RetrogeneDB ID: retro_cpor_39

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_3:58339032..58339389(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCPOG00000000171
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: FKBP2
• Ensembl ID: ENSCPOG00000002928
• Aliases: None
• Description: Peptidyl-prolyl cis-trans isomerase [Source:UniProtKB/TrEMBL;Acc:H0UZP2]

Sequence

>retro_cpor_39
ATGAGGCTACGCTGGGTCCTGACAGCATTGCCCATCTGCCTGAGTGCCCTGGCCACGGTCACGTGGTCTAGTGGCAAACG
GAAGCTGCAGATCGAGGCCAAGAAGCAGGTGGACCACAGTCCAACGTCCCGCGCAAGACAGACGTCTTGCACATGGCGCT
GCACAGGAAAGCTGGCAGATGCAACCAGGTTTAACAGAAGCTTTGCACAGAATCAGCCTTTTGTTTTCTTCTTTGACCCA
GGACAGGTCATCAACGGTTGGGACCAGAAATTGCTGCATATGTGTGGAGGGGAAAAGCAAAAGTTAGTAAGCCCATCTGA
GCCGGGATGGGGGAGCCCTACCCCAAAGATCCCAGGT

Alignment

ORF - retro_cpor_39 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.16 %
• Parental protein coverage: 86.43 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MRLSWVLTVLSICLSALATATGSEGKRKLQIGVKKRVDHCPIKSRKGDVLHMHYTGKLEDGTEFDSSLPQ
          MRL.WVLT.L.ICLSALAT.T.S.GKRKLQI..KK.VDH.P.............TGKL.D.T.F..S..Q
Retrocopy MRLRWVLTALPICLSALATVTWSSGKRKLQIEAKKQVDHSPTSRARQTSCTWRCTGKLADATRFNRSFAQ

Parental  NQPFVFSLGTGQVIKGWDQGLLGMCEGEKRKLVIPSELGYGERGAPPKIPG
          NQPFVF....GQVI.GWDQ.LL.MC.GEK.KLV.PSE.G.G.....PKIPG
Retrocopy NQPFVFFFDPGQVINGWDQKLLHMCGGEKQKLVSPSEPGWG--SPTPKIPG

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
SRP017611_brain	0.06 RPM	49.41 RPM
SRP017611_kidney	0.00 RPM	71.19 RPM
SRP017611_liver	0.00 RPM	30.47 RPM
SRP040447_lung	0.00 RPM	43.86 RPM
SRP040447_skeletal_muscle	0.00 RPM	13.61 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_39 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_39 was not experimentally validated.

Homology

Retrocopy orthology:

Cavia porcellus does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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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,