RetrogeneDB ID: retro_cpor_1234

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_6:5400393..5401143(+)
• Located in intron of: ENSCPOG00000008244

Retrocopy information

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

Parental gene information

• Parental gene symbol: MDM2
• Ensembl ID: ENSCPOG00000004323
• Aliases: None
• Description: None

Sequence

>retro_cpor_1234
GAGTGGTTTGATCAGAAATTCAGTCTCAGACCAATTCAGTGTGGAATTCGAAGTTGAAACTCTTGATTCAGAAGATCATA
GTCTTAGTAAAGGACAGGAACTCTCAGATGAAGATGATGAGGTATGTCAAGTTACTGTATATCAGGCAAGGGAAAATGAT
ACAGATTCATTTGAAGAAAGTCCCGAAATTTCCTTAGCTGACTATTGGAAGTGTGTATCATGCAGTGAAATGAATCCTTC
CCTTCCATCCCAATGCAGCAGATGTTGGGCCCTTCATGATAATTGGCTTCCTGAAGACAAAGGGAAAGATAAAGAGGAAA
TCCCTGGGAGAGCCAAATTAGAAAGCTCAACGGGGGCAGATAAGGGCTCAGACACGCTGCCCATGATTCCAGAGAGGCCT
GTGTTGATGAAAGTAATGATGGAATCACACAAGCCTCCCAGTCACAAGAAAGCCAGAATTGTTCTCAGGAGTCAACTTCT
ACTAGCACTTTTAATAGCAGCCAAGAAGATGGTAAAGAGTTTGAGAAGAAAGAAACACAACACAAAAGAGAAAATATGGA
ATCTAGTTTTCCCTTCAGTGCCACTGAACTTTGTGTGATTTGCCCAGGTCGACCTAAAAATGGTTGCATTGTTCATGGCA
AACGAAAATATCTTGGGTCATGTTTCATATGTGCAAAGAGGCAAAAGAAAAGAAATAAGCCTTGATCAGTATGTAGACAA
CCAATTCAAATGATTGTGCTAACTTACTTC

Alignment

ORF - retro_cpor_1234 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.8 %
• Parental protein coverage: 52.24 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  DWLDQ-DSVSDQFSVEFEVESLDSEDYSLSEEGQELSDEDDEVYRVTVFKTGESDTDSFEEDPEISLADY
          .W.DQ..SVSDQFSVEFEVE.LDSED.SLS..GQELSDEDDEV..VTV....E.DTDSFEE.PEISLADY
Retrocopy EWFDQ>NSVSDQFSVEFEVETLDSEDHSLSK-GQELSDEDDEVCQVTVYQARENDTDSFEESPEISLADY

Parental  WKCTSCNEMNPPLPSHCNRCWALRENWLPEEKGKDKGETPEKAELKNSSQADEGLDVPDGKKTL-ANDSK
          WKC.SC.EMNP.LPS.C.RCWAL..NWLPE....DKG....K.E...............G..TL.A.DS.
Retrocopy WKCVSCSEMNPSLPSQCSRCWALHDNWLPE----DKGK--DKEEIPGRAKLESSTGADKGSDTL<AHDSR

Parental  ESCVDENNDEVIQASQSQESEDYSQPSTSRSLVSSSQEDVKEFEKEETQDKEESVEFSFPLNAIEPCVIC
          E.CVDE.ND...QASQSQES...SQ.STS.S...SSQED.KEFEK.ETQ.K.E..E.SFP..A.E.CVIC
Retrocopy EACVDESNDGITQASQSQESQNCSQESTSTSTFNSSQEDGKEFEKKETQHKRENMESSFPFSATELCVIC

Parental  QGRPKNGCIVHGKTGHLMSCFTCAKKLKKRNKPCPVCRQPIQMIVLTYF
          .GRPKNGCIVHGK...L.SCF.CAK..KKRNKP..VCRQPIQMIVLTYF
Retrocopy PGRPKNGCIVHGKRKYLGSCFICAKRQKKRNKP*SVCRQPIQMIVLTYF

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	16.39 RPM
SRP017611_kidney	0.00 RPM	26.70 RPM
SRP017611_liver	0.00 RPM	20.72 RPM
SRP040447_lung	0.00 RPM	47.36 RPM
SRP040447_skeletal_muscle	0.00 RPM	18.15 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1234 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1234 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 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000004323	1 retrocopy	retro_cpor_1234 ,
Loxodonta africana	ENSLAFG00000005885	1 retrocopy	retro_lafr_715,
Otolemur garnettii	ENSOGAG00000034779	2 retrocopies	retro_ogar_1210, retro_ogar_49,
Ictidomys tridecemlineatus	ENSSTOG00000014702	1 retrocopy	retro_itri_1731,