.FVVYMCDLHTKIQIIN.PWSD.F
Retrocopy TDFSLTRKGFLLFAENILCLVILICFRASTAGYSF-SVTEMIFATI-FVVYMCDLHTKIQIINQPWSDCF

Parental  RTLVAAILYLITSIV
          .TLV..ILYLITSIV
Retrocopy *TLVVIILYLITSIV

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	2.52 RPM
ERP005899_muscle	0.00 RPM	59.60 RPM
SRP017611_brain	0.00 RPM	5.71 RPM
SRP017611_kidney	0.00 RPM	21.52 RPM
SRP017611_liver	0.00 RPM	2.27 RPM
SRP030211_testis	0.01 RPM	3.71 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_810 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_810 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_810 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 23 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000012288	1 retrocopy	retro_amel_1129,
Bos taurus	ENSBTAG00000016093	3 retrocopies	retro_btau_1574, retro_btau_73, retro_btau_810 ,
Bos taurus	ENSBTAG00000047654	1 retrocopy	retro_btau_1771,
Canis familiaris	ENSCAFG00000015798	1 retrocopy	retro_cfam_933,
Felis catus	ENSFCAG00000003820	2 retrocopies	retro_fcat_1547, retro_fcat_256,
Homo sapiens	ENSG00000102007	1 retrocopy	retro_hsap_3411,
Loxodonta africana	ENSLAFG00000004483	1 retrocopy	retro_lafr_427,
Macaca mulatta	ENSMMUG00000023022	1 retrocopy	retro_mmul_2124,
Mustela putorius furo	ENSMPUG00000013817	3 retrocopies	retro_mputfur_107, retro_mputfur_462, retro_mputfur_969,
Mus musculus	ENSMUSG00000031146	1 retrocopy	retro_mmus_94,
Nomascus leucogenys	ENSNLEG00000001317	1 retrocopy	retro_nleu_2887,
Otolemur garnettii	ENSOGAG00000003865	3 retrocopies	retro_ogar_2568, retro_ogar_2865, retro_ogar_473,
Pan troglodytes	ENSPTRG00000021885	1 retrocopy	retro_ptro_2316,
Rattus norvegicus	ENSRNOG00000039496	1 retrocopy	retro_rnor_2686,
Tursiops truncatus	ENSTTRG00000016968	2 retrocopies	retro_ttru_1586, retro_ttru_767,