RetrogeneDB ID: retro_cpor_1009

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_4:24017589..24017876(+)
• Located in intron of: ENSCPOG00000019749

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPL26
• Ensembl ID: ENSCPOG00000001315
• Aliases: None
• Description: None

Sequence

>retro_cpor_1009
CATTTCCATGTACCTCTCCACATTCACAGGAAGCATATGCCTTATCCTCTTTCCAAAGAGCTGAAGCAGAAGTACATTTG
ACTCATGCCTATCTAAAAAGATGATGAAGTTCAAGTTGTGCGAAGATACTATAAAGGTCAGCAAATCTGCAAAGCAGTCT
GCATCTATGGGAAGAAATACATTACCCATGCTGAATGGGTACAGTGGGAAAGGCTAACGGCATAACTGTCCACGTGGGTG
TTCCCCCCAGCAAGGTGGCTATCAATGGACAAAGCTTGCAAAAAGAT

Alignment

ORF - retro_cpor_1009 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.27 %
• Parental protein coverage: 66.9 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  HFNAPSHIRRKIMSSPLSKELRQKYNVRSMPIRKDDEVQVVRGHYKGQQIGKVVQVYRKKYVIYIERVQR
          HF..P.HI.RK.M..PLSKEL.QKY....MPI.KDDEVQVVR..YKGQQI.K.V..Y.KKY....E.VQ.
Retrocopy HFHVPLHIHRKHMPYPLSKELKQKY-I*LMPI*KDDEVQVVRRYYKGQQICKAVCIYGKKYITHAEWVQW

Parental  E-KANGTTVHVGIHPSKVVITRLKLDKD
          E.KANG.TVHVG..PSKV.I....L.KD
Retrocopy E<KANGITVHVGVPPSKVAINGQSLQKD

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	192.45 RPM
SRP017611_kidney	0.00 RPM	220.68 RPM
SRP017611_liver	0.00 RPM	156.48 RPM
SRP040447_lung	0.00 RPM	355.56 RPM
SRP040447_skeletal_muscle	0.00 RPM	353.86 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1009 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1009 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 17 parental genes, and 116 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000002453	7 retrocopies	retro_amel_1175, retro_amel_1535, retro_amel_1885, retro_amel_1934, retro_amel_360, retro_amel_499, retro_amel_900,
Bos taurus	ENSBTAG00000012344	2 retrocopies	retro_btau_1090, retro_btau_230,
Callithrix jacchus	ENSCJAG00000014372	8 retrocopies	retro_cjac_110, retro_cjac_119, retro_cjac_240, retro_cjac_250, retro_cjac_270, retro_cjac_297, retro_cjac_321, retro_cjac_362,
Cavia porcellus	ENSCPOG00000001315	10 retrocopies	retro_cpor_1009 , retro_cpor_1161, retro_cpor_1346, retro_cpor_1421, retro_cpor_1503, retro_cpor_1526, retro_cpor_167, retro_cpor_522, retro_cpor_585, retro_cpor_858,
Homo sapiens	ENSG00000161970	27 retrocopies	retro_hsap_1137, retro_hsap_1309, retro_hsap_1376, retro_hsap_1394, retro_hsap_191, retro_hsap_2108, retro_hsap_2165, retro_hsap_2253, retro_hsap_253, retro_hsap_267, retro_hsap_2946, retro_hsap_3118, retro_hsap_3260, retro_hsap_3324, retro_hsap_3490, retro_hsap_3700, retro_hsap_3803, retro_hsap_3813, retro_hsap_3914, retro_hsap_4043, retro_hsap_4061, retro_hsap_4874, retro_hsap_4932, retro_hsap_642, retro_hsap_691, retro_hsap_915, retro_hsap_998,
Gorilla gorilla	ENSGGOG00000023944	4 retrocopies	retro_ggor_2565, retro_ggor_270, retro_ggor_51, retro_ggor_974,
Macropus eugenii	ENSMEUG00000009891	7 retrocopies	retro_meug_1239, retro_meug_1538, retro_meug_1607, retro_meug_1827, retro_meug_262, retro_meug_322, retro_meug_534,
Myotis lucifugus	ENSMLUG00000002176	1 retrocopy	retro_mluc_232,
Macaca mulatta	ENSMMUG00000003448	22 retrocopies	retro_mmul_1117, retro_mmul_1361, retro_mmul_1398, retro_mmul_1497, retro_mmul_1710, retro_mmul_1773, retro_mmul_1899, retro_mmul_1986, retro_mmul_2052, retro_mmul_2163, retro_mmul_2332, retro_mmul_2344, retro_mmul_325, retro_mmul_360, retro_mmul_398, retro_mmul_405, retro_mmul_448, retro_mmul_548, retro_mmul_805, retro_mmul_903, retro_mmul_920, retro_mmul_992,
Monodelphis domestica	ENSMODG00000006201	2 retrocopies	retro_mdom_36, retro_mdom_64,
Nomascus leucogenys	ENSNLEG00000009981	1 retrocopy	retro_nleu_76,
Otolemur garnettii	ENSOGAG00000017070	3 retrocopies	retro_ogar_118, retro_ogar_255, retro_ogar_66,
Pan troglodytes	ENSPTRG00000008742	3 retrocopies	retro_ptro_1546, retro_ptro_2510, retro_ptro_73,
Rattus norvegicus	ENSRNOG00000004214	3 retrocopies	retro_rnor_213, retro_rnor_260, retro_rnor_273,
Sarcophilus harrisii	ENSSHAG00000006890	1 retrocopy	retro_shar_458,
Sus scrofa	ENSSSCG00000028850	9 retrocopies	retro_sscr_261, retro_sscr_363, retro_sscr_426, retro_sscr_427, retro_sscr_471, retro_sscr_485, retro_sscr_508, retro_sscr_609, retro_sscr_736,
Ictidomys tridecemlineatus	ENSSTOG00000021923	6 retrocopies	retro_itri_1113, retro_itri_1145, retro_itri_1206, retro_itri_1262, retro_itri_1670, retro_itri_811,