RetrogeneDB ID: retro_btau_1418

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 5:44306644..44306973(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FKBP2
• Ensembl ID: ENSBTAG00000013606
• Aliases: FKBP2, FKBP-2
• Description: Peptidyl-prolyl cis-trans isomerase FKBP2 [Source:UniProtKB/Swiss-Prot;Acc:Q32PA9]

Sequence

>retro_btau_1418
CAGAAGCTGCAGATCAGAGTCAAGAAACGCGTAGACCACTGTCTCATCAAATAGCGCAAAAGGTACATCCTGCACAGGCA
CTGCATGGGAAAGCTAGAAGATGGAACGGAGTTTGACAGCACCCTGCCCCGGAACCAACCATTTGTCTTCTCTCTCAGCA
CAGGCCAGCTCATCAAGGGTTGGGACCAGGGGCTGCTAGGGATGTGTGAGGGGAAAAGCAGAAGCTGGAGATTCCATCAG
AACTGGGTTATGGAGCACAGGGAGCTCCCCCAAAGATTCCAAGTGGTGCAGCCTTGGTGTTCTAGGTGGAGCTGCTCAAA
ATCCAGCAA

Alignment

ORF - retro_btau_1418 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.38 %
• Parental protein coverage: 67.9 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  RKLQIGVKKRVDHCPIKSRKGDVLHMHYTGKLEDGTEFDSSLPQNQPFVFSLGTGQVIKGWDQGLLGMCE
          .KLQI.VKKRVDHC.IK.RK...LH.H..GKLEDGTEFDS.LP.NQPFVFSL.TGQ.IKGWDQGLLGMCE
Retrocopy QKLQIRVKKRVDHCLIK*RKRYILHRHCMGKLEDGTEFDSTLPRNQPFVFSLSTGQLIKGWDQGLLGMCE

Parental  G-EKRKLVIPSELGYGERGAPPKIPGGATLVFEVELLKIER
          G.EK.KL.IPSELGYG..GAPPKIP.GA.LVF.VELLKI..
Retrocopy G<EKQKLEIPSELGYGAQGAPPKIPSGAALVF*VELLKIQQ

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	15.14 RPM
ERP005899_muscle	0.05 RPM	48.41 RPM
SRP017611_brain	0.00 RPM	44.45 RPM
SRP017611_kidney	0.06 RPM	40.19 RPM
SRP017611_liver	0.00 RPM	55.95 RPM
SRP030211_testis	0.19 RPM	94.28 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1418 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1418 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1418 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000000758	1 retrocopy	retro_acar_126,
Bos taurus	ENSBTAG00000013606	3 retrocopies	retro_btau_1418 , retro_btau_69, retro_btau_916,
Callithrix jacchus	ENSCJAG00000018124	2 retrocopies	retro_cjac_2030, retro_cjac_3853,
Cavia porcellus	ENSCPOG00000002928	1 retrocopy	retro_cpor_39,
Macaca mulatta	ENSMMUG00000012945	1 retrocopy	retro_mmul_1397,
Rattus norvegicus	ENSRNOG00000021153	1 retrocopy	retro_rnor_1034,