RetrogeneDB ID: retro_cpor_387

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_14:23535772..23536539(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: EEF1A1
• Ensembl ID: ENSCPOG00000004067
• Aliases: None
• Description: Elongation factor 1-alpha [Source:UniProtKB/TrEMBL;Acc:H0V2B3]

Sequence

>retro_cpor_387
ATAGGAAAGGAAAAGACTCACATTAATATCATTGTCACTGGACATGTGGATTCTGGCAAGTCCACCACTACTGGCATCTG
ATCTACAAGTGTGGTGGCATTGACAAAAGAACCATTGAAAAATTTGAGAAGGAGGCTGCTGAGGTAGGAAAGGGTTCCTT
TAAATATGCCTGGGTGTTGGATAAACTGAAAGCCAAGCGTGAGCGTGGTATCACCATCGACATCTCCCTGTGGAAATCTG
AGACCAGCAAGTACTACATGACTATCTTTAATGCCCCTGGACACAGAGACTTTATCAAAAACATGATTACAGGCACATCC
CAGGCTGACTGTGCTGTCCTGATTGTTGCTGCTGGTGTTGGTGAATTCGAAGCTGGTATCTCCAAGAATGGATAGACCTG
TGAGCATGATCTTCTGGCTTGTATTCTGGGTGTCAAACAACTAATTGTTGGTATTAACAAAATGGATTCCACTGAGCCAC
CCTCCAGCCAGAGGAGAAACAAGAAAATTGTTAAGCAAGTCAGCACCTACATTAAGAAAATCGGCTACAACCATGACACT
GTAAATTTTGTGCCAATTTCTGGTTGGAATGATGACAACATATTGGAGCCAAGCGCTAATATGCCTTAGTTCAAGGGATG
GAAGGTCACTGGTAAAGATGGCAGTGCTAGTGGAACCATACTGCTTAAAGCTTTGGATTGCATCCTTCCACCCACTCGCC
TTTGAGGCTGCCCCTCTAGGATATCTATAAAATTGGTGGTATTGATA

Alignment

ORF - retro_cpor_387 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.27 %
• Parental protein coverage: 55.41 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MGKEKTHINIVVIGHVDSGKSTTTG-HLIYKCGGIDKRTIEKFEKEAAEMGKGSFKYAWVLDKLKAERER
          .GKEKTHINI.V.GHVDSGKSTTTG.HLIYKCGGIDKRTIEKFEKEAAE.GKGSFKYAWVLDKLKA.RER
Retrocopy IGKEKTHINIIVTGHVDSGKSTTTG<HLIYKCGGIDKRTIEKFEKEAAEVGKGSFKYAWVLDKLKAKRER

Parental  GITIDISLWKFETSKYYVTIIDAPGHRDFIKNMITGTSQADCAVLIVAAGVGEFEAGISKNGQTREHALL
          GITIDISLWK.ETSKYY.TI..APGHRDFIKNMITGTSQADCAVLIVAAGVGEFEAGISKNG.T.EH.LL
Retrocopy GITIDISLWKSETSKYYMTIFNAPGHRDFIKNMITGTSQADCAVLIVAAGVGEFEAGISKNG*TCEHDLL

Parental  AYTLGVKQLIVGVNKMDSTEPPYSQKRYEEIVKEVSTYIKKIGYNPDTVAFVPISGWNGDNMLEPSANMP
          A..LGVKQLIVG.NKMDSTEPP.SQ.R...IVK.VSTYIKKIGYN.DTV.FVPISGWN.DN.LEPSANMP
Retrocopy ACILGVKQLIVGINKMDSTEPPSSQRRNKKIVKQVSTYIKKIGYNHDTVNFVPISGWNDDNILEPSANMP

Parental  WFKGWKVTRKDGNASGTTLLEALDCILPPTRPTDKPLRLPLQDVYKI
          .FKGWKVT.KDG.ASGT.LL.ALDCILPPTR....P.R.....V..I
Retrocopy *FKGWKVTGKDGSASGTILLKALDCILPPTRL*GCPSRISIKLVVLI

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	855.04 RPM
SRP017611_kidney	0.10 RPM	1991.99 RPM
SRP017611_liver	0.00 RPM	1852.07 RPM
SRP040447_lung	0.05 RPM	3418.91 RPM
SRP040447_skeletal_muscle	0.00 RPM	830.52 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_387 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_387 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 83 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000013249	1 retrocopy	retro_cfam_1007,
Callithrix jacchus	ENSCJAG00000010051	6 retrocopies	retro_cjac_1431, retro_cjac_3075, retro_cjac_34, retro_cjac_3735, retro_cjac_733, retro_cjac_97,
Cavia porcellus	ENSCPOG00000004067	15 retrocopies	retro_cpor_1150, retro_cpor_1162, retro_cpor_1191, retro_cpor_1256, retro_cpor_1393, retro_cpor_1492, retro_cpor_1499, retro_cpor_348, retro_cpor_381, retro_cpor_387 , retro_cpor_413, retro_cpor_709, retro_cpor_891, retro_cpor_918, retro_cpor_959,
Dipodomys ordii	ENSDORG00000009629	1 retrocopy	retro_dord_509,
Equus caballus	ENSECAG00000022260	1 retrocopy	retro_ecab_802,
Erinaceus europaeus	ENSEEUG00000000342	3 retrocopies	retro_eeur_407, retro_eeur_492, retro_eeur_625,
Loxodonta africana	ENSLAFG00000028081	1 retrocopy	retro_lafr_651,
Macaca mulatta	ENSMMUG00000004852	15 retrocopies	retro_mmul_1375, retro_mmul_1407, retro_mmul_1518, retro_mmul_1525, retro_mmul_1690, retro_mmul_1707, retro_mmul_1721, retro_mmul_1739, retro_mmul_1743, retro_mmul_1906, retro_mmul_2196, retro_mmul_2250, retro_mmul_323, retro_mmul_6, retro_mmul_848,
Monodelphis domestica	ENSMODG00000018533	4 retrocopies	retro_mdom_1053, retro_mdom_1146, retro_mdom_311, retro_mdom_792,
Mus musculus	ENSMUSG00000037742	15 retrocopies	retro_mmus_1349, retro_mmus_1518, retro_mmus_1667, retro_mmus_1783, retro_mmus_1816, retro_mmus_1849, retro_mmus_1850, retro_mmus_1864, retro_mmus_1909, retro_mmus_2363, retro_mmus_2583, retro_mmus_2902, retro_mmus_3249, retro_mmus_480, retro_mmus_483,
Nomascus leucogenys	ENSNLEG00000001476	6 retrocopies	retro_nleu_1492, retro_nleu_1584, retro_nleu_1754, retro_nleu_1901, retro_nleu_235, retro_nleu_829,
Pan troglodytes	ENSPTRG00000018347	1 retrocopy	retro_ptro_71,
Ictidomys tridecemlineatus	ENSSTOG00000007687	4 retrocopies	retro_itri_1509, retro_itri_1740, retro_itri_1816, retro_itri_195,
Vicugna pacos	ENSVPAG00000007637	9 retrocopies	retro_vpac_369, retro_vpac_404, retro_vpac_510, retro_vpac_511, retro_vpac_523, retro_vpac_544, retro_vpac_582, retro_vpac_592, retro_vpac_606,
Drosophila melanogaster	FBgn0000557	1 retrocopy	retro_dmel_9,