RetrogeneDB ID: retro_cpor_1256

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_6:49773561..49774355(-)
• 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_1256
ATGGGAAAGGAAACGATTCTCATTGATATCCTTGTCATTGGATTCATAGATTCAAGCAAGTCCACTACTACTGGCCATCT
CATTGACAAATTTGGCGGCACTGACAAAGAACCACTAAAAACTCTGAGAGGCAGGCTGCTGAGATGGGGAAGATTCCTTC
AAATATGCCTGGGTCTTGGATAAATTGAAAGCCAAGTGTGAGTGTGGTAAACCCATTGACATCTCCCTGTGGAAATTTGA
GATGAGTAATTATTATGTGACTATCACTGATGCTCCTGGACACAGAGACTTTATCAAAAGCATGATTGCAGGCACATTTC
AGGCTGACTGTGCTGTTCTGATTGTTGCTGCCATTGTTGGTGAATTCAAAGCTGGTATCTCCAAGAACGGGCAGACCCAT
GATCATGCCCTTCTGGCTTACATGCTGGGTGTGAAACAACTAACTGTCAGTGTTAACTAAATGGATTCCACTGAGCTAAC
CTTCAGCCAGAAGAGATACAAGGAAATTGTTAAAAAATTCAGCACCTTCATTAAGCAAATTGGCTACAATCCTGACATGG
TGGGTTTTATGCTAATTTCTAGTTGGAATGGTGACAGTATGCTGGACCTAAGAGCTAATATGCCTCAGTTCAAGGGATGG
AAGGTCTCTCATAAAAATGACATTGCCTTTGGAACTACACTGCTTGAAGCTTTGGATTACATACTTGCACCAACTCACCC
AACTGACAAACTATGGGGCTGCCTCCCCAGGATGCCTCCAAAATTGGTGGTATTGGTACCATCCTGTGGGAAAA

Alignment

ORF - retro_cpor_1256 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.85 %
• Parental protein coverage: 57.58 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MGKEKTHINIVVIGHVDSGKSTTTGHLIYKCGGIDK-RTIEKFEKEAAEMGK-GSFKYAWVLDKLKAERE
          MGKE...I.I.VIG..DS.KSTTTGHLI.K.GG.DK.RT....E..AAEMGK..SFKYAWVLDKLKA..E
Retrocopy MGKETILIDILVIGFIDSSKSTTTGHLIDKFGGTDK<RTTKNSERQAAEMGK<DSFKYAWVLDKLKAKCE

Parental  RGITIDISLWKFETSKYYVTIIDAPGHRDFIKNMITGTSQADCAVLIVAAGVGEFEAGISKNGQTREHAL
          .G..IDISLWKFE.S.YYVTI.DAPGHRDFIK.MI.GT.QADCAVLIVAA.VGEF.AGISKNGQT..HAL
Retrocopy CGKPIDISLWKFEMSNYYVTITDAPGHRDFIKSMIAGTFQADCAVLIVAAIVGEFKAGISKNGQTHDHAL

Parental  LAYTLGVKQLIVGVNKMDSTEPPYSQKRYEEIVKEVSTYIKKIGYNPDTVAFVPISGWNGDNMLEPSANM
          LAY.LGVKQL.V.VN.MDSTE...SQKRY.EIVK..ST.IK.IGYNPD.V.F..IS.WNGD.ML...ANM
Retrocopy LAYMLGVKQLTVSVN*MDSTELTFSQKRYKEIVKKFSTFIKQIGYNPDMVGFMLISSWNGDSMLDLRANM

Parental  PWFKGWKVTRKDGNASGTTLLEALDCILPPTRPTDK-PLRLPLQDVYKIGGIGTV-PVGR
          P.FKGWKV..K...A.GTTLLEALD.IL.PT.PTDK....LP.QD..KIGGIGT..PVG.
Retrocopy PQFKGWKVSHKNDIAFGTTLLEALDYILAPTHPTDK<TMGLPPQDASKIGGIGTI<PVGK

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	0.00 RPM	1991.99 RPM
SRP017611_liver	0.00 RPM	1852.07 RPM
SRP040447_lung	0.00 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_1256 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1256 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,