RetrogeneDB ID: retro_cpor_965

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_37:7444339..7444977(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ATPAF1
• Ensembl ID: ENSCPOG00000003349
• Aliases: None
• Description: None

Sequence

>retro_cpor_965
CACTGTAGGCAAGTTGAGTTCATAAAAAGTGTGGAGCAGAAAACAGATGCCTTGGAGAAATGGCCACTGAGCAAAGAATT
CACTAAAGACAGGACACTTGGTTCTGTCTTTAACACTGAGATGGTACAAGACAGAACTGAGAAGAACTAAACTAGATTTG
CAGGTTTTGCAGCAAAGATTCAGTCTATGCATTCCATTCATACAGAAAACTTTGATTTGGTCTGGCACTTGGCTCAGTCC
TCTCCAACATTTCTGGGAGTACTGCCACAAAGGGAAGGTTATGAGTTTTTCTTGGACAATGGGCAGATAGTGAACTCCAC
GTCATTGCTTGTATAAATATTCAGACCTAAGGGGACCCTACAACCTGCTAGTTGATTTTGTGTCACTACCCTGAACTTAA
GGAAGAACAAGGCATAGTACTGATGACAGCAGAAGTGGAGTCCACATTTCTGAATATTGCTGAAATACAGTGCATCACCA
ATCAAGTTCAGCTCTTCTCTGATGGTAAAGACACCTGTGGGTTTAAGGGCAAGTTTAAGTTCAGACCAATTTAACTCAAA
TATATGTCTGCCATTGCTGAAGTGGAGCACAGTGGATCTGCAGCAGAACTGAAACATACCTAGAACCAGGATGAGTCT

Alignment

ORF - retro_cpor_965 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.36 %
• Parental protein coverage: 66.56 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  YSRQGDFIKCVEQKTEALEKQPVSKGFTKDKTLSSIFNLEMVKDKTA-EEIKQIWQQYFAAKDTVYAV-I
          ..RQ..FIK.VEQKT.ALEK.P.SK.FTKD.TL.S.FN.EMV.D.T..EE...I....F..KD.VYA..I
Retrocopy HCRQVEFIKSVEQKTDALEKWPLSKEFTKDRTLGSVFNTEMVQDRTE<EELN*ICR--FCSKDSVYAF>I

Parental  PKEKFDLIWSRAQSCPTFLCALPRREGYEFFV-GQWTRTELHFTALINIQTRGDAAASQLILYHYPELKE
          ..E.FDL.W..AQS.PTFL..LP.REGYEFF..GQW...ELH..A.INIQT.GD.....LIL.HYPELKE
Retrocopy HTENFDLVWHLAQSSPTFLGVLPQREGYEFFL<GQWADSELHVIACINIQT*GDPTTC*LILCHYPELKE

Parental  EKGIVLMTAEMDSTFLNVTEAQCIANQVQLFYATDRKETYGLVETFNFRPNEFKYMSVIAELEQSGLGAK
          E.GIVLMTAE..STFLN..E.QCI.NQVQLF...D.K.T.G....F.FRP...KYMS.IAE.E.SG..A.
Retrocopy EQGIVLMTAEVESTFLNIAEIQCITNQVQLF--SDGKDTCGFKGKFKFRPI*LKYMSAIAEVEHSGSAAE

Parental  LKCTQNKDET
          LK.T.N.DE.
Retrocopy LKHT*NQDES

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	0.00 RPM	15.70 RPM
SRP017611_kidney	0.00 RPM	26.07 RPM
SRP017611_liver	0.00 RPM	13.80 RPM
SRP040447_lung	0.00 RPM	11.37 RPM
SRP040447_skeletal_muscle	0.00 RPM	19.43 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_965 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_965 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 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000000094	1 retrocopy	retro_btau_1192,
Cavia porcellus	ENSCPOG00000003349	1 retrocopy	retro_cpor_965 ,
Mustela putorius furo	ENSMPUG00000012737	1 retrocopy	retro_mputfur_1060,
Mus musculus	ENSMUSG00000028710	1 retrocopy	retro_mmus_1982,