RetrogeneDB ID: retro_btau_1557

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 7:12196307..12196839(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PLA2G12A
• Ensembl ID: ENSBTAG00000015230
• Aliases: None
• Description: group XIIA secretory phospholipase A2 precursor [Source:RefSeq peptide;Acc:NP_001091532]

Sequence

>retro_btau_1557
CTCCTCATCCCTCTCCTGACCACAGCTTTCAGGTGCCAGGAGCAGGCCCAGGCTACTGACTGGAGGGCTACCTTGCAGAC
TAACTAGAAGGGAATTCACAAGACAGACAAACGTCTGAACGCCATCTTGAACTTCCTGGGAGGTGAGCACCAGCTTTCCA
AGTATAAATGAGGGGATGGATCTAAGCCTTTCCCGTGTTATGATGATAAATCCTCCCCGCGAAATGGGTTTGGCTCTTCA
CTGTTTGGTGTCCATCTGAATATTAGCTTTCCTTCCCGGACAAAGTGCTGCAGCCAATGTGGCAGGTGCTATGGGATTTG
TGGCAAAATTAAAAAGGACTGTGATGAGGAGTACCAGTATTTTTCCTTCAAGATCTGTTGAGATGTGCAGACAACACTGG
GACCAACTCAGCATGTGAATGAAACCACAGTTGACCTCTTCACTGTCAGTGTTATACATTTAGGCTGCAAAGCATACCTG
GATAGCCAAGGAGCCTCCATGTAGCTCTCCATACAAAAGAAAAAAAGATCTT

Alignment

ORF - retro_btau_1557 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.22 %
• Parental protein coverage: 96.76 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LLVLFLTAGGRCQEQAQTTDWRATLKTIRNGVHKIDMYLNAALDLLGGEDGLCQYKCSDGSKPFPRYGYK
          LL...LT...RCQEQAQ.TDWRATL.T...G.HK.D..LNA.L..LGGE..L..YK..DGSKPFP.Y..K
Retrocopy LLIPLLTTAFRCQEQAQATDWRATLQTN*KGIHKTDKRLNAILNFLGGEHQLSKYK*GDGSKPFPCYDDK

Parental  PSPPNGCGSPLFGVHLNIGIPSLTKCCNQHDRCYETCGKSKNDCDEAFQSCLSKICRDVQKTLGLAQHVQ
          .SP.NG.GS.LFGVHLNI..PS.TKCC.Q..RCY..CGK.K.DCDE..Q....KIC.DVQ.TLG..QHV.
Retrocopy SSPRNGFGSSLFGVHLNISFPSRTKCCSQCGRCYGICGKIKKDCDEEYQYFSFKIC*DVQTTLGPTQHVN

Parental  ACETTVELLFDSVIHLGCKPYLDSQRAA-CRCRYEEKTDL
          ..ETTV.L...SVIHLGCK.YLDSQ.A..C...Y..K.DL
Retrocopy --ETTVDLFTVSVIHLGCKAYLDSQGAS>CSSPYKRKKDL

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	87.24 RPM
ERP005899_muscle	0.00 RPM	33.89 RPM
SRP017611_brain	0.00 RPM	25.90 RPM
SRP017611_kidney	0.00 RPM	34.44 RPM
SRP017611_liver	0.00 RPM	78.08 RPM
SRP030211_testis	0.00 RPM	19.49 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1557 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1557 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1557 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 29 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000015230	1 retrocopy	retro_btau_1557 ,
Callithrix jacchus	ENSCJAG00000016169	2 retrocopies	retro_cjac_1992, retro_cjac_3936,
Dasypus novemcinctus	ENSDNOG00000016573	7 retrocopies	retro_dnov_1694, retro_dnov_172, retro_dnov_1856, retro_dnov_1930, retro_dnov_2286, retro_dnov_2572, retro_dnov_434,
Homo sapiens	ENSG00000123739	1 retrocopy	retro_hsap_153,
Gorilla gorilla	ENSGGOG00000001082	2 retrocopies	retro_ggor_242, retro_ggor_929,
Loxodonta africana	ENSLAFG00000000852	2 retrocopies	retro_lafr_402, retro_lafr_718,
Mustela putorius furo	ENSMPUG00000008637	1 retrocopy	retro_mputfur_964,
Mus musculus	ENSMUSG00000027999	1 retrocopy	retro_mmus_2368,
Otolemur garnettii	ENSOGAG00000004686	1 retrocopy	retro_ogar_670,
Ochotona princeps	ENSOPRG00000014505	2 retrocopies	retro_opri_30, retro_opri_921,
Pan troglodytes	ENSPTRG00000016362	1 retrocopy	retro_ptro_817,
Sus scrofa	ENSSSCG00000009139	3 retrocopies	retro_sscr_622, retro_sscr_623, retro_sscr_670,
Tarsius syrichta	ENSTSYG00000004756	4 retrocopies	retro_tsyr_1366, retro_tsyr_376, retro_tsyr_487, retro_tsyr_493,
Vicugna pacos	ENSVPAG00000009842	1 retrocopy	retro_vpac_466,