RetrogeneDB ID: retro_btau_561

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 14:45945494..45946385(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FKBP4
• Ensembl ID: ENSBTAG00000007605
• Aliases: FKBP4, FKBP-4, FKBP-52
• Description: peptidyl-prolyl cis-trans isomerase FKBP4 [Source:RefSeq peptide;Acc:NP_001029494]

Sequence

>retro_btau_561
ATGGCCACCAAGGAGATGAAGGCGGCCAAGAGCAGGGAGCAGTTGGCACTGCAGCCCCTTGAGGGAGTGGACCTCAGCCC
TAAGCAGGATGAGGGTATGCTTGAGTTCATCAAGCAAGAAGGTCCTGGCATGGAAATGCCAATGATCGGGGACCGAGTCT
CTGTCCACTACAGGGGCTGGCTGCTGGATGGCACCAAGTTCCACTCCAGCCTGGACCGCAAGGACAGGGTCTCCTTTGAC
CTGGGGAGAGGGAAGGTCATCAAGGCTTGGGATGTTGCTGTAGCAACCATGAAGGCAGGCGAAGTGTGCCACATCACCTG
CAAGCCAGAGCATGCCTAGGGCTCAGCGGGCAGCCCTCCCAGGATCCCTCCCAAAGCCACACTTGTGTTTGAGGTGGAGT
TGTTGGAGTTCAAGGAAGAGGACCTGACAGACGAAGAAGACAGGGGATCATCAGGAGAGTACGGAGGCGATGGGGAGGGC
TATGCCAAGCCAGCGACAGCGCCACCCTGGAAGTTGCACTGGAAGGATACTTCGAGGACCAGATCTTTGACCCACGAGAG
CTCAGCTTTGAAGCTGGTGAGGGAGAAAGCATGCATCTTGCCCTGTGGGCTGGAGAAAGCCATTCAGTGTGTGGATAAAA
GAGAACATTCCATTGTGTATCTTAACACCTGTATGCTTTCAGCAATGCTGGGAAGGAGAAGTTCCAGATCCCACCAAATG
CTGAGCTGATGTACGAAATATAGCACAAGAATTTTTGAGAGGGCCAACAAGTCCGGGGCGATGAGTTCTGAGACCCTGGA
GCAGAGGACCGTAGTGAAGGAGCGAGGCACTGTGCTCTTCAAGGAAGGCAAGTACAAGCAAGCTGTGCTGCAGTGCAAGA
AGACTGTGTCC

Alignment

ORF - retro_btau_561 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.01 %
• Parental protein coverage: 64.92 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  MTAEETKAAESGAQSAPLRLEGVDISPKQDEGVLKVIKREGTGMETPMIGDRVFVHYTGWLLDGTKFDSS
          M...E.KAA.S..Q.A...LEGVD.SPKQDEG.L..IK.EG.GME.PMIGDRV.VHY.GWLLDGTKF.SS
Retrocopy MATKEMKAAKSREQLALQPLEGVDLSPKQDEGMLEFIKQEGPGMEMPMIGDRVSVHYRGWLLDGTKFHSS

Parental  LDRKDRFSFDLGKGEVIKAWDIAVATMKVGEVCHITCKPEYAYGLAGSPPKIPPNATLVFEVELFEFKGE
          LDRKDR.SFDLG.G.VIKAWD.AVATMK.GEVCHITCKPE.A.G.AGSPP.IPP.ATLVFEVEL.EFK.E
Retrocopy LDRKDRVSFDLGRGKVIKAWDVAVATMKAGEVCHITCKPEHA*GSAGSPPRIPPKATLVFEVELLEFKEE

Parental  DLTEEED-GGIIRRIRTR-GEGYAKP-NEGALVEVALEGYFKDQVFDRRELRFEVGEGESMD-LPCGLEK
          DLT.EED..GIIRR.R.R.GEGYAKP....A..EVALEGYF.DQ.FD.REL.FE.GEGESM..LPCGLEK
Retrocopy DLTDEED<QGIIRRVRRR>GEGYAKP<SDSATLEVALEGYFEDQIFDPRELSFEAGEGESMH>LPCGLEK

Parental  AIQRMEKGEHSIVYLKP-RYAFGSAGKEKFQIPPNAELKYEIHLKS-FEKAKESWEMSSEEKLEQSTIVK
          AIQ...K.EHSIVYL....YAF..AGKEKFQIPPNAEL.YEI..K..FE.A..S..MSS.E.LEQ.T.VK
Retrocopy AIQCVDKREHSIVYLNT<LYAFSNAGKEKFQIPPNAELMYEI*HKN>FERANKSGAMSS-ETLEQRTVVK

Parental  ERGTVYFKEGKYKQAVLQYKKIVS
          ERGTV.FKEGKYKQAVLQ.KK.VS
Retrocopy ERGTVLFKEGKYKQAVLQCKKTVS

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	75.84 RPM
ERP005899_muscle	0.00 RPM	228.52 RPM
SRP017611_brain	0.05 RPM	132.56 RPM
SRP017611_kidney	0.12 RPM	150.43 RPM
SRP017611_liver	0.00 RPM	127.84 RPM
SRP030211_testis	0.09 RPM	458.67 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_561 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_561 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_561 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 25 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000007605	1 retrocopy	retro_btau_561 ,
Bos taurus	ENSBTAG00000008303	4 retrocopies	retro_btau_1220, retro_btau_1265, retro_btau_128, retro_btau_1760,
Callithrix jacchus	ENSCJAG00000018746	1 retrocopy	retro_cjac_436,
Dasypus novemcinctus	ENSDNOG00000011244	1 retrocopy	retro_dnov_894,
Homo sapiens	ENSG00000004478	5 retrocopies	retro_hsap_3085, retro_hsap_4162, retro_hsap_4165, retro_hsap_4264, retro_hsap_4266,
Gorilla gorilla	ENSGGOG00000010471	4 retrocopies	retro_ggor_2120, retro_ggor_2852, retro_ggor_2854, retro_ggor_2855,
Macaca mulatta	ENSMMUG00000007405	1 retrocopy	retro_mmul_1969,
Nomascus leucogenys	ENSNLEG00000002835	1 retrocopy	retro_nleu_2291,
Pongo abelii	ENSPPYG00000004149	4 retrocopies	retro_pabe_2607, retro_pabe_2611, retro_pabe_3383, retro_pabe_3518,
Pan troglodytes	ENSPTRG00000004529	3 retrocopies	retro_ptro_2083, retro_ptro_3000, retro_ptro_3001,