RetrogeneDB ID: retro_btau_1585

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 7:74662605..74663084(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PPIL3
• Ensembl ID: ENSBTAG00000005416
• Aliases: None
• Description: peptidyl-prolyl cis-trans isomerase-like 3 [Source:RefSeq peptide;Acc:NP_001193493]

Sequence

>retro_btau_1585
TCGGTGACATTGCATACAGATGTAGGTGATATTAAAATAGAAGTCTTCTGTGAAAGGACACCCAAAACATCTGAAAATTT
CTTGGCTCTTTGTGCCAGTGATTACTACAATGGCTGTATATTTCATAGAAATATCAAGGGTTTCATGGTTCAAACGGGAG
ATCTGACAGGTACTGGAAGGGGAGGTAACAGTATCTGGGGCAAGAAGTTTGAAGAAGAATATAATGAACATCTTAAGCAC
AGTGTTAGAGGTGTTGTATCTATGGCTAATAATGGCCCAAATACCAATGGATCTCAGTTTTCATCACCTATGGGAAGCAG
CCACATCTGGACATGAAATACACAGTATTTGGCAAGGTGATAGATGGTCTGGAGACTCCAGATGAACTGGAGAAGTTACC
TGTAAATGAGAAGACATATCAACCTCTTAATGATGTACACATTAAGGATATAACTATTCATGCCAACCCATTTGCCCAG

Alignment

ORF - retro_btau_1585 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.93 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SVTLHTDVGDIKIEVFCEKGKKESQNFLALCASNYYNGCIFHRNIKGFMVQTGDPTGTGRGGNSIWGKKF
          SVTLHTDVGDIKIEVFCE...K.S.NFLALCAS.YYNGCIFHRNIKGFMVQTGD.TGTGRGGNSIWGKKF
Retrocopy SVTLHTDVGDIKIEVFCERTPKTSENFLALCASDYYNGCIFHRNIKGFMVQTGDLTGTGRGGNSIWGKKF

Parental  EDEYSEYLKHSVRGVVSMANNGPNTNGSQF-FITYGKQPHLDMKYTVFGKVIDGLETLDELEKLPVNEKT
          E.EY.E.LKHSVRGVVSMANNGPNTNGSQF.FITYGKQPHLDMKYTVFGKVIDGLET.DELEKLPVNEKT
Retrocopy EEEYNEHLKHSVRGVVSMANNGPNTNGSQF<FITYGKQPHLDMKYTVFGKVIDGLETPDELEKLPVNEKT

Parental  YRPLNDVHIKDITIHANPFAQ
          Y.PLNDVHIKDITIHANPFAQ
Retrocopy YQPLNDVHIKDITIHANPFAQ

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	8.00 RPM
ERP005899_muscle	0.69 RPM	5.86 RPM
SRP017611_brain	0.59 RPM	6.30 RPM
SRP017611_kidney	0.47 RPM	8.77 RPM
SRP017611_liver	0.45 RPM	6.12 RPM
SRP030211_testis	0.29 RPM	3.39 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1585 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1585 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1585 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000005917	1 retrocopy	retro_amel_1458,
Bos taurus	ENSBTAG00000002376	1 retrocopy	retro_btau_854,
Bos taurus	ENSBTAG00000004590	1 retrocopy	retro_btau_1530,
Bos taurus	ENSBTAG00000005416	1 retrocopy	retro_btau_1585 ,
Canis familiaris	ENSCAFG00000032245	1 retrocopy	retro_cfam_180,
Dasypus novemcinctus	ENSDNOG00000002364	1 retrocopy	retro_dnov_2477,
Dipodomys ordii	ENSDORG00000007389	1 retrocopy	retro_dord_575,
Monodelphis domestica	ENSMODG00000015037	1 retrocopy	retro_mdom_1025,
Tupaia belangeri	ENSTBEG00000000664	1 retrocopy	retro_tbel_4520,