RetrogeneDB ID: retro_btau_854

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 2:8844055..8844553(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSBTAG00000046000
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PPIL1
• Ensembl ID: ENSBTAG00000002376
• Aliases: None
• Description: Peptidyl-prolyl cis-trans isomerase-like 1 [Source:UniProtKB/Swiss-Prot;Acc:Q5E992]

Sequence

>retro_btau_854
ATGGCGGCGATTCCTCCAGACTCTTGGCAGCCGCCCAACGTGTACCTGGAGACCAGCATGGGGATCATCGTGCTGGAGCT
GTACTGGAAGGATGCTCCAAAGACCTGTAAGAACTTCGCTGAATTGGCTCATCGAGGTTACTACAATGGCACCAAATTCC
ACAGAATCATCAAAGACTTTATGATCCAGGGAGGTGACCCAACAGGGACAGGTCGAGGTGGTGCGTCTATCTATGGCAAG
CAGTTTGAAGATGAACTTTATCCAGACTTGAAATTCACAGGGGCTGGAATTCTCGCAATGGCCAATGCAGGGCCTGACAC
CAACGGCAGCCGGTTCTTTGTGACCCTGGCTCCCACCCAGCGGCTTGATGGCAAGCATACCATTTTTGGCCGTGTGTGTC
AGGGTATAGGCATGGTGAATCAAGTTGGAATGGTGGAAACAAACTCCCAGGACTGCCCCGTGGACGATGTGAAGATCATT
AAGGCATACCCTTCCGGG

Alignment

ORF - retro_btau_854 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.78 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAAIPPDSWQPPNVYLETSMGIIVLELYWKHAPKTCKNFAELARRGYYNGTKFHRIIKDFMIQGGDPTGT
          MAAIPPDSWQPPNVYLETSMGIIVLELYWK.APKTCKNFAELA.RGYYNGTKFHRIIKDFMIQGGDPTGT
Retrocopy MAAIPPDSWQPPNVYLETSMGIIVLELYWKDAPKTCKNFAELAHRGYYNGTKFHRIIKDFMIQGGDPTGT

Parental  GRGGASIYGKQFEDELHPDLKFTGAGILAMANAGPDTNGSQFFVTLAPTQWLDGKHTIFGRVCQGIGMVN
          GRGGASIYGKQFEDEL.PDLKFTGAGILAMANAGPDTNGS.FFVTLAPTQ.LDGKHTIFGRVCQGIGMVN
Retrocopy GRGGASIYGKQFEDELYPDLKFTGAGILAMANAGPDTNGSRFFVTLAPTQRLDGKHTIFGRVCQGIGMVN

Parental  RVGMVETNSQDRPVDDVKIIKAYPSG
          .VGMVETNSQD.PVDDVKIIKAYPSG
Retrocopy QVGMVETNSQDCPVDDVKIIKAYPSG

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	21.20 RPM
ERP005899_muscle	0.00 RPM	23.33 RPM
SRP017611_brain	0.00 RPM	15.53 RPM
SRP017611_kidney	0.06 RPM	32.24 RPM
SRP017611_liver	0.00 RPM	16.84 RPM
SRP030211_testis	0.00 RPM	18.04 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_854 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_854 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_854 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 22 parental genes, and 29 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000000213	1 retrocopy	retro_amel_30,
Bos taurus	ENSBTAG00000002376	1 retrocopy	retro_btau_854 ,
Bos taurus	ENSBTAG00000004590	1 retrocopy	retro_btau_1530,
Bos taurus	ENSBTAG00000005416	1 retrocopy	retro_btau_1585,
Choloepus hoffmanni	ENSCHOG00000006001	1 retrocopy	retro_chof_250,
Callithrix jacchus	ENSCJAG00000016094	1 retrocopy	retro_cjac_1302,
Erinaceus europaeus	ENSEEUG00000009371	1 retrocopy	retro_eeur_204,
Homo sapiens	ENSG00000137168	1 retrocopy	retro_hsap_2086,
Gorilla gorilla	ENSGGOG00000027071	1 retrocopy	retro_ggor_1630,
Loxodonta africana	ENSLAFG00000028161	2 retrocopies	retro_lafr_1187, retro_lafr_435,
Macropus eugenii	ENSMEUG00000000997	1 retrocopy	retro_meug_1008,
Myotis lucifugus	ENSMLUG00000002299	1 retrocopy	retro_mluc_69,
Monodelphis domestica	ENSMODG00000013502	2 retrocopies	retro_mdom_500, retro_mdom_997,
Mustela putorius furo	ENSMPUG00000014166	1 retrocopy	retro_mputfur_29,
Nomascus leucogenys	ENSNLEG00000010779	1 retrocopy	retro_nleu_2135,
Oryctolagus cuniculus	ENSOCUG00000007046	2 retrocopies	retro_ocun_1493, retro_ocun_1759,
Otolemur garnettii	ENSOGAG00000011275	3 retrocopies	retro_ogar_1484, retro_ogar_2850, retro_ogar_939,
Ochotona princeps	ENSOPRG00000006059	3 retrocopies	retro_opri_1054, retro_opri_238, retro_opri_641,
Procavia capensis	ENSPCAG00000015572	1 retrocopy	retro_pcap_426,
Pongo abelii	ENSPPYG00000016554	1 retrocopy	retro_pabe_2009,
Pan troglodytes	ENSPTRG00000018111	1 retrocopy	retro_ptro_1535,
Sus scrofa	ENSSSCG00000030390	1 retrocopy	retro_sscr_472,