RetrogeneDB ID: retro_cpor_1022

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_4:3842634..3843476(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ARMC10
• Ensembl ID: ENSCPOG00000019936
• Aliases: None
• Description: None

Sequence

>retro_cpor_1022
TGGGCAGAGCACTGCTGCAGGTTAGGGGTGGCAGGCCTGGCCCTGGACACGGGGACCAGCTTCTGCCTCTCACGGTCCAC
AGAAGATTTACCCAGTAGCTCATACAATGATGACTTAAATGCTGAACAACTTGAGAAACTTCTTTACTCACTGGAGTCCA
CTGAGAATCCTATAGTTACTGAAAATGCCTTGATCACTCTGGTTAACAATGTGGCCTTTTCAGCCAAACCAGCTATTATT
CGTGATCTGGGTGGTGTTCCAATTGTTGAAAATTAAATCAACAATCCAAACCACAGCATTAAAGAGAAAGCTTTAAATGC
ACTAGATAACTTGAGCGTGAATGTTAAAAACCAAATCAAGATAAAGATTTTCATCAGTAAAGTCCATGAGGGTGTCCTGT
CCGGTCCCTTGAACTCTGCTGCATAGCTGGCTGCCCTGAGACTGTTGACAAATGTGACAGTCACCAGTGAGCGCCAGCAC
ACTCTGAGCAGTTACCTCGCAAGCCTGTTCCATGTGTTAATGACCGGAAATGCCAAAACCAAGGTTCAAGTTCTGAAGCT
GCTTGTGAATTTGTCTGAAAATCCGGCCATGACAGAGGACTTCTCAGGGCCCAAGTGGACTTGGGGTTCCTTTCCCTTTT
TGAAGGCCACATAGCACAGGAGATTCTTCTTCTAGTACTTACACTGTTTCAGAATATAAGTAACCGCCTCAGAGTGGGAG
GCCGTTCAGCTGCTCAGCTTCCTTTCCTGAAAGGTTCATTGTTTTCCCTATTATATGGAGAAGAATGTGTCCAGCACATG
AAAGCTTTAGTTTAGCATCATGATGTGGATGTGAGAGAAAAG

Alignment

ORF - retro_cpor_1022 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.78 %
• Parental protein coverage: 78.81 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  WKNNCTCHSLRARIRLLSKKRLLRKGDQEDLTNGSYNDVLNAEQLRKLLYLLESTEDPIITEKALVTLGN
          W...C.C....A...L............EDL...SYND.LNAEQL.KLLY.LESTE.PI.TE.AL.TL.N
Retrocopy WAEHC-CRLGVAGLALDTGTSFCLSRSTEDLPSSSYNDDLNAEQLEKLLYSLESTENPIVTENALITLVN

Parental  SAAFSTNQAIIRELGGIPIIGSKINSPNHSIKEKALNALNNLSVNVENQIKIKVFVSRVCEDVLSSPPDS
          ..AFS...AIIR.LGG.PI....IN.PNHSIKEKALNAL.NLSVNV.NQIKIK.F.S.V.E.VLS.P..S
Retrocopy NVAFSAKPAIIRDLGGVPIVEN*INNPNHSIKEKALNALDNLSVNVKNQIKIKIFISKVHEGVLSGPLNS

Parental  AAQLAGLRLLTNMTVTNAHQHLLSTAVADLFGLLLAANGNTKVQVLKLLVNLSENPAMTE-GLLSAQVDA
          AA.LA.LRLLTN.TVT...QH.LS...A.LF..L...N..TKVQVLKLLVNLSENPAMTE.GLL.AQVD.
Retrocopy AA*LAALRLLTNVTVTSERQHTLSSYLASLFHVLMTGNAKTKVQVLKLLVNLSENPAMTE<GLLRAQVDL

Parental  SFLSLFDGHVAQEILLRVLTLFQNINNCLRV---EAVQPPFPEGSLFSLLYGEECVQKMKALVNHHEVDV
          .FLSLF.GH.AQEILL.VLTLFQNI.N.LRV....A.Q.PF..GSLFSLLYGEECVQ.MKALV.HH.VDV
Retrocopy GFLSLFEGHIAQEILLLVLTLFQNISNRLRVGGRSAAQLPFLKGSLFSLLYGEECVQHMKALV*HHDVDV

Parental  REK
          REK
Retrocopy REK

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	1.96 RPM
SRP017611_kidney	0.00 RPM	2.09 RPM
SRP017611_liver	0.00 RPM	0.87 RPM
SRP040447_lung	0.25 RPM	1.39 RPM
SRP040447_skeletal_muscle	0.20 RPM	0.50 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1022 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1022 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 9 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000004247	1 retrocopy	retro_cfam_1264,
Choloepus hoffmanni	ENSCHOG00000002095	1 retrocopy	retro_chof_2665,
Callithrix jacchus	ENSCJAG00000021208	2 retrocopies	retro_cjac_1758, retro_cjac_2104,
Cavia porcellus	ENSCPOG00000019936	1 retrocopy	retro_cpor_1022 ,
Homo sapiens	ENSG00000170632	1 retrocopy	retro_hsap_2815,
Microcebus murinus	ENSMICG00000010160	1 retrocopy	retro_mmur_638,
Myotis lucifugus	ENSMLUG00000006088	3 retrocopies	retro_mluc_1587, retro_mluc_1825, retro_mluc_624,
Mus musculus	ENSMUSG00000038525	3 retrocopies	retro_mmus_1292, retro_mmus_2256, retro_mmus_969,
Vicugna pacos	ENSVPAG00000008914	1 retrocopy	retro_vpac_19,