RetrogeneDB ID: retro_btau_1446

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 6:8031524..8032114(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSBTAG00000010010
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PRDX1
• Ensembl ID: ENSBTAG00000003642
• Aliases: PRDX1, PRX1
• Description: Peroxiredoxin-1 [Source:UniProtKB/Swiss-Prot;Acc:Q5E947]

Sequence

>retro_btau_1446
ATGTCTTCAGGAAATGTGAAAATTGGGCATCCTGCCCCCCAGTTCAAAACTACAACCATTATGCCAGATGGTCAGTTCAA
AGATATGTCTGTCTGACCACAAAGGAAGATACGTTGTGTTCTTCTTTTACCCTCTTGACTTCGCCTTTGTGTGCCCCATG
GAGCTCCTTGCTTTCAGTGATAGGGCAGAAGAATTTAAGAAACTCAACTACCAAGTAACTGGTGCTTCTTTGGGTTCTCA
CTTCTGTCACCTGGCGTGGATCAACATACCCAAGAAACAAGGAAGGCTGGGGGCCATGCACATTCCCTTGATATCAGAGC
CCGAGCGCACCGTTGCTCAGTACTGTGGGGTCTTAAAGGCTGATGAGGGCTTCTCATTCAGGAACCTTTTTACTATTGAT
GGTAAAGGTATCTTTCCACAGATTACCATAAACAACCTTCCTGTTGGCCGCTCTGTGGATGAGACACTGAGACTAGTTCA
GGCCTTTCCGCTTCACTGACACATATGGGGACGTGCCAGTGCGCTGGAAGCCTGGTGGTGATACCAAGAAGCCTGATGCC
CAGAGCAAAGAATATTTCTCTAATCAGAAG

Alignment

ORF - retro_btau_1446 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.15 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MSSGNA-KIGHRAPQFKATAVMPDGQFKDISLADYKGKYVVFFFYPLDFTFVCPTEIIAFSDRAEEFKKL
          MSSGN..K.G...P..K..........K.I.L.D.KG.YVVFFFYPLDF.FVCP.E..AFSDRAEEFKKL
Retrocopy MSSGNV>KLGILPPSSKLQPLCQMVSSK-ICLSDHKGRYVVFFFYPLDFAFVCPMELLAFSDRAEEFKKL

Parental  NCQVIGASVDSHFCHLAWINTPKKQGGLGPMNIPLISDPKRTIAQDYGVLKADEGISFRGLFIIDDKGIL
          N.QV.GAS..SHFCHLAWIN.PKKQG.LG.M.IPLIS.P.RT.AQ..GVLKADEG.SFR.LF.ID.KGI.
Retrocopy NYQVTGASLGSHFCHLAWINIPKKQGRLGAMHIPLISEPERTVAQYCGVLKADEGFSFRNLFTIDGKGIF

Parental  RQITINDLPVGRSVDETLRLVQAF-QFTDKHGEVCPAGWKPGSDTIKPDVQKSKEYFSKQK
          .QITIN.LPVGRSVDETLRLVQAF..FTD..G.V.P..WKPG.DT.KPD.Q.SKEYFS.QK
Retrocopy PQITINNLPVGRSVDETLRLVQAF>RFTDTYGDV-PVRWKPGGDTKKPDAQ-SKEYFSNQK

