RetrogeneDB ID: retro_cpor_1159

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_51:728697..729171(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MEMO1
• Ensembl ID: ENSCPOG00000012278
• Aliases: None
• Description: None

Sequence

>retro_cpor_1159
GGCCTGCAGCTGCATGCACAGCTAGAAGGTTGGCTCTCCCAAGTGCAGTCTATGAAAAAATGTGCTTAGAGCCATTATTG
CACCCTGCACAGAATATACACACTGTGGGTCTTGTCCTGCCAATGCTTACAAACAAGTGGATCTATCTCTTACCTGAAGA
ATTTTCATCCTTGGATCTTTGCATCATGTACCCCTCTCACCAATTGTACTATCCAGTGTGGATATATGCAGTATACCTCT
ATATGGTGTTTGTACTGATCAAAAGATTTATGGAGAGCTATGAAAGACAGGAATATTTGAACAAATGTCTCTACAGACAG
ATTAAGATGACAACAGTATTGAAATGCATTTGCCTTATACAAGTAAAGCCATGGAAAGCCATAAGAATGAGTTTACCATT
ATTCCTGTACTGGTTGGAACTCTGGGTGAGTCAAAAGACCAGGAAGTGAAAAACTCTTTAGTAAATATCTAGCA

Alignment

ORF - retro_cpor_1159 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.38 %
• Parental protein coverage: 79.4 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  GPQLNAQLEGWLSQVQSTKRPA-RAIIAPHAGYTYCGSCAAHAYKQVDPSITRRIFILGPSHHVPLSRCA
          G.QL.AQLEGWLSQVQS.K..A.RAIIAP...YT.CGSC.A.AYKQVD.S.T.RIFILG..HHVPLS...
Retrocopy GLQLHAQLEGWLSQVQSMKKCA>RAIIAPCTEYTHCGSCPANAYKQVDLSLT*RIFILGSLHHVPLSPIV

Parental  LSSVDIYRTPLYDLRIDQKIYGELWKTGMFERMSLQTDEDEHSIEMHLPYTAKAMESHKDEFTIIPVLVG
          LSSVDI...PLY....DQKIYGEL.KTG.FE.MSLQTD.D..SIEMHLPYT.KAMESHK.EFTIIPVLVG
Retrocopy LSSVDICSIPLYGVCTDQKIYGEL*KTGIFEQMSLQTD*DDNSIEMHLPYTSKAMESHKNEFTIIPVLVG

Parental  ALSESKEQEF-GKLFSKYLA
          .L.ESK.QE...KLFSKYLA
Retrocopy TLGESKDQEV<EKLFSKYLA

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	0.17 RPM	7.53 RPM
SRP017611_kidney	0.00 RPM	8.27 RPM
SRP017611_liver	0.04 RPM	8.44 RPM
SRP040447_lung	0.00 RPM	7.31 RPM
SRP040447_skeletal_muscle	0.00 RPM	11.21 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1159 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1159 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 5 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000012339	2 retrocopies	retro_chof_2257, retro_chof_2552,
Cavia porcellus	ENSCPOG00000012278	1 retrocopy	retro_cpor_1159 ,
Dasypus novemcinctus	ENSDNOG00000001254	1 retrocopy	retro_dnov_253,
Oryctolagus cuniculus	ENSOCUG00000005878	3 retrocopies	retro_ocun_1441, retro_ocun_1663, retro_ocun_928,
Pteropus vampyrus	ENSPVAG00000011427	1 retrocopy	retro_pvam_184,