RetrogeneDB ID: retro_cpor_1242

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_6:1850549..1851178(-)
• Located in intron of: ENSCPOG00000021935

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPL13
• Ensembl ID: ENSCPOG00000027348
• Aliases: None
• Description: 60S ribosomal protein L13 [Source:UniProtKB/TrEMBL;Acc:H0W636]

Sequence

>retro_cpor_1242
ATGATGCCCAGCCAGAATAACAGGATTCTGAAGCCCCACTTCCACAAGGACTGGCAGCAGCACGTGCCACATGGTTCAGT
CAGTCAGCTTGGAAGATCTGTAGGCACAAGGCCCAACAGGCAAAAGCGTGCTGTGTAGCCCTCGCTCCTTGTCCAGACCC
ATCTGGGCCATCGTGCACTGTCCCACGATGTGATACACACTAAGGCCCAAGCCAGCAGGGCCTTCAGACTGGCGGAGCTG
CAGGTGACTGGTATTCACAAGAAGACAGCCCAGACCATTGCATCTTGGTGGACCCAAGGTGGCAGAATAAATCTACCAAG
TCTCTGCAGGCCACCGTGCAGCAGCTCAGAGGGCACTGCTCCAAACTCATCCTCTTCCCCAGGAAGCTGTCAGCCCCCAG
GGAGAGACATAGCTCTGCTGAAGAACTCAAATTGACTACCCGGCTCTCAGGACCAGTGATGCGGTTCAGGAACATCTACA
AGAAGGAGAAGGCCAGGGTCATCACAGAGGAGGAAAAGAGCTTCAAGGCCTTTGCCATTCTGTGCATGGATCATGCCAAT
GCCCATCTCTTTGGCATCTGGGCATAGAGAGCCAAGGAAGCTGCAGAGCAGGACACTGAGAAGAAAAAA

Alignment

ORF - retro_cpor_1242 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.37 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MAPSRNGMILKPHFHKDWQRRV-ATWFNQPARKIRRRKARQAKARRIA-PRPASGPIRPIVRCPTVRY-H
          M.PS.N..ILKPHFHKDWQ..V.ATWF.Q.A.KI.R.KA.QAKA...A.PR..S.PI..IV.CPT..Y.H
Retrocopy MMPSQNNRILKPHFHKDWQQHV<ATWFSQSAWKICRHKAQQAKACCVA<PRSLSRPIWAIVHCPTM*Y<H

Parental  TKVRAGRGFSLEELRVAGIHKKVARTIG-ISVDPRRRNKSTESLQANVQRLKEYRSKLILFPRKPSAPKK
          TK..A.R.F.L.EL.V.GIHKK.A.TI..I.VDPR..NKST.SLQA.VQ.L....SKLILFPRK.SAP..
Retrocopy TKAQASRAFRLAELQVTGIHKKTAQTIA<ILVDPRWQNKSTKSLQATVQQLRGHCSKLILFPRKLSAPRE

Parental  GDSSAEELKLATQLTGPVMPIRNVYKKEKARVITEEEKNFKAFASLRMARANARLFGIRAKRAKEAAEQD
          ..SSAEELKL.T.L.GPVM..RN.YKKEKARVITEEEK.FKAFA.L.M..ANA.LFGI.A.RAKEAAEQD
Retrocopy RHSSAEELKLTTRLSGPVMRFRNIYKKEKARVITEEEKSFKAFAILCMDHANAHLFGIWA*RAKEAAEQD