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	21.99 RPM
ERP005899_muscle	0.00 RPM	350.10 RPM
SRP017611_brain	0.00 RPM	66.74 RPM
SRP017611_kidney	0.18 RPM	135.61 RPM
SRP017611_liver	0.00 RPM	15.93 RPM
SRP030211_testis	0.30 RPM	95.05 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1446 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1446 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1446 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 32 parental genes, and 86 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000013632	2 retrocopies	retro_amel_1116, retro_amel_539,
Bos taurus	ENSBTAG00000003642	2 retrocopies	retro_btau_1299, retro_btau_1446 ,
Bos taurus	ENSBTAG00000006165	1 retrocopy	retro_btau_439,
Bos taurus	ENSBTAG00000008731	1 retrocopy	retro_btau_562,
Canis familiaris	ENSCAFG00000004567	5 retrocopies	retro_cfam_1313, retro_cfam_270, retro_cfam_577, retro_cfam_834, retro_cfam_988,
Choloepus hoffmanni	ENSCHOG00000003358	5 retrocopies	retro_chof_1140, retro_chof_134, retro_chof_1714, retro_chof_2035, retro_chof_2450,
Ciona intestinalis	ENSCING00000003002	1 retrocopy	retro_cint_8,
Callithrix jacchus	ENSCJAG00000004807	2 retrocopies	retro_cjac_1201, retro_cjac_2884,
Cavia porcellus	ENSCPOG00000014137	3 retrocopies	retro_cpor_1079, retro_cpor_290, retro_cpor_398,
Dasypus novemcinctus	ENSDNOG00000018488	1 retrocopy	retro_dnov_2071,
Dipodomys ordii	ENSDORG00000008975	1 retrocopy	retro_dord_727,
Equus caballus	ENSECAG00000008678	1 retrocopy	retro_ecab_81,
Echinops telfairi	ENSETEG00000007922	11 retrocopies	retro_etel_112, retro_etel_1157, retro_etel_1245, retro_etel_1442, retro_etel_1838, retro_etel_2121, retro_etel_2122, retro_etel_308, retro_etel_367, retro_etel_460, retro_etel_556,
Felis catus	ENSFCAG00000028484	1 retrocopy	retro_fcat_1714,
Homo sapiens	ENSG00000117450	1 retrocopy	retro_hsap_4230,
Macropus eugenii	ENSMEUG00000006820	4 retrocopies	retro_meug_1694, retro_meug_1711, retro_meug_2059, retro_meug_662,
Macaca mulatta	ENSMMUG00000006221	1 retrocopy	retro_mmul_762,
Monodelphis domestica	ENSMODG00000002382	2 retrocopies	retro_mdom_1787, retro_mdom_555,
Mus musculus	ENSMUSG00000028691	5 retrocopies	retro_mmus_1466, retro_mmus_1659, retro_mmus_1786, retro_mmus_3129, retro_mmus_3167,
Nomascus leucogenys	ENSNLEG00000014524	2 retrocopies	retro_nleu_1040, retro_nleu_1627,
Oryctolagus cuniculus	ENSOCUG00000005951	2 retrocopies	retro_ocun_1064, retro_ocun_1124,
Otolemur garnettii	ENSOGAG00000002303	4 retrocopies	retro_ogar_1219, retro_ogar_1333, retro_ogar_1588, retro_ogar_486,
Pongo abelii	ENSPPYG00000001411	1 retrocopy	retro_pabe_3409,
Pan troglodytes	ENSPTRG00000000675	1 retrocopy	retro_ptro_2874,
Pteropus vampyrus	ENSPVAG00000015001	1 retrocopy	retro_pvam_179,
Rattus norvegicus	ENSRNOG00000017194	8 retrocopies	retro_rnor_1401, retro_rnor_1488, retro_rnor_1574, retro_rnor_1656, retro_rnor_1736, retro_rnor_2063, retro_rnor_2292, retro_rnor_2401,
Sorex araneus	ENSSARG00000004703	5 retrocopies	retro_sara_153, retro_sara_370, retro_sara_399, retro_sara_633, retro_sara_95,
Sus scrofa	ENSSSCG00000003914	1 retrocopy	retro_sscr_719,
Ictidomys tridecemlineatus	ENSSTOG00000023413	2 retrocopies	retro_itri_631, retro_itri_817,
Tupaia belangeri	ENSTBEG00000015997	4 retrocopies	retro_tbel_3922, retro_tbel_4017, retro_tbel_4024, retro_tbel_4669,
Tarsius syrichta	ENSTSYG00000011031	1 retrocopy	retro_tsyr_1781,
Tursiops truncatus	ENSTTRG00000008858	4 retrocopies	retro_ttru_1350, retro_ttru_1878, retro_ttru_234, retro_ttru_36,