RetrogeneDB ID: retro_cpor_273

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_112:3986308..3986508(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HSPE1
• Ensembl ID: ENSCPOG00000027474
• Aliases: None
• Description: None

Sequence

>retro_cpor_273
AAAAAAGCCTTAAGGAAAACTACTGAAGCAACAATAACTGTAGCATAATCAGTCTTCAAAGGAAAGGGTGGACAGATTCA
ACCAGTTAGTTTAAAATCTGAAGACAAAATTCTTTTCCCAAAATATGAGGGAACCAAAGTAGTTCTAAATGGAAAAAGAT
TTATTTCTTATTTAGAGATGATGACATTTTTAGAAAGTAT

Alignment

ORF - retro_cpor_273 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 55.88 %
• Parental protein coverage: 64.71 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  EKSQGKVLQATVVAVGSGSKGKGGEIQPVSVKVGDKVLLPEYGGTKVVLD-DKDYF-LFRDGDILGKY
          .K...K...AT.....S..KGKGG.IQPVS.K..DK.L.P.Y.GTKVVL...KD.F.LFRD.DI..KY
Retrocopy KKALRKTTEATITVA*SVFKGKGGQIQPVSLKSEDKILFPKYEGTKVVLN>EKDLF>LFRDDDIFRKY

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	30.02 RPM
SRP017611_kidney	0.00 RPM	149.60 RPM
SRP017611_liver	0.00 RPM	94.84 RPM
SRP040447_lung	0.00 RPM	27.26 RPM
SRP040447_skeletal_muscle	0.00 RPM	44.11 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_273 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_273 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 9 parental genes, and 110 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000013769	18 retrocopies	retro_amel_1027, retro_amel_1083, retro_amel_1084, retro_amel_1100, retro_amel_133, retro_amel_1504, retro_amel_1513, retro_amel_1623, retro_amel_1699, retro_amel_1819, retro_amel_199, retro_amel_23, retro_amel_269, retro_amel_310, retro_amel_329, retro_amel_491, retro_amel_506, retro_amel_922,
Bos taurus	ENSBTAG00000012589	4 retrocopies	retro_btau_1118, retro_btau_624, retro_btau_760, retro_btau_801,
Cavia porcellus	ENSCPOG00000027474	3 retrocopies	retro_cpor_1431, retro_cpor_273 , retro_cpor_649,
Dasypus novemcinctus	ENSDNOG00000013246	27 retrocopies	retro_dnov_1088, retro_dnov_1117, retro_dnov_1214, retro_dnov_1375, retro_dnov_1391, retro_dnov_1405, retro_dnov_1412, retro_dnov_1428, retro_dnov_1445, retro_dnov_1546, retro_dnov_1647, retro_dnov_1652, retro_dnov_1686, retro_dnov_1821, retro_dnov_2176, retro_dnov_2291, retro_dnov_2413, retro_dnov_2569, retro_dnov_2625, retro_dnov_2652, retro_dnov_418, retro_dnov_481, retro_dnov_483, retro_dnov_490, retro_dnov_524, retro_dnov_554, retro_dnov_966,
Dipodomys ordii	ENSDORG00000011071	19 retrocopies	retro_dord_153, retro_dord_158, retro_dord_162, retro_dord_191, retro_dord_207, retro_dord_216, retro_dord_219, retro_dord_296, retro_dord_368, retro_dord_403, retro_dord_417, retro_dord_462, retro_dord_492, retro_dord_525, retro_dord_535, retro_dord_583, retro_dord_740, retro_dord_744, retro_dord_755,
Loxodonta africana	ENSLAFG00000000057	1 retrocopy	retro_lafr_69,
Otolemur garnettii	ENSOGAG00000034434	24 retrocopies	retro_ogar_1018, retro_ogar_1441, retro_ogar_1512, retro_ogar_1690, retro_ogar_1744, retro_ogar_1899, retro_ogar_191, retro_ogar_1921, retro_ogar_200, retro_ogar_2030, retro_ogar_2129, retro_ogar_2310, retro_ogar_235, retro_ogar_2439, retro_ogar_2636, retro_ogar_2928, retro_ogar_3088, retro_ogar_3350, retro_ogar_3419, retro_ogar_389, retro_ogar_777, retro_ogar_824, retro_ogar_829, retro_ogar_834,
Rattus norvegicus	ENSRNOG00000014868	6 retrocopies	retro_rnor_1094, retro_rnor_1320, retro_rnor_1334, retro_rnor_2245, retro_rnor_2296, retro_rnor_984,
Vicugna pacos	ENSVPAG00000005805	8 retrocopies	retro_vpac_173, retro_vpac_209, retro_vpac_292, retro_vpac_299, retro_vpac_329, retro_vpac_410, retro_vpac_443, retro_vpac_46,