Parental  VEKKK
          .EKKK
Retrocopy TEKKK

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	0.17 RPM	127.28 RPM
SRP017611_kidney	0.10 RPM	222.67 RPM
SRP017611_liver	0.04 RPM	140.46 RPM
SRP040447_lung	0.20 RPM	314.10 RPM
SRP040447_skeletal_muscle	0.00 RPM	301.96 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1242 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1242 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 127 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000017072	1 retrocopy	retro_acar_70,
Canis familiaris	ENSCAFG00000019840	5 retrocopies	retro_cfam_1135, retro_cfam_1919, retro_cfam_2122, retro_cfam_565, retro_cfam_897,
Callithrix jacchus	ENSCJAG00000009672	5 retrocopies	retro_cjac_2607, retro_cjac_2961, retro_cjac_4054, retro_cjac_663, retro_cjac_747,
Cavia porcellus	ENSCPOG00000027348	4 retrocopies	retro_cpor_1014, retro_cpor_1192, retro_cpor_1242 , retro_cpor_491,
Echinops telfairi	ENSETEG00000015057	4 retrocopies	retro_etel_1240, retro_etel_1382, retro_etel_1606, retro_etel_703,
Felis catus	ENSFCAG00000003338	4 retrocopies	retro_fcat_1946, retro_fcat_706, retro_fcat_852, retro_fcat_866,
Homo sapiens	ENSG00000167526	12 retrocopies	retro_hsap_1377, retro_hsap_1810, retro_hsap_2070, retro_hsap_2430, retro_hsap_2485, retro_hsap_2824, retro_hsap_3207, retro_hsap_3281, retro_hsap_3443, retro_hsap_4074, retro_hsap_478, retro_hsap_951,
Gorilla gorilla	ENSGGOG00000025427	6 retrocopies	retro_ggor_1548, retro_ggor_1963, retro_ggor_2231, retro_ggor_2732, retro_ggor_562, retro_ggor_767,
Microcebus murinus	ENSMICG00000008191	4 retrocopies	retro_mmur_249, retro_mmur_288, retro_mmur_779, retro_mmur_908,
Myotis lucifugus	ENSMLUG00000010950	6 retrocopies	retro_mluc_1431, retro_mluc_1436, retro_mluc_1549, retro_mluc_2022, retro_mluc_891, retro_mluc_991,
Monodelphis domestica	ENSMODG00000003663	4 retrocopies	retro_mdom_1001, retro_mdom_416, retro_mdom_439, retro_mdom_674,
Mus musculus	ENSMUSG00000000740	23 retrocopies	retro_mmus_1091, retro_mmus_1522, retro_mmus_1533, retro_mmus_1854, retro_mmus_2074, retro_mmus_2163, retro_mmus_2186, retro_mmus_2321, retro_mmus_2333, retro_mmus_2351, retro_mmus_25, retro_mmus_2668, retro_mmus_2718, retro_mmus_3097, retro_mmus_3274, retro_mmus_3453, retro_mmus_3489, retro_mmus_3500, retro_mmus_355, retro_mmus_3711, retro_mmus_692, retro_mmus_732, retro_mmus_863,
Nomascus leucogenys	ENSNLEG00000015774	13 retrocopies	retro_nleu_1156, retro_nleu_1202, retro_nleu_2299, retro_nleu_238, retro_nleu_2457, retro_nleu_2530, retro_nleu_2657, retro_nleu_273, retro_nleu_2732, retro_nleu_2885, retro_nleu_3016, retro_nleu_789, retro_nleu_892,
Ornithorhynchus anatinus	ENSOANG00000006729	1 retrocopy	retro_oana_78,
Otolemur garnettii	ENSOGAG00000026444	3 retrocopies	retro_ogar_1165, retro_ogar_1831, retro_ogar_1853,
Pan troglodytes	ENSPTRG00000008480	12 retrocopies	retro_ptro_1175, retro_ptro_1382, retro_ptro_1402, retro_ptro_1438, retro_ptro_1914, retro_ptro_2219, retro_ptro_2242, retro_ptro_2336, retro_ptro_2761, retro_ptro_359, retro_ptro_658, retro_ptro_946,
Pteropus vampyrus	ENSPVAG00000015130	6 retrocopies	retro_pvam_1174, retro_pvam_1289, retro_pvam_1344, retro_pvam_228, retro_pvam_58, retro_pvam_616,
Rattus norvegicus	ENSRNOG00000015335	14 retrocopies	retro_rnor_1054, retro_rnor_1260, retro_rnor_158, retro_rnor_160, retro_rnor_1719, retro_rnor_1720, retro_rnor_1834, retro_rnor_1848, retro_rnor_2471, retro_rnor_2574, retro_rnor_2608, retro_rnor_2787, retro_rnor_2854, retro_rnor_682,