RetrogeneDB ID: retro_btau_1530

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 7:39892262..39892790(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PPIH
• Ensembl ID: ENSBTAG00000004590
• Aliases: None
• Description: Peptidyl-prolyl cis-trans isomerase H [Source:UniProtKB/Swiss-Prot;Acc:Q0P5D0]

Sequence

>retro_btau_1530
ATGGCAGTGGCAAATTCAAGCCCTGTCAATCCCATGGTATTCTTTGATGACAGCATTGGCGGCCAGGAAGTTGGCCACAT
GAAGACTGAACTCTTTGCAGACATTGTGCCTAAGACTGCCGAGAATTTTAGGCAGTTCTACACAGAATTCAGAAAAGATG
GGGTTCCAATAAGCTACAAAGGGAGCACCTTCCACAGGGTCATAAAAGATTTCATGATTCAGGGTGGAGATTTTGTTAAT
GGAGATGGTACTTGAGTCACCAGTATCTACTGGGGGCCATTCGCAGATGATAATTTTAAGCTTAGATACTCAGCTCCAGG
CCTGCTTTCCATGACAAACAGCGGTCCCAGTACAAATGGCTGCCAGCTTTTCATCACCTGCTCTGAGTGTGATTGGCTAG
ATGGGAAGCTCATGGTGTTTGGAAAAATCATTGATGGACTTTTGGTGATGAGAAAGATTGAGAATGTTCCCACAGGCCCC
AACAATAAGACCAAGCTGCCTCTGGTGATCTCACAGTGTGGGGAGATT

Alignment

ORF - retro_btau_1530 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.14 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAVANSSPVNPVVFFDVSIGGQEVGRMKIELFADVVPKTAENFRQFCTGEFRKDGVPIGYKGSTFHRVIK
          MAVANSSPVNP.VFFD.SIGGQEVG.MK.ELFAD.VPKTAENFRQF.T.EFRKDGVPI.YKGSTFHRVIK
Retrocopy MAVANSSPVNPMVFFDDSIGGQEVGHMKTELFADIVPKTAENFRQFYT-EFRKDGVPISYKGSTFHRVIK

Parental  DFMIQGGDFVNGDGTGVASIYRGPFADENFKLRHSAPGLLSMANSGPSTNGCQFFITCSKCDWLDGKHVV
          DFMIQGGDFVNGDGT.V.SIY.GPFAD.NFKLR.SAPGLLSM.NSGPSTNGCQ.FITCS.CDWLDGK..V
Retrocopy DFMIQGGDFVNGDGT*VTSIYWGPFADDNFKLRYSAPGLLSMTNSGPSTNGCQLFITCSECDWLDGKLMV

Parental  FGKIIDGLLVMRKIENVPTGPNNKPKLPVVISQCGEM
          FGKIIDGLLVMRKIENVPTGPNNK.KLP.VISQCGE.
Retrocopy FGKIIDGLLVMRKIENVPTGPNNKTKLPLVISQCGEI

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	7.64 RPM
ERP005899_muscle	0.00 RPM	16.47 RPM
SRP017611_brain	0.00 RPM	18.87 RPM
SRP017611_kidney	0.00 RPM	12.51 RPM
SRP017611_liver	0.00 RPM	6.04 RPM
SRP030211_testis	0.02 RPM	24.96 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1530 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1530 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1530 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 21 parental genes, and 43 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000000526	1 retrocopy	retro_amel_1481,
Bos taurus	ENSBTAG00000002376	1 retrocopy	retro_btau_854,
Bos taurus	ENSBTAG00000004590	1 retrocopy	retro_btau_1530 ,
Bos taurus	ENSBTAG00000005416	1 retrocopy	retro_btau_1585,
Callithrix jacchus	ENSCJAG00000003145	5 retrocopies	retro_cjac_129, retro_cjac_1886, retro_cjac_2205, retro_cjac_3120, retro_cjac_4110,
Cavia porcellus	ENSCPOG00000008214	8 retrocopies	retro_cpor_1511, retro_cpor_785, retro_cpor_786, retro_cpor_794, retro_cpor_795, retro_cpor_796, retro_cpor_797, retro_cpor_798,
Dipodomys ordii	ENSDORG00000016152	3 retrocopies	retro_dord_151, retro_dord_173, retro_dord_447,
Homo sapiens	ENSG00000171960	2 retrocopies	retro_hsap_4740, retro_hsap_928,
Gorilla gorilla	ENSGGOG00000022507	2 retrocopies	retro_ggor_2945, retro_ggor_748,
Macropus eugenii	ENSMEUG00000001691	1 retrocopy	retro_meug_1699,
Myotis lucifugus	ENSMLUG00000025400	2 retrocopies	retro_mluc_1922, retro_mluc_2243,
Macaca mulatta	ENSMMUG00000013129	1 retrocopy	retro_mmul_1124,
Mustela putorius furo	ENSMPUG00000013966	2 retrocopies	retro_mputfur_285, retro_mputfur_542,
Nomascus leucogenys	ENSNLEG00000012313	2 retrocopies	retro_nleu_1242, retro_nleu_289,
Oryctolagus cuniculus	ENSOCUG00000011453	1 retrocopy	retro_ocun_1195,
Procavia capensis	ENSPCAG00000011139	1 retrocopy	retro_pcap_81,
Pongo abelii	ENSPPYG00000001467	2 retrocopies	retro_pabe_3686, retro_pabe_797,
Pan troglodytes	ENSPTRG00000000614	2 retrocopies	retro_ptro_3155, retro_ptro_644,
Pteropus vampyrus	ENSPVAG00000005500	1 retrocopy	retro_pvam_107,
Ictidomys tridecemlineatus	ENSSTOG00000000115	2 retrocopies	retro_itri_1248, retro_itri_412,
Tarsius syrichta	ENSTSYG00000003182	2 retrocopies	retro_tsyr_224, retro_tsyr_647,