RetrogeneDB ID: retro_cpor_534

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_180:412498..412972(+)
• Located in intron of: ENSCPOG00000003397

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPS11
• Ensembl ID: ENSCPOG00000015145
• Aliases: None
• Description: None

Sequence

>retro_cpor_534
ATGGTGGACATTCAGACAGAACGCGCCTATCAGAAAACACCGACTATCTTCCAAAACAAGAAGAGGGTGCTGCTGGGAGA
AACTGGCAAGGAGAAGCTCCCTCGGTACTATAAGAACATTGGTCTGGGCTTCAAGACTCTTAAAGAGGTCATCAAGGGCA
CCTATATCGATAAAAAATGCCCCTTTACCAGGAATGTCTCCATTCGAGGGCAGATCCTATCTGGTGTGGTGACCAAGATG
AAGATGCAAAGGACCACTGTCATCCGCTGAGACTATCTCCACTACATCCGCAAATATAATCACTTTGAGAAGCGTCACAA
GTACATGTCCGTGCACCTGTCACCCTGCTTCAGGGAAGTCCAGATTGGAGACATCGCCAATGTGGGCGAGTGCAGGCCAC
TGAGTAAGACAGTGTGCTTCAATGTGCTTAAGGTCACCAAGGCCACCGGTACCAAGAAGCAGTTCCAGAAGTTC

Alignment

ORF - retro_cpor_534 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.87 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MADIQTERAYQKQPTIFQNKKRVLLGETGKEKLPRYYKNIGLGFKTPKEAIEGTYIDKKCPFTGNVSIRG
          M.DIQTERAYQK.PTIFQNKKRVLLGETGKEKLPRYYKNIGLGFKT.KE.I.GTYIDKKCPFT.NVSIRG
Retrocopy MVDIQTERAYQKTPTIFQNKKRVLLGETGKEKLPRYYKNIGLGFKTLKEVIKGTYIDKKCPFTRNVSIRG

Parental  RILSGVVTKMKMQRTIVIRRDYLHYIRKYNRFEKRHKNMSVHLSPCFRDVQIGDIVTVGECRPLSKTVRF
          .ILSGVVTKMKMQRT.VIR.DYLHYIRKYN.FEKRHK.MSVHLSPCFR.VQIGDI..VGECRPLSKTV.F
Retrocopy QILSGVVTKMKMQRTTVIR*DYLHYIRKYNHFEKRHKYMSVHLSPCFREVQIGDIANVGECRPLSKTVCF

Parental  NVLKVTKAAGTKKQFQKF
          NVLKVTKA.GTKKQFQKF
Retrocopy NVLKVTKATGTKKQFQKF

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	75.69 RPM
SRP017611_kidney	0.10 RPM	179.02 RPM
SRP017611_liver	0.22 RPM	120.40 RPM
SRP040447_lung	0.10 RPM	254.98 RPM
SRP040447_skeletal_muscle	0.01 RPM	329.08 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_534 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_534 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 20 parental genes, and 110 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000014020	13 retrocopies	retro_amel_1038, retro_amel_1071, retro_amel_1398, retro_amel_1406, retro_amel_1475, retro_amel_246, retro_amel_262, retro_amel_317, retro_amel_64, retro_amel_757, retro_amel_759, retro_amel_764, retro_amel_859,
Bos taurus	ENSBTAG00000013924	5 retrocopies	retro_btau_1282, retro_btau_1369, retro_btau_1499, retro_btau_1529, retro_btau_888,
Canis familiaris	ENSCAFG00000003631	9 retrocopies	retro_cfam_126, retro_cfam_1333, retro_cfam_1572, retro_cfam_1656, retro_cfam_1669, retro_cfam_1900, retro_cfam_1955, retro_cfam_2121, retro_cfam_248,
Callithrix jacchus	ENSCJAG00000000069	1 retrocopy	retro_cjac_340,
Cavia porcellus	ENSCPOG00000015145	1 retrocopy	retro_cpor_534 ,
Danio rerio	ENSDARG00000053058	1 retrocopy	retro_drer_15,
Equus caballus	ENSECAG00000000370	1 retrocopy	retro_ecab_868,
Erinaceus europaeus	ENSEEUG00000003392	1 retrocopy	retro_eeur_75,
Homo sapiens	ENSG00000142534	6 retrocopies	retro_hsap_1017, retro_hsap_1068, retro_hsap_230, retro_hsap_2449, retro_hsap_4242, retro_hsap_4674,
Loxodonta africana	ENSLAFG00000016217	2 retrocopies	retro_lafr_622, retro_lafr_658,
Monodelphis domestica	ENSMODG00000013434	7 retrocopies	retro_mdom_1185, retro_mdom_1284, retro_mdom_1421, retro_mdom_1950, retro_mdom_636, retro_mdom_922, retro_mdom_978,
Mustela putorius furo	ENSMPUG00000002599	10 retrocopies	retro_mputfur_1402, retro_mputfur_1507, retro_mputfur_200, retro_mputfur_306, retro_mputfur_345, retro_mputfur_485, retro_mputfur_491, retro_mputfur_626, retro_mputfur_781, retro_mputfur_897,
Otolemur garnettii	ENSOGAG00000004627	7 retrocopies	retro_ogar_1290, retro_ogar_1813, retro_ogar_1910, retro_ogar_2037, retro_ogar_2573, retro_ogar_2640, retro_ogar_840,
Procavia capensis	ENSPCAG00000004146	2 retrocopies	retro_pcap_333, retro_pcap_54,
Pongo abelii	ENSPPYG00000025860	5 retrocopies	retro_pabe_1800, retro_pabe_3396, retro_pabe_3631, retro_pabe_855, retro_pabe_889,
Pan troglodytes	ENSPTRG00000011299	1 retrocopy	retro_ptro_88,
Rattus norvegicus	ENSRNOG00000020595	18 retrocopies	retro_rnor_1132, retro_rnor_1159, retro_rnor_1261, retro_rnor_1299, retro_rnor_1363, retro_rnor_1414, retro_rnor_1435, retro_rnor_1451, retro_rnor_1635, retro_rnor_1790, retro_rnor_2000, retro_rnor_2647, retro_rnor_385, retro_rnor_394, retro_rnor_538, retro_rnor_737, retro_rnor_835, retro_rnor_989,
Sorex araneus	ENSSARG00000003236	2 retrocopies	retro_sara_11, retro_sara_469,
Ictidomys tridecemlineatus	ENSSTOG00000023443	2 retrocopies	retro_itri_1033, retro_itri_805,
Tupaia belangeri	ENSTBEG00000016677	16 retrocopies	retro_tbel_125, retro_tbel_1361, retro_tbel_1753, retro_tbel_2071, retro_tbel_2207, retro_tbel_2808, retro_tbel_2947, retro_tbel_319, retro_tbel_3401, retro_tbel_3571, retro_tbel_3600, retro_tbel_3742, retro_tbel_449, retro_tbel_604, retro_tbel_801, retro_tbel_836,