RetrogeneDB ID: retro_btau_777

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 19:3185954..3186398(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: BT.52802
• Ensembl ID: ENSBTAG00000000205
• Aliases: None
• Description: monocyte to macrophage differentiation protein [Source:RefSeq peptide;Acc:NP_001069069]

Sequence

>retro_btau_777
AGGTTTCAGAATCGATTCCAGCAGTTCATGAATCACTGGGCCCAGCCAAAGGCCGCTACAAGCCAACAGGTTACAAACAT
GCTGCTAACTGTTACACACATGCATTCCTCATTGCTCCGGCCATTGTGGGCAGTACCCTCCTTCACCAGCTATCTGATGA
CTGCTGGGAAAAGATAACAACTTGGATTTATGGAATGGACCTCTGTGCCTTCTTCATCATTTCCACAGATTTCACATCAT
GTCATGGAAAAAGTAGCACCGTTAAGGACAGTAAAGCATTGCTTTTACATGTATTATAGAATGGTTATCTATTTCTTCAT
TGCTGCATCTTACACTCCATGGGTAAATCTCCATGCACTTGGATCCCTGGCATCTCATATGCATTGGTTTATTTGGCTCA
TGGCAGCTGGAGGAACCATTTATGTATTTCTCTACCATGAAAAA

Alignment

ORF - retro_btau_777 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.67 %
• Parental protein coverage: 62.18 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  RFQICFYRFMNHRA-PANGRYKPTCYEHAANCYTHAFLIVPAIVGSALLHRLSDDCWEKITAWIYGMGLC
          RFQ..F..FMNH.A.PA.GRYKPT.Y.HAANCYTHAFLI.PAIVGS.LLH.LSDDCWEKIT.WIYGM.LC
Retrocopy RFQNRFQQFMNHWA<PAKGRYKPTGYKHAANCYTHAFLIAPAIVGSTLLHQLSDDCWEKITTWIYGMDLC

Parental  ALFIVSTVF-HIVAWKKSHLRTVEHWFHMCDRMVIYFFIAASYAPWLNLRELGPLASHMRWFIWLMAAGG
          A.FI.ST.F.H.V..K...LRTV.H.F.M..RMVIYFFIAASY.PW.NL..LG.LASHM.WFIWLMAAGG
Retrocopy AFFIISTDF>HHVMEKVAPLRTVKHCFYMYYRMVIYFFIAASYTPWVNLHALGSLASHMHWFIWLMAAGG

Parental  TIYVFLYHEK
          TIYVFLYHEK
Retrocopy TIYVFLYHEK

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	3.39 RPM
ERP005899_muscle	0.00 RPM	8.92 RPM
SRP017611_brain	0.00 RPM	64.77 RPM
SRP017611_kidney	0.00 RPM	11.91 RPM
SRP017611_liver	0.00 RPM	2.34 RPM
SRP030211_testis	0.00 RPM	29.36 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_777 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_777 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_777 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000000205	1 retrocopy	retro_btau_777 ,
Choloepus hoffmanni	ENSCHOG00000013437	1 retrocopy	retro_chof_1814,
Dasypus novemcinctus	ENSDNOG00000017248	1 retrocopy	retro_dnov_2313,
Macropus eugenii	ENSMEUG00000007054	1 retrocopy	retro_meug_714,
Myotis lucifugus	ENSMLUG00000012876	1 retrocopy	retro_mluc_289,
Monodelphis domestica	ENSMODG00000014847	5 retrocopies	retro_mdom_1029, retro_mdom_1569, retro_mdom_1591, retro_mdom_670, retro_mdom_951,
Oryctolagus cuniculus	ENSOCUG00000010549	1 retrocopy	retro_ocun_222,
Otolemur garnettii	ENSOGAG00000005902	2 retrocopies	retro_ogar_3070, retro_ogar_3071,
Procavia capensis	ENSPCAG00000004969	1 retrocopy	retro_pcap_231,
Ictidomys tridecemlineatus	ENSSTOG00000016227	1 retrocopy	retro_itri_913,
Tursiops truncatus	ENSTTRG00000007915	1 retrocopy	retro_ttru_469,