RetrogeneDB ID: retro_cpor_1228

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_59:6246165..6246499(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: C16ORF87
• Ensembl ID: ENSCPOG00000010228
• Aliases: None
• Description: None

Sequence

>retro_cpor_1228
TTAAATGCAAAACACTCAGAGAAATCACCGTCTTCTACAGAAAACAAGAATGACGCCAAGAGGAGGCAAACAGAGAGAGT
TAGGAGAGAGAAGATAAATTCTACAGTAAATAAAGATTTACAAAACAAAAAGAGGTCTTGAAGTAACAGCCATTCAGATC
ATATCAGATGAGGAAGAGAAAAACCTAAAAGTGCATCTGTCAAAAACAGGAGGGAGAGAGAAACAGGAAGAGGAAACTGA
CATCTATACTAACCTTCCTGATGAAAAGGCTTTCGTATTTTCAGTCACCTTGGCAGAAATAAATAGAAAAATTATCAATC
AAAGACTTATTCTC

Alignment

ORF - retro_cpor_1228 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.95 %
• Parental protein coverage: 76.87 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LNAKHSEKSPSSTENKHEAKRRRTERVRREKINSTVNKDLENRKRSRSNSHSDHIRRGRGRPKSASAKKH
          LNAKHSEKSPSSTENK..AKRR.TERVRREKINSTVNKDL.N.KRS.SNSHSDHIR.GR..PKSAS.K..
Retrocopy LNAKHSEKSPSSTENKNDAKRRQTERVRREKINSTVNKDLQNKKRS*SNSHSDHIR*GREKPKSASVKNR

Parental  EE-EREKQEKEIDIYANLSDEKAFVFSVALAEINRKIINQRLIL
          .E.E......E.DIY.NL.DEKAFVFSV.LAEINRKIINQRLIL
Retrocopy RE>EKQEE--ETDIYTNLPDEKAFVFSVTLAEINRKIINQRLIL

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	7.76 RPM
SRP017611_kidney	0.00 RPM	6.49 RPM
SRP017611_liver	0.00 RPM	6.01 RPM
SRP040447_lung	0.00 RPM	4.59 RPM
SRP040447_skeletal_muscle	0.00 RPM	3.34 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1228 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1228 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.

---

Parental genes homology:

Parental genes homology involve 5 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000003679	1 retrocopy	retro_cfam_1054,
Cavia porcellus	ENSCPOG00000010228	2 retrocopies	retro_cpor_1197, retro_cpor_1228 ,
Dasypus novemcinctus	ENSDNOG00000006412	2 retrocopies	retro_dnov_1512, retro_dnov_2463,
Tupaia belangeri	ENSTBEG00000013316	2 retrocopies	retro_tbel_3011, retro_tbel_305,
Tarsius syrichta	ENSTSYG00000008921	1 retrocopy	retro_tsyr_1758,