RetrogeneDB ID: retro_cpor_1494

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_9:17576130..17576469(-)
• Located in intron of: ENSCPOG00000011621

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPL34
• Ensembl ID: ENSCPOG00000000802
• Aliases: None
• Description: None

Sequence

>retro_cpor_1494
CAGCACTTGACTTACCACTGTAGGCTCTCCTACAACACAGCCTCTAACAAAACTAGGCTGTCCCGAACCCCAGGGAACAG
AATTGTTTACCTCTACACCAAGGTCGGGAAGGCCCCCAAGTCCATGTGTGGCATGTGCCCAGGCAGGTTTCGAGGGGTTC
ATGCAGTGCACCCTAAAGTTCTCATGCGACTGTCTAAGACAAAGAAGCAGGTCAGCAGGGCCACAGGGGCTCCATGTGTG
CCAAGTGTGTCCATGACACGGAACAAGCGTGCTTTCCTTATTGAGGAGCAGAAAATCGTGGTGAAGGTGTTGAAGGCACA
GGCGCAGAGTCAGAAGGCC

Alignment

ORF - retro_cpor_1494 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.07 %
• Parental protein coverage: 97.44 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  QRLTYRRRLSYNTASNKTRLSRTPGNRIVYLYTKKVGKAPKSACGVCPGRLRGVRAVRPKVLMRLSKTKK
          Q.LTY..RLSYNTASNKTRLSRTPGNRIVYLYTK.VGKAPKS.CG.CPGR.RGV.AV.PKVLMRLSKTKK
Retrocopy QHLTYHCRLSYNTASNKTRLSRTPGNRIVYLYTK-VGKAPKSMCGMCPGRFRGVHAVHPKVLMRLSKTKK

Parental  HVSRAYG-GSMCAKCVRD-RIKRAFLIEEQKIVVKVLKAQAQSQKA
          .VSRA.G.GSMCAKCV.D.R.KRAFLIEEQKIVVKVLKAQAQSQKA
Retrocopy QVSRATG<GSMCAKCVHD>RNKRAFLIEEQKIVVKVLKAQAQSQKA

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	0.98 RPM	90.42 RPM
SRP017611_kidney	0.10 RPM	142.90 RPM
SRP017611_liver	0.13 RPM	86.97 RPM
SRP040447_lung	0.08 RPM	189.84 RPM
SRP040447_skeletal_muscle	0.18 RPM	148.17 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1494 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1494 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 16 parental genes, and 144 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000001758	20 retrocopies	retro_amel_1151, retro_amel_1298, retro_amel_1402, retro_amel_147, retro_amel_1595, retro_amel_1670, retro_amel_1678, retro_amel_1755, retro_amel_240, retro_amel_368, retro_amel_388, retro_amel_410, retro_amel_477, retro_amel_655, retro_amel_690, retro_amel_739, retro_amel_874, retro_amel_936, retro_amel_949, retro_amel_978,
Bos taurus	ENSBTAG00000014226	13 retrocopies	retro_btau_1017, retro_btau_1141, retro_btau_1280, retro_btau_1303, retro_btau_1372, retro_btau_1476, retro_btau_1738, retro_btau_288, retro_btau_404, retro_btau_465, retro_btau_628, retro_btau_712, retro_btau_904,
Cavia porcellus	ENSCPOG00000000802	6 retrocopies	retro_cpor_139, retro_cpor_1494 , retro_cpor_402, retro_cpor_485, retro_cpor_694, retro_cpor_732,
Dasypus novemcinctus	ENSDNOG00000011179	26 retrocopies	retro_dnov_1172, retro_dnov_1775, retro_dnov_2020, retro_dnov_2025, retro_dnov_2079, retro_dnov_2127, retro_dnov_2137, retro_dnov_2275, retro_dnov_2385, retro_dnov_2501, retro_dnov_252, retro_dnov_262, retro_dnov_2627, retro_dnov_2651, retro_dnov_325, retro_dnov_339, retro_dnov_430, retro_dnov_553, retro_dnov_565, retro_dnov_59, retro_dnov_606, retro_dnov_635, retro_dnov_658, retro_dnov_862, retro_dnov_88, retro_dnov_978,
Gadus morhua	ENSGMOG00000009982	1 retrocopy	retro_gmor_31,
Loxodonta africana	ENSLAFG00000032615	6 retrocopies	retro_lafr_1039, retro_lafr_1232, retro_lafr_182, retro_lafr_298, retro_lafr_306, retro_lafr_733,
Macropus eugenii	ENSMEUG00000009361	3 retrocopies	retro_meug_1012, retro_meug_1754, retro_meug_1775,
Macaca mulatta	ENSMMUG00000011901	1 retrocopy	retro_mmul_162,
Monodelphis domestica	ENSMODG00000020601	3 retrocopies	retro_mdom_1690, retro_mdom_774, retro_mdom_836,
Mustela putorius furo	ENSMPUG00000008873	17 retrocopies	retro_mputfur_1028, retro_mputfur_1095, retro_mputfur_1130, retro_mputfur_1170, retro_mputfur_12, retro_mputfur_1242, retro_mputfur_1305, retro_mputfur_1480, retro_mputfur_1501, retro_mputfur_360, retro_mputfur_378, retro_mputfur_475, retro_mputfur_517, retro_mputfur_557, retro_mputfur_562, retro_mputfur_852, retro_mputfur_923,
Pongo abelii	ENSPPYG00000014988	18 retrocopies	retro_pabe_1171, retro_pabe_1351, retro_pabe_1609, retro_pabe_1630, retro_pabe_1859, retro_pabe_2338, retro_pabe_2560, retro_pabe_2784, retro_pabe_2931, retro_pabe_3330, retro_pabe_3352, retro_pabe_3375, retro_pabe_3788, retro_pabe_385, retro_pabe_420, retro_pabe_566, retro_pabe_77, retro_pabe_827,
Pelodiscus sinensis	ENSPSIG00000003295	1 retrocopy	retro_psin_60,
Sarcophilus harrisii	ENSSHAG00000001357	1 retrocopy	retro_shar_799,
Sarcophilus harrisii	ENSSHAG00000002052	3 retrocopies	retro_shar_131, retro_shar_324, retro_shar_419,
Tupaia belangeri	ENSTBEG00000003574	24 retrocopies	retro_tbel_1109, retro_tbel_1298, retro_tbel_1337, retro_tbel_1532, retro_tbel_1781, retro_tbel_1857, retro_tbel_1941, retro_tbel_213, retro_tbel_2162, retro_tbel_2165, retro_tbel_2372, retro_tbel_2391, retro_tbel_2601, retro_tbel_279, retro_tbel_335, retro_tbel_3606, retro_tbel_3984, retro_tbel_4059, retro_tbel_4398, retro_tbel_657, retro_tbel_74, retro_tbel_901, retro_tbel_974, retro_tbel_983,
Xenopus tropicalis	ENSXETG00000021095	1 retrocopy	retro_xtro_5,