RetrogeneDB ID: retro_cpor_1343

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_70:232023..232334(-)
• Located in intron of: ENSCPOG00000026559

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPL36
• Ensembl ID: ENSCPOG00000022839
• Aliases: None
• Description: 60S ribosomal protein L36 [Source:UniProtKB/TrEMBL;Acc:H0WCA3]

Sequence

>retro_cpor_1343
ATGGCTCTGCGCTAGCCCATGGCCATGGGCCTCAACAAGGGGACAAGGTGACCAAGAATGTGAGCAAACTGAGGCACAGT
CCCTGCGGTGGATGTCTCACCAAGCACACCGAGTTCATGCGGGTCATGACCCAGGAGGTATGCGGCTTTGCCCTCTGCGA
GCTGTGCACCTTGGAGCTGCTCAAGGTCTCCAAGGACAAGTGGGTCCTCAAGCTCATCAAGAAAAGGGTTGGGATGCACA
TTTGTGCCCAGAGGAAGCAGGAGAAGCTAAGTAACAAGGTGACCACTGAGGAAGGCAGCTGCAAAAAGGAC

Alignment

ORF - retro_cpor_1343 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.55 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MALRYPMAVGLNKG-HKVTKNVSKPRHSRRRGRLTKHTKFVRDMIREVCGFAPYERRAMELLKVSKDKRA
          MALR.PMA.GLNKG..KVTKNVSK.RHS...G.LTKHT.F.R.M..EVCGFA..E....ELLKVSKDK..
Retrocopy MALR*PMAMGLNKG<DKVTKNVSKLRHSPCGGCLTKHTEFMRVMTQEVCGFALCELCTLELLKVSKDKWV

Parental  LKFIKKRVVGTHIRAKRKREELSNVLAAMRKAAAKKD
          LK.IKKR.VG.HI.A.RK.E.LSN..........KKD
Retrocopy LKLIKKR-VGMHICAQRKQEKLSNKVTT-EEGSCKKD

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	26.52 RPM
SRP017611_kidney	0.00 RPM	76.95 RPM
SRP017611_liver	0.00 RPM	29.77 RPM
SRP040447_lung	0.03 RPM	134.73 RPM
SRP040447_skeletal_muscle	0.00 RPM	135.84 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1343 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1343 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 18 parental genes, and 101 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000012349	6 retrocopies	retro_amel_1222, retro_amel_1581, retro_amel_1935, retro_amel_748, retro_amel_799, retro_amel_835,
Bos taurus	ENSBTAG00000001794	3 retrocopies	retro_btau_139, retro_btau_238, retro_btau_81,
Callithrix jacchus	ENSCJAG00000017072	2 retrocopies	retro_cjac_280, retro_cjac_52,
Cavia porcellus	ENSCPOG00000022839	3 retrocopies	retro_cpor_1317, retro_cpor_1343 , retro_cpor_857,
Dasypus novemcinctus	ENSDNOG00000005163	8 retrocopies	retro_dnov_19, retro_dnov_2160, retro_dnov_311, retro_dnov_313, retro_dnov_457, retro_dnov_578, retro_dnov_595, retro_dnov_631,
Felis catus	ENSFCAG00000011838	5 retrocopies	retro_fcat_1152, retro_fcat_1168, retro_fcat_1216, retro_fcat_406, retro_fcat_94,
Gorilla gorilla	ENSGGOG00000015365	11 retrocopies	retro_ggor_1514, retro_ggor_1613, retro_ggor_180, retro_ggor_2211, retro_ggor_2535, retro_ggor_2620, retro_ggor_34, retro_ggor_487, retro_ggor_60, retro_ggor_82, retro_ggor_885,
Latimeria chalumnae	ENSLACG00000015161	1 retrocopy	retro_lcha_47,
Macropus eugenii	ENSMEUG00000002743	4 retrocopies	retro_meug_1318, retro_meug_176, retro_meug_261, retro_meug_283,
Monodelphis domestica	ENSMODG00000001275	2 retrocopies	retro_mdom_1353, retro_mdom_148,
Mustela putorius furo	ENSMPUG00000006166	6 retrocopies	retro_mputfur_1423, retro_mputfur_150, retro_mputfur_1562, retro_mputfur_747, retro_mputfur_749, retro_mputfur_773,
Mus musculus	ENSMUSG00000057863	9 retrocopies	retro_mmus_151, retro_mmus_1601, retro_mmus_1900, retro_mmus_1912, retro_mmus_193, retro_mmus_2864, retro_mmus_3379, retro_mmus_38, retro_mmus_652,
Otolemur garnettii	ENSOGAG00000027049	12 retrocopies	retro_ogar_1348, retro_ogar_18, retro_ogar_184, retro_ogar_2256, retro_ogar_2278, retro_ogar_2332, retro_ogar_2537, retro_ogar_2592, retro_ogar_3278, retro_ogar_358, retro_ogar_795, retro_ogar_888,
Pongo abelii	ENSPPYG00000009431	12 retrocopies	retro_pabe_1194, retro_pabe_137, retro_pabe_1639, retro_pabe_1792, retro_pabe_1834, retro_pabe_1898, retro_pabe_216, retro_pabe_3081, retro_pabe_3173, retro_pabe_318, retro_pabe_3443, retro_pabe_3688,
Rattus norvegicus	ENSRNOG00000033473	5 retrocopies	retro_rnor_11, retro_rnor_17, retro_rnor_170, retro_rnor_369, retro_rnor_687,
Sarcophilus harrisii	ENSSHAG00000013492	8 retrocopies	retro_shar_185, retro_shar_347, retro_shar_543, retro_shar_557, retro_shar_592, retro_shar_615, retro_shar_716, retro_shar_819,
Sus scrofa	ENSSSCG00000030010	2 retrocopies	retro_sscr_849, retro_sscr_960,
Ictidomys tridecemlineatus	ENSSTOG00000020518	2 retrocopies	retro_itri_43, retro_itri_593,