RetrogeneDB ID: retro_cpor_385

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_14:16061447..16061787(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCPOG00000022733
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: GCSH
• Ensembl ID: ENSCPOG00000009983
• Aliases: None
• Description: None

Sequence

>retro_cpor_385
CCCTGTGAACATAGTTATTGGGAATGGTGGCCGTAGGCAGGTGCCATGGGGATGCTGCGAACTGAACCAGCTCCACTTCC
AGTGAGTAAATTCACGGAGAAACAGGAATGGATAACAACAGAAAATGGAACAGCGGGACTCAGCAATTTTTCACAGCATG
ATTTGAGGGATATTTACTGTAGTCTGCCTGACGGTGGGCCAAGATTGAAAAATCAAGATGAATTTTGTGCTTTGGAAAGT
GTGAAAGCTGCCTTTGAAGTCTCCCCTCCTCTTACTAGGAAAAACAACCAAAGGTGAGAAAGCACTTGCAGAAAATCCAG
GGCTTGTCAAGAAGTCTTGT

Alignment

ORF - retro_cpor_385 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.12 %
• Parental protein coverage: 65.9 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  PCAIRPWRLW--AGAVRSLRTGSALLAMRKFTEKHEWVTTENGIGTVGISNFAQEALGDVVYCSLPEVGT
          PC....W..W..AGA...LRT..A.L...KFTEK.EW.TTENG..T.G.SNF.Q..L.D..YCSLP..G.
Retrocopy PCEHSYWEWWP*AGAMGMLRTEPAPLPVSKFTEKQEWITTENG--TAGLSNFSQHDLRDI-YCSLPDGGP

Parental  KLKKHDEFGALESVKAASELYSPLS-GEVTEINEALAENPGLVNKSC
          .LK..DEF.ALESVKAA.E...PL..G..T....ALAENPGLV.KSC
Retrocopy RLKNQDEFCALESVKAAFEVSPPLT>GKTTKGEKALAENPGLVKKSC

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	16.39 RPM
SRP017611_kidney	0.00 RPM	46.80 RPM
SRP017611_liver	0.00 RPM	39.17 RPM
SRP040447_lung	0.00 RPM	9.89 RPM
SRP040447_skeletal_muscle	0.00 RPM	13.78 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_385 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_385 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 21 parental genes, and 159 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000008905	1 retrocopy	retro_acar_75,
Ailuropoda melanoleuca	ENSAMEG00000013959	5 retrocopies	retro_amel_1362, retro_amel_1877, retro_amel_229, retro_amel_432, retro_amel_80,
Bos taurus	ENSBTAG00000006795	8 retrocopies	retro_btau_1128, retro_btau_12, retro_btau_1483, retro_btau_1543, retro_btau_1628, retro_btau_246, retro_btau_265, retro_btau_94,
Canis familiaris	ENSCAFG00000020014	5 retrocopies	retro_cfam_1249, retro_cfam_1543, retro_cfam_358, retro_cfam_618, retro_cfam_732,
Choloepus hoffmanni	ENSCHOG00000002434	37 retrocopies	retro_chof_1011, retro_chof_1019, retro_chof_1123, retro_chof_1213, retro_chof_1324, retro_chof_1410, retro_chof_1482, retro_chof_1550, retro_chof_163, retro_chof_1647, retro_chof_1659, retro_chof_1690, retro_chof_1705, retro_chof_1722, retro_chof_178, retro_chof_1781, retro_chof_1787, retro_chof_219, retro_chof_2264, retro_chof_2289, retro_chof_2319, retro_chof_2412, retro_chof_2466, retro_chof_2494, retro_chof_2632, retro_chof_2657, retro_chof_283, retro_chof_335, retro_chof_361, retro_chof_362, retro_chof_363, retro_chof_419, retro_chof_433, retro_chof_477, retro_chof_597, retro_chof_755, retro_chof_931,
Cavia porcellus	ENSCPOG00000009983	3 retrocopies	retro_cpor_1240, retro_cpor_385 , retro_cpor_463,
Dipodomys ordii	ENSDORG00000007831	1 retrocopy	retro_dord_645,
Felis catus	ENSFCAG00000013038	8 retrocopies	retro_fcat_1007, retro_fcat_1112, retro_fcat_1294, retro_fcat_1435, retro_fcat_1627, retro_fcat_1920, retro_fcat_215, retro_fcat_354,
Loxodonta africana	ENSLAFG00000015586	3 retrocopies	retro_lafr_554, retro_lafr_822, retro_lafr_900,
Myotis lucifugus	ENSMLUG00000005783	12 retrocopies	retro_mluc_1151, retro_mluc_1221, retro_mluc_1466, retro_mluc_1538, retro_mluc_1659, retro_mluc_1685, retro_mluc_2089, retro_mluc_2090, retro_mluc_2139, retro_mluc_2314, retro_mluc_2411, retro_mluc_709,
Macaca mulatta	ENSMMUG00000013088	5 retrocopies	retro_mmul_1192, retro_mmul_2202, retro_mmul_661, retro_mmul_840, retro_mmul_960,
Mustela putorius furo	ENSMPUG00000009677	4 retrocopies	retro_mputfur_1434, retro_mputfur_1492, retro_mputfur_349, retro_mputfur_809,
Mus musculus	ENSMUSG00000034424	8 retrocopies	retro_mmus_1880, retro_mmus_2144, retro_mmus_2235, retro_mmus_3062, retro_mmus_3303, retro_mmus_3459, retro_mmus_3610, retro_mmus_3703,
Nomascus leucogenys	ENSNLEG00000026844	1 retrocopy	retro_nleu_365,
Procavia capensis	ENSPCAG00000005820	1 retrocopy	retro_pcap_207,
Pteropus vampyrus	ENSPVAG00000009956	8 retrocopies	retro_pvam_1253, retro_pvam_1474, retro_pvam_1481, retro_pvam_194, retro_pvam_552, retro_pvam_583, retro_pvam_78, retro_pvam_958,
Rattus norvegicus	ENSRNOG00000011535	6 retrocopies	retro_rnor_1217, retro_rnor_1218, retro_rnor_1400, retro_rnor_1910, retro_rnor_2691, retro_rnor_557,
Sarcophilus harrisii	ENSSHAG00000005529	1 retrocopy	retro_shar_239,
Ictidomys tridecemlineatus	ENSSTOG00000016433	2 retrocopies	retro_itri_31, retro_itri_34,
Tupaia belangeri	ENSTBEG00000000056	27 retrocopies	retro_tbel_1426, retro_tbel_1716, retro_tbel_1766, retro_tbel_1846, retro_tbel_1923, retro_tbel_2026, retro_tbel_2074, retro_tbel_2168, retro_tbel_2315, retro_tbel_2426, retro_tbel_2489, retro_tbel_2515, retro_tbel_2573, retro_tbel_2769, retro_tbel_3007, retro_tbel_3025, retro_tbel_311, retro_tbel_3140, retro_tbel_3458, retro_tbel_3852, retro_tbel_3924, retro_tbel_4173, retro_tbel_4727, retro_tbel_597, retro_tbel_601, retro_tbel_609, retro_tbel_825,
Tarsius syrichta	ENSTSYG00000000248	13 retrocopies	retro_tsyr_119, retro_tsyr_1311, retro_tsyr_1367, retro_tsyr_1833, retro_tsyr_2023, retro_tsyr_2173, retro_tsyr_309, retro_tsyr_328, retro_tsyr_363, retro_tsyr_429, retro_tsyr_439, retro_tsyr_587, retro_tsyr_643,