RetrogeneDB ID: retro_cpor_247

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_11:18383585..18384564(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: LPCAT4
• Ensembl ID: ENSCPOG00000023492
• Aliases: None
• Description: None

Sequence

>retro_cpor_247
GGAGGCAAGTGGCCCCAGGTACTATTCTTTCCCAAAGGCACGTGTTCTAACAAGAAGGCTCTGCTTAAATTCAAACCAGG
AGCCTTCATTGCAGGGGGTGCCTGTCATCCGCTACCCCAAGAGTCTGGATACCACCAGCTGGGCATGAAGGGGCCCTGGA
GTGCTCAAGGTGCTGTGGCTCACAGCTTCTCAGCCCTGTAGCATTGTGGATGTGGAGTTCCTCCCCGTGTATCAGCCCAG
CCCTGAGGAGAGCAGGAACCCCACCCTGTATGCCAGCAATGTCCAGCGGATCATGGCACAGGCCCTGGGCATTCCAGCCA
CTGAGTGTGAGTTTGTGGGCAGTTTGCCTGCCATTGTGGTTGGCCGGCTGAGGGTAGCTTTGGAGCCACAGCTCTGGGAG
CTGGGAAAGGTGCTTCAGAAGGCAGGCTTGTTACCTGGTTGTGTGGATGCTGAGGCAGAGACAGGCCAGAGTCCAATGAT
CAGCCAGAAGGAGTTTGCCAGGCAGCTACAGCTCTTGGGCCCTCAGACTGTGGCTGGTGCCTTCAGTTACTTCCAGTAGG
ATGCCAGCGGTTTGGTGGACTTCCAAGATGTGGTACTTGTGCCAGCAGCTTTGGATGGAGGCAGGAGCCTGGAGGGTCTG
ACTCGCCTGGCCTTTGAGCTGTTTGCTGTAGAGCACACAGAGGGACCTGGCCATCTGTTGTACCAAGATGGTGTCAGTGC
CATCCTGCACCTGCTGCTGGGCTCGCCCCGCCCTGCTGCCACAACTCTGCATGCTGAGCTGTGCCAGCCAGAAGCCAGCC
ATAGCCTCTCACTCTGTCAGTTCCAGAACTTCTCCCTCCACGACCCGCTCTATGGGAAGCTCTTCACACCTACCTGCACC
CCCTCCACACTGCTCGAGGCACCTGCCAGGTGCCTTGTCCCCATGCAGCCCCCTGCTCTGGCCGACGGGACTATGCAGGC
TCCCAAGCAGAAGGGCGAC

Alignment

ORF - retro_cpor_247 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.97 %
• Parental protein coverage: 63.48 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  GGKWPQVLFFPEGTCSNKKALLKFKPGAFIAG-VPVQPVLIRYPNSLDTTSWAWRGPGVLKVLWLTASQP
          GGKWPQVLFFP.GTCSNKKALLKFKPGAFIAG.VPV....IRYP.SLDTTSWA.RGPGVLKVLWLTASQP
Retrocopy GGKWPQVLFFPKGTCSNKKALLKFKPGAFIAG>VPV----IRYPKSLDTTSWA*RGPGVLKVLWLTASQP

Parental  CSIVDVEFLPVYQPSPEESRDPTLYANNVQRVMAQALGIPATECEFVGSLPVIVVGRLKVALEPQLWELG
          CSIVDVEFLPVYQPSPEESR.PTLYA.NVQR.MAQALGIPATECEFVGSLP.IVVGRL.VALEPQLWELG
Retrocopy CSIVDVEFLPVYQPSPEESRNPTLYASNVQRIMAQALGIPATECEFVGSLPAIVVGRLRVALEPQLWELG

Parental  KVLQKAGLSPGCVDAEAEPGRSRMISQEEFARQLQLLDPQTVAGAFSYFQQDASGLVDFRDVALALAALD
          KVLQKAGL.PGCVDAEAE.G.S.MISQ.EFARQLQLL.PQTVAGAFSYFQ.DASGLVDF.DV.L..AALD
Retrocopy KVLQKAGLLPGCVDAEAETGQSPMISQKEFARQLQLLGPQTVAGAFSYFQ*DASGLVDFQDVVLVPAALD

Parental  GGRSLEDLTRLAFELFAEEQTEGPGRLLYEDGFSTILHLLLGSPRPAATTLHAELCQAGASHGLSLCQFQ
          GGRSLE.LTRLAFELFA.E.TEGPG.LLY.DG.S.ILHLLLGSPRPAATTLHAELCQ..ASH.LSLCQFQ
Retrocopy GGRSLEGLTRLAFELFAVEHTEGPGHLLYQDGVSAILHLLLGSPRPAATTLHAELCQPEASHSLSLCQFQ

Parental  NFSLHDPLYGKLFS-TYLHPPHTARGTCPVPGASPRSPP-ALANGTVQAPKQKGD
          NFSLHDPLYGKLF..TYLHP.HTARGTC.VP...P...P.ALA.GT.QAPKQKGD
Retrocopy NFSLHDPLYGKLFT<TYLHPLHTARGTCQVP--CPHAAP>ALADGTMQAPKQKGD

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	116.82 RPM
SRP017611_kidney	0.00 RPM	5.34 RPM
SRP017611_liver	0.00 RPM	3.26 RPM
SRP040447_lung	0.00 RPM	12.48 RPM
SRP040447_skeletal_muscle	0.00 RPM	1.36 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_247 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_247 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000023492	1 retrocopy	retro_cpor_247 ,
Oryctolagus cuniculus	ENSOCUG00000006180	1 retrocopy	retro_ocun_1422,