RetrogeneDB ID: retro_btau_889

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 2:112637713..112638362(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PSMA2
• Ensembl ID: ENSBTAG00000000990
• Aliases: None
• Description: Proteasome subunit alpha type-2 [Source:UniProtKB/Swiss-Prot;Acc:Q3T0Y5]

Sequence

>retro_btau_889
ATCCACTTTGAATACCGTTTGGCTGCTGTAGCTGGAGGAATCCCTTCAGTGAAAACTATAGCTGCAAATGGTATAGTATC
AGCAACCGAGAAGAAACAGAAATCCATTCTGTAGGATGAGTGTCAAGAACACAGTGTGGAAGCAATGACCGAGCACTGAG
GTTTGATGTGCGGTGGCATGAGCTCACATCGCTGAGTGCTGGTGCAAAGAGTTGGGAAACCAGCTCAGCCACACTGTCTT
GTTTCCCGAGAACCCACTGTCACAACTCTGCTGGTACAGAGCATAACTTCTGTGATTCAAGGATACACTCAGCCAGGTGG
TGTTCCTTCACTTGGAGGGTTTTCTTTTTTTTTTGGTTGGAATGATGAGGGACGATCATATTTATTTCAGTCACATCCAT
CTAGGCCTTACTTTGCCTGGAAAGTCACATCAATGGGAAAGAACTATGTAACTGGGAAAACTTCTCCTTAAGAAAATATG
TAAACAAGATCTGTAACTTGAAGATGCCACCCGTACAGCCAAATTAACCCTAAAGGAAAGCTTGGAAGGGCAGAGGAGAA
AAGATTACATAGCAGCAGGAATCTGCAGTGAAGCCAGCCTTCCCAGTCTTACACCAGCTAAAGTTAAGAATTAGTTGGCT
GCCATAGCA

Alignment

ORF - retro_btau_889 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.53 %
• Parental protein coverage: 91.88 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VQIEYALAAVAGGAPSVGIKAANGVVLATEKKQKSILYDERSVHKVEPITKHIGLVYSGMGPDYRVLVHR
          ...EY.LAAVAGG.PSV...AANG.V.ATEKKQKSIL.DE...H.VE..T.H.GL...GM.....VLV.R
Retrocopy IHFEYRLAAVAGGIPSVKTIAANGIVSATEKKQKSIL*DECQEHSVEAMTEH*GLMCGGMSSHR*VLVQR

Parental  ARKLAQQYYLVYQEPIPTAQLVQRVASVMQEYTQSGGVRPFGVSLLICGWN-EGRPYLFQSDPSGAYFAW
          ..K.AQ...LV..EP..T..LVQ...SV.Q.YTQ.GGV...G......GWN.EGR.YLFQS.PS..YFAW
Retrocopy VGKPAQPHCLVSREPTVTTLLVQSITSVIQGYTQPGGVPSLGGXXXXXGWNDEGRSYLFQSHPSRPYFAW

Parental  KATAMGKNYVNGKT-FLEKRYNEDLELEDAIHTAILTLKESFEGQMTEDNIEVGICNEAGFRRLTPTEVK
          K.T.MGKNYV.GKT..L.K....DL.LEDA..TA.LTLKES.EGQ...D.I..GIC.EA....LTP..VK
Retrocopy KVTSMGKNYVTGKT>LLKKICKQDL*LEDATRTAKLTLKESLEGQRRKDYIAAGICSEASLPSLTPAKVK

Parental  DYLAAIA
          ..LAAIA
Retrocopy N*LAAIA

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	41.02 RPM
ERP005899_muscle	0.00 RPM	53.32 RPM
SRP017611_brain	0.00 RPM	19.14 RPM
SRP017611_kidney	0.00 RPM	36.93 RPM
SRP017611_liver	0.00 RPM	43.64 RPM
SRP030211_testis	0.00 RPM	38.38 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_889 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_889 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_889 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Sus scrofa	retro_sscr_1082

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Parental genes homology:

Parental genes homology involve 24 parental genes, and 46 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000009433	3 retrocopies	retro_amel_1029, retro_amel_1336, retro_amel_1379,
Bos taurus	ENSBTAG00000000990	3 retrocopies	retro_btau_296, retro_btau_384, retro_btau_889 ,
Choloepus hoffmanni	ENSCHOG00000000644	1 retrocopy	retro_chof_893,
Callithrix jacchus	ENSCJAG00000007730	4 retrocopies	retro_cjac_1096, retro_cjac_1868, retro_cjac_2583, retro_cjac_852,
Cavia porcellus	ENSCPOG00000013134	1 retrocopy	retro_cpor_1512,
Dasypus novemcinctus	ENSDNOG00000011910	2 retrocopies	retro_dnov_2202, retro_dnov_724,
Echinops telfairi	ENSETEG00000015835	2 retrocopies	retro_etel_1569, retro_etel_2022,
Homo sapiens	ENSG00000106588	2 retrocopies	retro_hsap_2199, retro_hsap_908,
Gorilla gorilla	ENSGGOG00000006538	1 retrocopy	retro_ggor_735,
Myotis lucifugus	ENSMLUG00000010086	2 retrocopies	retro_mluc_1050, retro_mluc_135,
Macaca mulatta	ENSMMUG00000022451	2 retrocopies	retro_mmul_1114, retro_mmul_923,
Mustela putorius furo	ENSMPUG00000018145	1 retrocopy	retro_mputfur_548,
Mus musculus	ENSMUSG00000015671	4 retrocopies	retro_mmus_1104, retro_mmus_1105, retro_mmus_1215, retro_mmus_1320,
Nomascus leucogenys	ENSNLEG00000003177	1 retrocopy	retro_nleu_329,
Oryctolagus cuniculus	ENSOCUG00000012092	1 retrocopy	retro_ocun_774,
Otolemur garnettii	ENSOGAG00000016805	1 retrocopy	retro_ogar_197,
Ochotona princeps	ENSOPRG00000011793	2 retrocopies	retro_opri_135, retro_opri_791,
Pongo abelii	ENSPPYG00000017612	2 retrocopies	retro_pabe_2076, retro_pabe_783,
Pan troglodytes	ENSPTRG00000019120	2 retrocopies	retro_ptro_1670, retro_ptro_628,
Rattus norvegicus	ENSRNOG00000049920	2 retrocopies	retro_rnor_2041, retro_rnor_2769,
Sus scrofa	ENSSSCG00000020769	3 retrocopies	retro_sscr_1082, retro_sscr_419, retro_sscr_440,
Ictidomys tridecemlineatus	ENSSTOG00000013334	1 retrocopy	retro_itri_223,
Tarsius syrichta	ENSTSYG00000014299	2 retrocopies	retro_tsyr_132, retro_tsyr_246,
Tursiops truncatus	ENSTTRG00000005649	1 retrocopy	retro_ttru_356,