RetrogeneDB ID: retro_cpor_246

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_11:12346928..12347301(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCPOG00000014693
• Aliases: None
• Description: None

Sequence

>retro_cpor_246
GGCCTTGTTCACACCAAGACAGTGAAGAAGACAGCCAGGTCATCACTTAGAAGTACTACATGCCTCTGAGCAACGAGTTT
GAGACCTACAGGCACGTGTGTGAGGAGACCACCACACACACCCCAGCAAGAAGCTTCGAAACAAGATAGGAGGATATGTC
ACACGTCTGATGAAGCAGATCCAGATGGCCCTGTACAGGAATTTCCATCAAGCTATAAGTGGAGGGAAAGAAAGAGAGAT
AATTCTGTCCCTGAGTGCTCAGCCTTGGGTCAGGAAATCACTGAGGTAGACTCTGACACTAAAGAAATGCTGACACTTTT
GGACTTTGGCAGCCTCTCCACCTGCAGGTCATGCAGCTACCATCGGGATGAAT

Alignment

ORF - retro_cpor_246 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.94 %
• Parental protein coverage: 93.33 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 7

Retrocopy - Parental Gene Alignment:

Parental  GRVRTKTVKKAAR-VIIEKYYTRLGNDFHTNKRVCEEIAI-IPSKKLRNK-IAGYVTHLMKRIQR-GPVR
          G.V.TKTVKK.AR.VI..KYY..L.N.F.T...VCEE.....P........I.GYVT.LMK.IQ..GPV.
Retrocopy GLVHTKTVKKTAR<VIT*KYYMPLSNEFETYRHVCEETTTHTPARSFETR<IGGYVTRLMKQIQM<GPVQ

Parental  -GISIKLQEE-ERERRDNYVPEVSALDQEIIEVDPDTKEMLKLLDFGSLS-NLQVTQ-PTVGMN
          .GISIKL..E.ER..RDN.VPE.SAL.QEI.EVD.DTKEML.LLDFGSLS..LQV.Q..T.GMN
Retrocopy <GISIKL*VE>ER-KRDNSVPECSALGQEITEVDSDTKEMLTLLDFGSLS<HLQVMQ<ATIGMN

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	0.06 RPM	73.28 RPM
SRP017611_kidney	0.00 RPM	114.42 RPM
SRP017611_liver	0.00 RPM	90.67 RPM
SRP040447_lung	0.03 RPM	165.83 RPM
SRP040447_skeletal_muscle	0.01 RPM	132.79 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_246 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_246 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 93 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000012225	4 retrocopies	retro_acar_128, retro_acar_154, retro_acar_177, retro_acar_81,
Ailuropoda melanoleuca	ENSAMEG00000014122	5 retrocopies	retro_amel_1571, retro_amel_1662, retro_amel_179, retro_amel_431, retro_amel_492,
Bos taurus	ENSBTAG00000000622	4 retrocopies	retro_btau_1014, retro_btau_568, retro_btau_731, retro_btau_884,
Canis familiaris	ENSCAFG00000013053	9 retrocopies	retro_cfam_1032, retro_cfam_1234, retro_cfam_1680, retro_cfam_1707, retro_cfam_217, retro_cfam_240, retro_cfam_307, retro_cfam_491, retro_cfam_82,
Cavia porcellus	ENSCPOG00000014693	3 retrocopies	retro_cpor_1472, retro_cpor_246 , retro_cpor_440,
Dasypus novemcinctus	ENSDNOG00000012633	6 retrocopies	retro_dnov_1183, retro_dnov_1296, retro_dnov_2140, retro_dnov_2636, retro_dnov_416, retro_dnov_673,
Equus caballus	ENSECAG00000024902	1 retrocopy	retro_ecab_92,
Felis catus	ENSFCAG00000002358	7 retrocopies	retro_fcat_1060, retro_fcat_1354, retro_fcat_1419, retro_fcat_1549, retro_fcat_288, retro_fcat_436, retro_fcat_710,
Homo sapiens	ENSG00000182774	11 retrocopies	retro_hsap_1516, retro_hsap_1743, retro_hsap_2150, retro_hsap_2702, retro_hsap_3172, retro_hsap_3477, retro_hsap_3570, retro_hsap_3588, retro_hsap_3719, retro_hsap_464, retro_hsap_925,
Homo sapiens	ENSG00000184779	5 retrocopies	retro_hsap_2559, retro_hsap_2854, retro_hsap_3233, retro_hsap_3909, retro_hsap_4110,
Loxodonta africana	ENSLAFG00000031717	5 retrocopies	retro_lafr_1105, retro_lafr_1204, retro_lafr_359, retro_lafr_573, retro_lafr_634,
Myotis lucifugus	ENSMLUG00000022830	3 retrocopies	retro_mluc_1202, retro_mluc_1347, retro_mluc_1949,
Macaca mulatta	ENSMMUG00000011327	6 retrocopies	retro_mmul_116, retro_mmul_194, retro_mmul_200, retro_mmul_266, retro_mmul_67, retro_mmul_99,
Monodelphis domestica	ENSMODG00000002011	9 retrocopies	retro_mdom_1482, retro_mdom_1923, retro_mdom_1928, retro_mdom_330, retro_mdom_342, retro_mdom_422, retro_mdom_425, retro_mdom_645, retro_mdom_762,
Mustela putorius furo	ENSMPUG00000015571	5 retrocopies	retro_mputfur_218, retro_mputfur_388, retro_mputfur_476, retro_mputfur_57, retro_mputfur_681,
Oryctolagus cuniculus	ENSOCUG00000006370	1 retrocopy	retro_ocun_90,
Pongo abelii	ENSPPYG00000006888	3 retrocopies	retro_pabe_108, retro_pabe_194, retro_pabe_72,
Rattus norvegicus	ENSRNOG00000019106	6 retrocopies	retro_rnor_19, retro_rnor_23, retro_rnor_276, retro_rnor_285, retro_rnor_289, retro_rnor_84,