RetrogeneDB ID: retro_btau_619

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 16:37710406..37710792(+)
• Located in intron of: ENSBTAG00000002689

Retrocopy information

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

Parental gene information

• Parental gene symbol: PFDN6
• Ensembl ID: ENSBTAG00000010723
• Aliases: None
• Description: Prefoldin subunit 6 [Source:UniProtKB/Swiss-Prot;Acc:Q17Q89]

Sequence

>retro_btau_619
ATGGCTGAGCTAATCCAGAAGAAGCTACAGGGAGAAGTGGAGAAATATCAACAGCTGCAGAAGGACTTGAGTAAATCCGT
GTCAGGGAGGCAGAAACTAGAGGTACAACTAACAGAAAATAATATCATGAAGGAGGAACTGGCTCTACTGGATGGGTCCA
ATGTGGTGTTTAAACTTCTGGGGCCCATACTGGTCAAACAGGAGCTGGGGGAATCTCGGGCCACAGTGGGTAAAAGGCTG
GACTACATCACAGCTGAGATTAAGTGATATGAATCCCAGCTCCGGGATCTAGAGCGTCAGTCAGAACAACAGAGGGAGAC
CTTTGCTCAGCTGCAACAGGAGTTTCAGACTGCCCAGGCAGCAGAGGCAGGGCTCCTGGGAAGGCC

Alignment

ORF - retro_btau_619 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.54 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAELIQKKLQGEVEKYQQLQKDLSKSMSGRQKLEAQLTENNIVKEELALLDGSNVVFKLLGPVLVKQELG
          MAELIQKKLQGEVEKYQQLQKDLSKS.SGRQKLE.QLTENNI.KEELALLDGSNVVFKLLGP.LVKQELG
Retrocopy MAELIQKKLQGEVEKYQQLQKDLSKSVSGRQKLEVQLTENNIMKEELALLDGSNVVFKLLGPILVKQELG

Parental  EARATVGKRLDYITAEIKRYESQLRDLEQQSEQQRETLAQLQQEFQRAQAAKAG-APGKA
          E.RATVGKRLDYITAEIK.YESQLRDLE.QSEQQRET.AQLQQEFQ.AQAA.AG.APGKA
Retrocopy ESRATVGKRLDYITAEIK*YESQLRDLERQSEQQRETFAQLQQEFQTAQAAEAG<APGKA

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	15.86 RPM
ERP005899_muscle	0.00 RPM	20.53 RPM
SRP017611_brain	0.00 RPM	29.19 RPM
SRP017611_kidney	0.06 RPM	23.00 RPM
SRP017611_liver	0.00 RPM	17.74 RPM
SRP030211_testis	0.05 RPM	80.01 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_619 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_619 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_619 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 17 parental genes, and 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000001576	2 retrocopies	retro_amel_221, retro_amel_824,
Bos taurus	ENSBTAG00000010723	1 retrocopy	retro_btau_619 ,
Canis familiaris	ENSCAFG00000000956	2 retrocopies	retro_cfam_1749, retro_cfam_1981,
Cavia porcellus	ENSCPOG00000019520	1 retrocopy	retro_cpor_570,
Dipodomys ordii	ENSDORG00000013828	1 retrocopy	retro_dord_453,
Felis catus	ENSFCAG00000028199	1 retrocopy	retro_fcat_1784,
Macropus eugenii	ENSMEUG00000016778	1 retrocopy	retro_meug_1930,
Microcebus murinus	ENSMICG00000000922	1 retrocopy	retro_mmur_1520,
Mustela putorius furo	ENSMPUG00000002364	1 retrocopy	retro_mputfur_608,
Mus musculus	ENSMUSG00000024309	1 retrocopy	retro_mmus_1930,
Oryctolagus cuniculus	ENSOCUG00000010559	1 retrocopy	retro_ocun_711,
Otolemur garnettii	ENSOGAG00000028341	4 retrocopies	retro_ogar_1185, retro_ogar_2023, retro_ogar_3508, retro_ogar_85,
Ochotona princeps	ENSOPRG00000000983	1 retrocopy	retro_opri_12,
Pteropus vampyrus	ENSPVAG00000001910	1 retrocopy	retro_pvam_391,
Rattus norvegicus	ENSRNOG00000000473	2 retrocopies	retro_rnor_2216, retro_rnor_2869,
Sorex araneus	ENSSARG00000006330	2 retrocopies	retro_sara_338, retro_sara_453,
Tupaia belangeri	ENSTBEG00000013280	1 retrocopy	retro_tbel_454,