RetrogeneDB ID: retro_cpor_1223

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_59:74327..74591(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: LYRM2
• Ensembl ID: ENSCPOG00000015625
• Aliases: None
• Description: None

Sequence

>retro_cpor_1223
ATGGCCACCTCCTGCTTACCCTAGACATGTTGACACTAAATCAGTTCCTGAGAAGGCAACAAGTTCTCCTACTCTAAATA
AGGATTTTGCAAGCAATCTGGCAAGTTCCAAATGCATCTGATTTGCAAATACCTGAATAACTAGGCAAGGGAAGAATTCA
AATGAAATAAAAGTGCCACAGAAAAGGACACTATCTGAATGATGATTACTCAAGACATTATCCAGCTAAAGGAGTTAGAA
AAAACACTTGCATTAGCAAAATCT

Alignment

ORF - retro_cpor_1223 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.78 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAASRLP-PGTLTLKQFLRRQQVLLLYRRILQAIRQVPNACDR-KYLQNWAREEFKRNKSATEEDTIQMM
          MA.S.LP....LTL.QFLRRQQVLLL..RILQAI.QVPNA.D..KYL.N.AREEFK.NKSATE.DTI.MM
Retrocopy MATSCLP<LDMLTLNQFLRRQQVLLL*IRILQAIWQVPNASDL>KYLNN*AREEFK*NKSATEKDTI*MM

Parental  ITQGNIQLKELEKTLALAKS
          ITQ..IQLKELEKTLALAKS
Retrocopy ITQDIIQLKELEKTLALAKS

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	7.13 RPM
SRP017611_kidney	0.00 RPM	6.91 RPM
SRP017611_liver	0.00 RPM	3.96 RPM
SRP040447_lung	0.00 RPM	3.76 RPM
SRP040447_skeletal_muscle	0.00 RPM	9.45 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1223 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1223 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 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000000905	1 retrocopy	retro_cjac_2485,
Cavia porcellus	ENSCPOG00000015625	4 retrocopies	retro_cpor_1169, retro_cpor_1223 , retro_cpor_925, retro_cpor_946,
Homo sapiens	ENSG00000083099	1 retrocopy	retro_hsap_2054,
Macropus eugenii	ENSMEUG00000009916	1 retrocopy	retro_meug_2134,