RetrogeneDB ID: retro_cpor_321

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_123:3512864..3513367(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCPOG00000019917
• Aliases: None
• Description: None

Sequence

>retro_cpor_321
ATGAACCCTTGGTCTCTTTATTTAAATATGGATCCACGATATCTTGTGCAGGATACTGATGCATTTATTTTACTGACTGG
AGCTAATAAAACCCAAGGCAGGTTTGAAATGGCCTTCTCTGCCACTGGGGGATGTTGCATGACGGGCACTGCATTTGTAG
CAGTGAACCGTCTTCAGCTAGGATTGAAGGAAACCCAGAATATGGCCTGGTCCAAACCAAGAAATGGACAGGTTTTGAAT
ATGGTGACTAGGCAAGGGGCACTGTGGGCCAGTGTTTTTGGTCCGTTGGCTTTGCTCGACAGTGCATTTGGTGTTATCAT
TGAGAAAACACAAGGAGCAGAAGATAATCTGAACACTGGCAGCCAGAACCATGGCAGGCATCAGCGCACAGGTGGGCTTC
CAGGGGTTGCATGAGGGAGTCTGGCAGGCATAACACTACCAGTCTGCGTGCACTCTGTGACAACTGGGAGCACAGGAAAG
GCTCCTTGCTCCCCCAGCCACTC

Alignment

ORF - retro_cpor_321 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.67 %
• Parental protein coverage: 81.82 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MNPLSPYLNVDPRYLVQDTDEFILPTGANKTRGRFELAFFTIGGCCMTGAAFGAVNGLRLGLKETQNMAW
          MNP.S.YLN.DPRYLVQDTD.FIL.TGANKT.GRFE.AF...GGCCMTG.AF.AVN.L.LGLKETQNMAW
Retrocopy MNPWSLYLNMDPRYLVQDTDAFILLTGANKTQGRFEMAFSATGGCCMTGTAFVAVNRLQLGLKETQNMAW

Parental  SKPRNVQILNMVTRQGALWANTLGSLALLYSAFGVIIEKTRGAEDDLNTVAAGTMTGMLYKCTGGLRGVA
          SKPRN.Q.LNMVTRQGALWA...G.LALL.SAFGVIIEKT.GAED.LNT...G.........TGGL.GVA
Retrocopy SKPRNGQVLNMVTRQGALWASVFGPLALLDSAFGVIIEKTQGAEDNLNT---GSQNHGRHQRTGGLPGVA

Parental  RGGLAGLTL-TGLYALYNNWEHMKGSLLHQSL
          .G.LAG.TL.T.L.AL..NWEH.KGSLL.Q.L
Retrocopy *GSLAGITL<TSLRALCDNWEHRKGSLLPQPL

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	17.25 RPM
SRP017611_kidney	0.00 RPM	32.66 RPM
SRP017611_liver	0.00 RPM	17.67 RPM
SRP040447_lung	0.00 RPM	14.63 RPM
SRP040447_skeletal_muscle	0.00 RPM	40.36 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_321 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_321 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 15 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000007501	1 retrocopy	retro_amel_1488,
Canis familiaris	ENSCAFG00000029477	1 retrocopy	retro_cfam_329,
Choloepus hoffmanni	ENSCHOG00000007073	1 retrocopy	retro_chof_797,
Callithrix jacchus	ENSCJAG00000013336	1 retrocopy	retro_cjac_2965,
Cavia porcellus	ENSCPOG00000019917	2 retrocopies	retro_cpor_1013, retro_cpor_321 ,
Monodelphis domestica	ENSMODG00000002661	2 retrocopies	retro_mdom_1202, retro_mdom_860,
Mus musculus	ENSMUSG00000013701	1 retrocopy	retro_mmus_2,
Oryctolagus cuniculus	ENSOCUG00000000525	1 retrocopy	retro_ocun_73,
Otolemur garnettii	ENSOGAG00000015393	1 retrocopy	retro_ogar_2627,
Ochotona princeps	ENSOPRG00000005255	2 retrocopies	retro_opri_520, retro_opri_920,
Procavia capensis	ENSPCAG00000015914	1 retrocopy	retro_pcap_181,
Rattus norvegicus	ENSRNOG00000019811	3 retrocopies	retro_rnor_1804, retro_rnor_225, retro_rnor_661,
Sorex araneus	ENSSARG00000010335	1 retrocopy	retro_sara_86,
Sus scrofa	ENSSSCG00000025276	1 retrocopy	retro_sscr_404,
Ictidomys tridecemlineatus	ENSSTOG00000007041	1 retrocopy	retro_itri_1043,