RetrogeneDB ID: retro_cpor_690

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_23:26813636..26814000(-)
• Located in intron of: ENSCPOG00000005122

Retrocopy information

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

Parental gene information

• Parental gene symbol: NIPSNAP3B
• Ensembl ID: ENSCPOG00000009373
• Aliases: None
• Description: None

Sequence

>retro_cpor_690
AAATACGATAGGTTTGCTCATCAAACTGCAGTCTGGAAAGTTCTGGCCAAAGATAAAGGAATGATGAGAACAATTCCTCG
TTCCAAATTGGGCTCACAGGAGTGAGATTACTTATGCTGTCCTTTGGTGCAAAATGGAAAGGCCTACAAAAGTGGGAGTC
TATGAACCGCTACTTTTCAGATGAAACCTGGCCGTCCAGCTCTGTGGGGGGATGCATTTAAAAGGACAATTCATACGCAG
ATAGGTGGAGGCTACAGAAAACTACTCGCTGTCCTCTACACAGAGTTTGGAGCACTCAACAGAGTTCACGTTCTTCGGTG
GCAGGAGAGCAGCTGGGCGAAGGGCCTCGTGCAGATCCCAGAGT

Alignment

ORF - retro_cpor_690 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.91 %
• Parental protein coverage: 55.02 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  KYVNSSHKRTAVRKALTKDKEWQ-EQFLGPNLAHIDKQECEITYLVPWCKIEKPTKEGVYE-LATFHMKP
          KY....H..TAV.K.L.KDK....EQFL.PN.AH......EITY.V.WCK.E.PTK.GVYE..ATF.MKP
Retrocopy KYDRFAHQ-TAVWKVLAKDKGMM>EQFLVPNWAH----RSEITYAVLWCKMERPTKVGVYE<TATFQMKP

Parental  GGPALWGDAFKRAVHSHVNRGYTKLIGVFHTEYGTLNRVHVLWWHES-ADSRAAGRHES
          G.PALWGDAFKR..H.....GY.KL..V..TE.G.LNRVHVL.W.ES.A..RA..R..S
Retrocopy GRPALWGDAFKRTIHTQIGGGYRKLLAVLYTEFGALNRVHVLRWQES>AGRRASCRSQS

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	9.66 RPM
SRP017611_kidney	0.00 RPM	14.55 RPM
SRP017611_liver	0.00 RPM	12.14 RPM
SRP040447_lung	0.00 RPM	6.41 RPM
SRP040447_skeletal_muscle	0.00 RPM	7.41 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_690 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_690 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 8 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000014253	1 retrocopy	retro_acar_133,
Canis familiaris	ENSCAFG00000023949	1 retrocopy	retro_cfam_295,
Cavia porcellus	ENSCPOG00000009373	1 retrocopy	retro_cpor_690 ,
Dasypus novemcinctus	ENSDNOG00000000943	1 retrocopy	retro_dnov_482,
Echinops telfairi	ENSETEG00000016120	1 retrocopy	retro_etel_1335,
Myotis lucifugus	ENSMLUG00000010147	1 retrocopy	retro_mluc_924,
Oryctolagus cuniculus	ENSOCUG00000007880	1 retrocopy	retro_ocun_1385,
Tursiops truncatus	ENSTTRG00000012307	1 retrocopy	retro_ttru_1702,