RetrogeneDB ID: retro_cpor_1088

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_45:1713914..1714621(-)
• Located in intron of: ENSCPOG00000004192

Retrocopy information

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

Parental gene information

• Parental gene symbol: EIF4A1
• Ensembl ID: ENSCPOG00000004900
• Aliases: None
• Description: None

Sequence

>retro_cpor_1088
GACAATGGCCCAGATGGGATGAAGGCTGAAGGTGTCACTGAGAGTAACCAATATGAGACTGTTGACAAGCTTTGATGATA
TGAATCTCTCAGAGTCACTCCTCCATGGCATCTATGCTGATGGTTTTGAGAAATCCTCTGCCATCCAGCAGCATGCTATT
TTTCCTTGTATCAACGGTTATGATGTGATTGCTCAAGCCCAGTCTGGGACCAGGAAAATGGCCACATTTGCTATATTTAT
TCTGCAAAAGATTGAGTTAGATCTAAAGGCTACCCGGGCTTTGGTTCTGTCTCCCACTGGAGAATTGGCTCAGCAGACAC
AAAGGTGGTTATGGCTTTAGGAGATCACATGAGTGCCTCATGTTGTGCCTGTAATGGGGGCACCAATGTGCGTGCTGAAG
TCCAGACACTGCAGATGGAAGCTCCTCATACCATTGTAGGAACCCTGGCTGCAAGTTTGATACACTTAACTGGAGATACT
TGTGTCCCAAATACATTAAGATGTTTGTGTTAGACGAAGCTGATGAAATGTTGAGCCGTGGATTCAAGGATCAGATTTAT
GATATATTACAAACCCTCAACAGCAACACCCAGGTAGTTTTGCTGTCAGCTTCTGATGTGCTAGAGGTGACCAAGAAGTT
CATGAGAGACTCTATTTGGATTCTCGTCAAGAAAGAAGAGTTGACCCTGGAAGGTATCTGCCAATTC

Alignment

ORF - retro_cpor_1088 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.64 %
• Parental protein coverage: 60.05 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  DNGPDGMEPEGVIESNWNEIVD-SFDDMNLSESLLRGIYAYGFEKPSAIQQRAILPCIKGYDVIAQAQSG
          DNGPDGM..EGV.ESN..E.VD.SFDDMNLSESLL.GIYA.GFEK.SAIQQ.AI.PCI.GYDVIAQAQSG
Retrocopy DNGPDGMKAEGVTESNQYETVD>SFDDMNLSESLLHGIYADGFEKSSAIQQHAIFPCINGYDVIAQAQSG

Parental  TGKTATFAISILQQIELDLKATQALVLAPTRELAQQIQ-KVVMALGDYMGASCHACIGGTNVRAEVQKLQ
          T.K.ATFAI.ILQ.IELDLKAT.ALVL.PT.ELAQQ.Q.KVVMALGD.M.ASC.AC.GGTNVRAEVQ.LQ
Retrocopy TRKMATFAIFILQKIELDLKATRALVLSPTGELAQQTQ<KVVMALGDHMSASCCACNGGTNVRAEVQTLQ

Parental  MEAPHIIVGT-PGRVFDMLNRRYLSPKYIKMFVLDEADEMLSRGFKDQIYDIFQKLNSNTQVVLLSATMP
          MEAPH.IVGT.PG..FD.LN.RYL.PKYIKMFVLDEADEMLSRGFKDQIYDI.Q.LNSNTQVVLLSA...
Retrocopy MEAPHTIVGT<PGCKFDTLNWRYLCPKYIKMFVLDEADEMLSRGFKDQIYDILQTLNSNTQVVLLSA---

Parental  SDVLEVTKKFMRDPIRILVKKEELTLEGIRQF
          SDVLEVTKKFMRD.I.ILVKKEELTLEGI.QF
Retrocopy SDVLEVTKKFMRDSIWILVKKEELTLEGICQF

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	70.00 RPM
SRP017611_kidney	0.00 RPM	101.34 RPM
SRP017611_liver	0.00 RPM	68.47 RPM
SRP040447_lung	0.08 RPM	240.38 RPM
SRP040447_skeletal_muscle	0.01 RPM	76.46 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1088 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1088 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 16 parental genes, and 66 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000004900	1 retrocopy	retro_cpor_1088 ,
Cavia porcellus	ENSCPOG00000011183	1 retrocopy	retro_cpor_639,
Erinaceus europaeus	ENSEEUG00000003581	1 retrocopy	retro_eeur_610,
Felis catus	ENSFCAG00000024897	1 retrocopy	retro_fcat_370,
Homo sapiens	ENSG00000161960	10 retrocopies	retro_hsap_1004, retro_hsap_1182, retro_hsap_1252, retro_hsap_1270, retro_hsap_1796, retro_hsap_2520, retro_hsap_4836, retro_hsap_4873, retro_hsap_4931, retro_hsap_610,
Gorilla gorilla	ENSGGOG00000024702	8 retrocopies	retro_ggor_1321, retro_ggor_1572, retro_ggor_3015, retro_ggor_537, retro_ggor_798, retro_ggor_920, retro_ggor_983, retro_ggor_998,
Macropus eugenii	ENSMEUG00000010780	2 retrocopies	retro_meug_158, retro_meug_179,
Myotis lucifugus	ENSMLUG00000003415	3 retrocopies	retro_mluc_1047, retro_mluc_1229, retro_mluc_1805,
Macaca mulatta	ENSMMUG00000013499	1 retrocopy	retro_mmul_1280,
Monodelphis domestica	ENSMODG00000007090	3 retrocopies	retro_mdom_1282, retro_mdom_326, retro_mdom_711,
Mus musculus	ENSMUSG00000059796	7 retrocopies	retro_mmus_1810, retro_mmus_1853, retro_mmus_2320, retro_mmus_2473, retro_mmus_3122, retro_mmus_325, retro_mmus_527,
Nomascus leucogenys	ENSNLEG00000009547	7 retrocopies	retro_nleu_2109, retro_nleu_2117, retro_nleu_230, retro_nleu_2470, retro_nleu_2769, retro_nleu_440, retro_nleu_701,
Pan troglodytes	ENSPTRG00000008694	10 retrocopies	retro_ptro_1201, retro_ptro_1465, retro_ptro_2954, retro_ptro_3112, retro_ptro_3247, retro_ptro_450, retro_ptro_750, retro_ptro_810, retro_ptro_862, retro_ptro_870,
Rattus norvegicus	ENSRNOG00000030628	3 retrocopies	retro_rnor_1059, retro_rnor_2213, retro_rnor_2306,
Sorex araneus	ENSSARG00000006017	7 retrocopies	retro_sara_224, retro_sara_383, retro_sara_461, retro_sara_567, retro_sara_6, retro_sara_605, retro_sara_89,
Ictidomys tridecemlineatus	ENSSTOG00000024814	1 retrocopy	retro_itri_610,