RetrogeneDB ID: retro_cpor_230

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_103:1005069..1005491(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCPOG00000008581
• Aliases: None
• Description: None

Sequence

>retro_cpor_230
GAAAGCTGGCATTTGCTGGCAGACCGGTGCCTGGGATTACAGCAGAACCAGATGACAGCAACATCATTGTTTTCACTTGG
TTGTTGCTGGTCTCCAGGATTCTCCCTTTAAAGGAGGGACTTTTAAACTTGAACTATTTCTGCCAGAAGAATTTCCAGTA
ACAGTACCGAAAGTATGTTTCACGACCACAACTTATCATCCTAATGTAGACAAGCTGGGAAGAATATGTTTAGGTATTTT
GAAAGATAAATGGTCACCAGCACTGCAGATCTGCACAGTTCTGCTACTGATCCTGGCTTTGTTCAGTGCTCCTAATCCAG
ATGACCCTTAACAAATGATGTAGCAGAGCATGGAAGACCAATGAAGCCCAAGCCATAGAAACAACTAGCACATGGACTTG
GCTATATGCCATAAATAATATT

Alignment

ORF - retro_cpor_230 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.66 %
• Parental protein coverage: 93.42 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  ETQRLLAE-PVPGIKAEPDESNA-RYFHVVIAGPQDSPFEGGTFKLELFLPEEYPMAAPKVRFMTKIYHP
          E...LLA..PVPGI.AEPD.SN....FH.V.AG.QDSPF.GGTFKLELFLPEE.P...PKV.F.T..YHP
Retrocopy ESWHLLAD<PVPGITAEPDDSNI<HCFHLVVAGLQDSPFKGGTFKLELFLPEEFPVTVPKVCFTTTTYHP

Parental  NVDKLGRICLDILKDKWSPALQIRTVLLSIQALLSAPNPDD-PLANDVAEQ-WKTNEAQAIETARAWTRL
          NVDKLGRICL.ILKDKWSPALQI.TVLL.I.AL.SAPNPDD.PL.NDVAE..WKTNEAQAIET...WT.L
Retrocopy NVDKLGRICLGILKDKWSPALQICTVLLLILALFSAPNPDD<PLTNDVAEH<WKTNEAQAIETTSTWTWL

Parental  YAMNNI
          YA.NNI
Retrocopy YAINNI

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	20.82 RPM
SRP017611_kidney	0.00 RPM	12.98 RPM
SRP017611_liver	0.00 RPM	8.88 RPM
SRP040447_lung	0.00 RPM	17.43 RPM
SRP040447_skeletal_muscle	0.00 RPM	16.93 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_230 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_230 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 29 parental genes, and 110 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000009833	1 retrocopy	retro_amel_507,
Bos taurus	ENSBTAG00000021767	2 retrocopies	retro_btau_1173, retro_btau_1614,
Canis familiaris	ENSCAFG00000006177	1 retrocopy	retro_cfam_196,
Callithrix jacchus	ENSCJAG00000002979	8 retrocopies	retro_cjac_141, retro_cjac_2121, retro_cjac_3142, retro_cjac_3148, retro_cjac_3216, retro_cjac_3241, retro_cjac_3329, retro_cjac_425,
Cavia porcellus	ENSCPOG00000008581	5 retrocopies	retro_cpor_1548, retro_cpor_230 , retro_cpor_24, retro_cpor_655, retro_cpor_750,
Dasypus novemcinctus	ENSDNOG00000018952	9 retrocopies	retro_dnov_1002, retro_dnov_1066, retro_dnov_1107, retro_dnov_1185, retro_dnov_1487, retro_dnov_1977, retro_dnov_2598, retro_dnov_277, retro_dnov_492,
Echinops telfairi	ENSETEG00000001882	5 retrocopies	retro_etel_1008, retro_etel_1417, retro_etel_1593, retro_etel_1661, retro_etel_2136,
Felis catus	ENSFCAG00000004260	2 retrocopies	retro_fcat_1477, retro_fcat_1598,
Homo sapiens	ENSG00000177889	3 retrocopies	retro_hsap_1392, retro_hsap_17, retro_hsap_3124,
Gorilla gorilla	ENSGGOG00000024332	4 retrocopies	retro_ggor_1079, retro_ggor_2140, retro_ggor_2720, retro_ggor_2969,
Loxodonta africana	ENSLAFG00000028985	1 retrocopy	retro_lafr_57,
Macropus eugenii	ENSMEUG00000002944	7 retrocopies	retro_meug_1236, retro_meug_1287, retro_meug_1453, retro_meug_1473, retro_meug_162, retro_meug_2009, retro_meug_31,
Microcebus murinus	ENSMICG00000014081	4 retrocopies	retro_mmur_1351, retro_mmur_220, retro_mmur_267, retro_mmur_611,
Myotis lucifugus	ENSMLUG00000009982	2 retrocopies	retro_mluc_2166, retro_mluc_453,
Macaca mulatta	ENSMMUG00000020634	3 retrocopies	retro_mmul_1587, retro_mmul_234, retro_mmul_72,
Monodelphis domestica	ENSMODG00000009451	2 retrocopies	retro_mdom_133, retro_mdom_1485,
Mus musculus	ENSMUSG00000074781	6 retrocopies	retro_mmus_1031, retro_mmus_2656, retro_mmus_3031, retro_mmus_3294, retro_mmus_3510, retro_mmus_524,
Nomascus leucogenys	ENSNLEG00000005695	2 retrocopies	retro_nleu_1078, retro_nleu_2279,
Oryctolagus cuniculus	ENSOCUG00000011287	1 retrocopy	retro_ocun_100,
Otolemur garnettii	ENSOGAG00000034461	7 retrocopies	retro_ogar_1502, retro_ogar_2178, retro_ogar_406, retro_ogar_408, retro_ogar_566, retro_ogar_584, retro_ogar_732,
Pongo abelii	ENSPPYG00000004832	4 retrocopies	retro_pabe_113, retro_pabe_1152, retro_pabe_2580, retro_pabe_3326,
Pan troglodytes	ENSPTRG00000005297	3 retrocopies	retro_ptro_2112, retro_ptro_3253, retro_ptro_956,
Pteropus vampyrus	ENSPVAG00000013734	2 retrocopies	retro_pvam_1420, retro_pvam_358,
Sorex araneus	ENSSARG00000005945	3 retrocopies	retro_sara_174, retro_sara_438, retro_sara_695,
Sarcophilus harrisii	ENSSHAG00000007776	1 retrocopy	retro_shar_105,
Sus scrofa	ENSSSCG00000000908	4 retrocopies	retro_sscr_101, retro_sscr_369, retro_sscr_698, retro_sscr_699,
Tupaia belangeri	ENSTBEG00000012497	10 retrocopies	retro_tbel_108, retro_tbel_1208, retro_tbel_1235, retro_tbel_1727, retro_tbel_2393, retro_tbel_2732, retro_tbel_275, retro_tbel_3151, retro_tbel_4655, retro_tbel_849,
Tarsius syrichta	ENSTSYG00000008800	5 retrocopies	retro_tsyr_1476, retro_tsyr_1754, retro_tsyr_207, retro_tsyr_348, retro_tsyr_5,
Tursiops truncatus	ENSTTRG00000003311	3 retrocopies	retro_ttru_1235, retro_ttru_286, retro_ttru_702,