RetrogeneDB ID: retro_cpor_289

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_12:25257339..25258383(+)
• Located in intron of: ENSCPOG00000005727

Retrocopy information

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

Parental gene information

• Parental gene symbol: ABCE1
• Ensembl ID: ENSCPOG00000007367
• Aliases: None
• Description: None

Sequence

>retro_cpor_289
TGCCCCTTTGGCACCTTATCAATTGTCAATTTACCAAGCAACTTGGAAGAAGAAACAACACAGTGATATTGTGCCAGCGC
CTTCAAACTTCACAGGTCTCCTGTCCCTCATGTAAGTGAAGTCTTGGGATTAGTTGGAACTATTGGTATTGGAAAATCAA
CAGCATAAAAAATTTTAGCAGGAAAGCAAAAGCCGACCTTGAAAAGTATGATGATCCTCTTTATCTGCAGGAGATTCTGA
CTTACTTCCATGGATCTGAATTAAAAAATTACTTTATTAAGATTCTGAAACATGATCTAAAGTCTATTATCAAATCAATA
TATGGGTCAGATTACCAAGAATGCAAAGGGGACAATAGAGTCTATTTTGGATTGAAAGGATAAAACAAAGACACGTGGAA
TTGTATGTCAACAGATTGATTTAACCCATTTTAAAGAATAAAATGTTGAAGATCTTTCAGGAGAATTGCAGAGATTCTCT
TATGTTGTTGTTTACATACAGAAAGCTGATATTTTCATGTGTGATGAGCCCTCTAGATACCTAGATGTCAAGCTGTGTTT
AAGAATGCTATTATTATTATTCAATCTCTGATAGATTCAGATAGATATATCACTGTGGTGGAGCATGATCTAAGTGTATG
ACACTATCTCTCTGAGTTCATTTGTTGTTAACCATGATGTACTGAGTACTCCCAATGTTATCACTATGCCTTTAAGTGTA
ATAGAAAGCATAAATATTTTTGGATGGCTTTTTCAAACAGAAAATTTGAGATTCTGAAATACATTGCTTGTTAAAGTAAT
GAAACAGCAAATGAAGTTAAGTTAAAAAGTTGTGTTTGTATAAATATTCAGGAATGGATAAAATGGTAGAAATTGAGCTA
GTAATTAAAATTGGAGAGTTTGCTGATTCTGAAATATGGTGATGATGGAGGAAAATGATACAGGTAAAATGAGATTTTTC
AGAATGCTTGCTGGGAGAGTGAAACCTGATGAAGGAGGGGAACTACCAGTTCTAAATGTCAGATGTAAGCCACAAAGTCA
GTCC

Alignment

ORF - retro_cpor_289 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.68 %
• Parental protein coverage: 58.93 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 8

Retrocopy - Parental Gene Alignment:

Parental  CPFGALSIVNLPSNLEKETTHRYCANAFKLHRLPIPRPGEVLGLVGTNGIGKSTALKILAGKQKP-NLGK
          CPFG.LSIVNLPSNLE.ETT..YCA.AFKLHR.P.P...EVLGLVGT.GIGKSTA.KILAGKQKP..L.K
Retrocopy CPFGTLSIVNLPSNLEEETTQ*YCASAFKLHRSPVPHVSEVLGLVGTIGIGKSTA*KILAGKQKP<DLEK

Parental  YDDPPDWQEILTYFRGSELQNYFTKILEDDLKAIIKPQYVD-QIPKAAKG-TVGSILDRKDETKTQAIVC
          YDDP...QEILTYF.GSEL.NYF.KIL..DLK.IIK..Y.....P....G.T..SILD.KD.TKT..IVC
Retrocopy YDDPLYLQEILTYFHGSELKNYFIKILKHDLKSIIKSIYGS<RLPRMQRG<TIESILD*KDKTKTRGIVC

Parental  QQLDLTHLKERNVEDLSGGELQRFACAVVCIQKADIFMFDEPSSYLDVKQRL-KAAI-TIRSLINPDRYI
          QQ.DLTH.KE.NVEDLS.GELQRF...VV.IQKADIFM.DEPS.YLDVK..L.K.AI..I.SLI..DRYI
Retrocopy QQIDLTHFKE*NVEDLS-GELQRFSYVVVYIQKADIFMCDEPSRYLDVKLCL<KNAIIIIQSLIDSDRYI

Parental  IVVEHDLSVLDYLSDFICC-LYGVPSAYGVVTMPFSVREGINIFLDGYVPTENLRFRDASLVFKVA-ETA
          .VVEHDLSV..YLS.FICC....V.S...V.TMP.SV.E.INIF......TENLRF....LV.KV..ETA
Retrocopy TVVEHDLSV*HYLSEFICC>NHDVLSTPNVITMPLSVIESINIF-GWLFQTENLRF*NTLLV-KVM<ETA

Parental  NEEE-VKKMCMYKYPGMKKKMGEFELAIVAGEFTDSEI-MVMLGENGTGKTTFIRMLAGRLKPDEGGEVP
          NE...VKK.C.YKY.GM..KM.E.EL.I..GEF.DSEI.MVM..EN.TGK..F.RMLAGR.KPDEGGE.P
Retrocopy NEVK<VKKLCLYKYSGM-DKMVEIELVIKIGEFADSEI<MVMMEENDTGKMRFFRMLAGRVKPDEGGELP

Parental  VLNVSYKPQKIS
          VLNV..KPQ..S
Retrocopy VLNVRCKPQSQS

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	41.53 RPM
SRP017611_kidney	0.00 RPM	50.35 RPM
SRP017611_liver	0.04 RPM	37.39 RPM
SRP040447_lung	0.10 RPM	31.32 RPM
SRP040447_skeletal_muscle	0.00 RPM	25.80 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_289 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_289 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 10 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000004534	1 retrocopy	retro_chof_1280,
Cavia porcellus	ENSCPOG00000007367	1 retrocopy	retro_cpor_289 ,
Homo sapiens	ENSG00000164163	1 retrocopy	retro_hsap_3826,
Macaca mulatta	ENSMMUG00000004433	1 retrocopy	retro_mmul_1628,
Mus musculus	ENSMUSG00000058355	1 retrocopy	retro_mmus_1503,
Nomascus leucogenys	ENSNLEG00000005460	1 retrocopy	retro_nleu_2125,
Oryctolagus cuniculus	ENSOCUG00000001821	2 retrocopies	retro_ocun_1925, retro_ocun_668,
Procavia capensis	ENSPCAG00000006183	1 retrocopy	retro_pcap_90,
Pongo abelii	ENSPPYG00000015097	1 retrocopy	retro_pabe_3067,
Pan troglodytes	ENSPTRG00000016481	1 retrocopy	retro_ptro_2603,