RetrogeneDB ID: retro_btau_1325

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 4:84662875..84663548(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSBTAG00000031464
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PRDX6
• Ensembl ID: ENSBTAG00000004855
• Aliases: PRDX6, AOP2
• Description: Peroxiredoxin-6 [Source:UniProtKB/Swiss-Prot;Acc:O77834]

Sequence

>retro_btau_1325
ATGCTGGGAGATCTCCTCCTCGGGGACGAGGCTCCCAACTTCGAGGCAAATACTCCCATCGGCCGCATCCGTTTCCACGA
CTATCTGGGAGACTCATGGGGCATTCTCTCCTCCCATCCTCGGGACTTTACCACTGTGTGCACCACGGAGCTCGGCAGAG
CAGCAAAGCTGGCACCAGAATTTGCCAAGAGAAATGTTATGATGATTGCTCTTTCCATAGACAGTGTGGAAGACCATCTT
GCATGGAGCAAGGATATCAATGCTTACAATGGTGAAGGGCCCACAGAAAAGTTACCTTTTCCCATCATTGATGATAAGAA
TCGGGACCTTGCCATCCAGTTGGGCATGCTGGACCCAGCAGAGAAAGACAAAAAGGACATGCCTGAGACTTCTCGTGTGG
TGTTTATTTTTGGTCCTGATAAGAAACTGAAACTGTCCATCCTCTACCCAGCTACCACTGGGCAGGAACTTTGATGAGAT
TCTCAGAGTAATTATCTCTCTCCAGCTGACGGCAGAAAAGAGGGTGGCCACCCCGGTTGACTGGAAGAATGGGGACAGCG
TGATGGTCCTTCCAACCGTCCCTGAAGAGGAAGCCAAAAAACTTTTCCCTAAAGGAGTCTTCACCAAAGAGCTCCCATCT
GGCAAGAAATACCTCCGCTACACACCCCAGCCA

Alignment

ORF - retro_btau_1325 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.22 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MPGGLLLGDEAPNFEANTTIGRIRFHDYLGDSWGILFSHPRDFTPVCTTELGRAAKLAPEFAKRNVKMIA
          M.G.LLLGDEAPNFEANT.IGRIRFHDYLGDSWGIL.SHPRDFT.VCTTELGRAAKLAPEFAKRNV.MIA
Retrocopy MLGDLLLGDEAPNFEANTPIGRIRFHDYLGDSWGILSSHPRDFTTVCTTELGRAAKLAPEFAKRNVMMIA

Parental  LSIDSVEDHLAWSKDINAYNGEEPTEKLPFPIIDDKNRDLAIQLGMLDPAEKDEKGMPVTARVVFIFGPD
          LSIDSVEDHLAWSKDINAYNGE.PTEKLPFPIIDDKNRDLAIQLGMLDPAEKD.K.MP.T.RVVFIFGPD
Retrocopy LSIDSVEDHLAWSKDINAYNGEGPTEKLPFPIIDDKNRDLAIQLGMLDPAEKDKKDMPETSRVVFIFGPD

Parental  KKLKLSILYPATT-GRNFDEILRVIISLQLTAEKRVATPVDWKNGDSVMVLPTIPEEEAKKLFPKGVFTK
          KKLKLSILYPATT.GRNFDEILRVIISLQLTAEKRVATPVDWKNGDSVMVLPT.PEEEAKKLFPKGVFTK
Retrocopy KKLKLSILYPATT>GRNFDEILRVIISLQLTAEKRVATPVDWKNGDSVMVLPTVPEEEAKKLFPKGVFTK

Parental  ELPSGKKYLRYTPQP
          ELPSGKKYLRYTPQP
Retrocopy ELPSGKKYLRYTPQP

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	204.75 RPM
ERP005899_muscle	0.21 RPM	332.47 RPM
SRP017611_brain	0.05 RPM	118.17 RPM
SRP017611_kidney	0.24 RPM	378.92 RPM
SRP017611_liver	0.00 RPM	100.28 RPM
SRP030211_testis	0.09 RPM	55.44 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1325 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1325 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1325 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 21 parental genes, and 40 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000015560	1 retrocopy	retro_amel_493,
Bos taurus	ENSBTAG00000004855	2 retrocopies	retro_btau_1325 , retro_btau_1477,
Canis familiaris	ENSCAFG00000014579	1 retrocopy	retro_cfam_492,
Choloepus hoffmanni	ENSCHOG00000011367	6 retrocopies	retro_chof_1143, retro_chof_1361, retro_chof_1364, retro_chof_225, retro_chof_2483, retro_chof_2598,
Callithrix jacchus	ENSCJAG00000009355	6 retrocopies	retro_cjac_1903, retro_cjac_2188, retro_cjac_3008, retro_cjac_3239, retro_cjac_3830, retro_cjac_4000,
Cavia porcellus	ENSCPOG00000011091	1 retrocopy	retro_cpor_623,
Equus caballus	ENSECAG00000022468	1 retrocopy	retro_ecab_215,
Erinaceus europaeus	ENSEEUG00000004040	1 retrocopy	retro_eeur_475,
Homo sapiens	ENSG00000117592	2 retrocopies	retro_hsap_1046, retro_hsap_3017,
Gorilla gorilla	ENSGGOG00000026357	1 retrocopy	retro_ggor_2086,
Macaca mulatta	ENSMMUG00000008776	1 retrocopy	retro_mmul_1928,
Monodelphis domestica	ENSMODG00000004032	2 retrocopies	retro_mdom_462, retro_mdom_661,
Mustela putorius furo	ENSMPUG00000004648	1 retrocopy	retro_mputfur_1328,
Mus musculus	ENSMUSG00000026701	2 retrocopies	retro_mmus_181, retro_mmus_2334,
Nomascus leucogenys	ENSNLEG00000015278	2 retrocopies	retro_nleu_2244, retro_nleu_917,
Pan troglodytes	ENSPTRG00000042455	1 retrocopy	retro_ptro_70,
Pteropus vampyrus	ENSPVAG00000002596	2 retrocopies	retro_pvam_1389, retro_pvam_805,
Rattus norvegicus	ENSRNOG00000002896	3 retrocopies	retro_rnor_2084, retro_rnor_754, retro_rnor_806,
Sarcophilus harrisii	ENSSHAG00000003248	1 retrocopy	retro_shar_478,
Tarsius syrichta	ENSTSYG00000010073	2 retrocopies	retro_tsyr_1395, retro_tsyr_193,
Tursiops truncatus	ENSTTRG00000008478	1 retrocopy	retro_ttru_1274,