RetrogeneDB ID: retro_cpor_298

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_12:13299494..13300158(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPLP0
• Ensembl ID: ENSCPOG00000021812
• Aliases: None
• Description: None

Sequence

>retro_cpor_298
TCCCTCCTGCTGATGGGTGAGAACACCGTGACATGCAGGGCCATCCGAGGACATCTGGAGAGCAGCCTAGCTCTGGAGAA
ACTGTTGCATCATATGGGGGGAACATGGGCTTTATGTTCATCAAGGAGGCCCTCCCTGAGATTAGGGATGTGCTGAGGCC
ATTAAGGTGCCAGCTGCTGTCTGTGTTGGTGCCATTGCACCATGTGAAGTCACTGTGCTGGCCCAGAACGCTGGTCTGAG
ACCTGAGAAGACCTCCTTTCAGACTCTGGGCATCACTATGAAAATCTCCAGGGGCACCATTGAAATCCTGAGTGATACAC
ACCCGATCTAACTGGAGACAGAGTAGGAGCCAGCAAGGCCACCTTCCTGGACATGTTGAACATCTCCCCTTTCTCCTTTG
GGCTGATCATCCAGCATGTGTTTGACAGCGGTGGCATCTACACCCTGAAGTGCTGGCATTGCAGAGGAAACTGCATTCTC
GCTTTCTGGAGGGCGTCTTCGATGTGCCATTGTTTGTCTGCAGATCAGTTACCCAAAGATTGCATCAAGGCCTCAATGGG
TACAAATGGGTCCTGGCTTTGTCTTGGAGACTGATTCCACCTTCCCACCTGCTGAAAGAAAAGTCAAGGCCTTCTTGGCT
GACCCATCTGCATTTGTGGCTGCT

Alignment

ORF - retro_cpor_298 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.67 %
• Parental protein coverage: 76.25 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  AVVLMGKNTMMRKAIRGHLENNPALEKLLPHIRG-NVGFVFTKEDLTEIRDMLL-ANKVPAAARAGAIAP
          ...LMG.NT....AIRGHLE...ALEKLL.H..G.N.GF.F.KE.L.EIRD.L..A.KVPAA...GAIAP
Retrocopy SLLLMGENTVTCRAIRGHLESSLALEKLLHHMGG<NMGFMFIKEALPEIRDVLR<AIKVPAAVCVGAIAP

Parental  CEVTVPAQNTGLGPEKTSFFQALGITTKISRGTIEILSDVQLI-KTGDKVGASEATLLNMLNISPFSFGL
          CEVTV.AQN.GL.PEKTSF.Q.LGIT.KISRGTIEILSD...I..TGD.VGAS.AT.L.MLNISPFSFGL
Retrocopy CEVTVLAQNAGLRPEKTSF-QTLGITMKISRGTIEILSDTHPI<LTGDRVGASKATFLDMLNISPFSFGL

Parental  IIQQVFDNGSIY-NPEVLDITEETLHSRFLEGVRNV-ASVCLQIGYPTVASVPHSIINGYKRVLALSVET
          IIQ.VFD.G.IY..PEVL......LHSRFLEGV..V.A.VCLQI.YP..AS.P.....G...VL....ET
Retrocopy IIQHVFDSGGIY<HPEVLAL-QRKLHSRFLEGVFDV<AIVCLQISYPKIASRPQWVQMGPGFVL----ET

Parental  DYTFPLAE-KVKAFLADPSAFAPA
          D.TFP.AE.KVKAFLADPSAF..A
Retrocopy DSTFPPAERKVKAFLADPSAFVAA

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	149.89 RPM
SRP017611_kidney	0.00 RPM	358.97 RPM
SRP017611_liver	0.00 RPM	282.27 RPM
SRP040447_lung	0.00 RPM	571.00 RPM
SRP040447_skeletal_muscle	0.00 RPM	890.77 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_298 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_298 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 19 parental genes, and 66 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000003756	2 retrocopies	retro_acar_111, retro_acar_115,
Choloepus hoffmanni	ENSCHOG00000002745	2 retrocopies	retro_chof_1115, retro_chof_2341,
Callithrix jacchus	ENSCJAG00000008677	3 retrocopies	retro_cjac_1693, retro_cjac_2840, retro_cjac_786,
Cavia porcellus	ENSCPOG00000021812	5 retrocopies	retro_cpor_298 , retro_cpor_449, retro_cpor_475, retro_cpor_498, retro_cpor_601,
Erinaceus europaeus	ENSEEUG00000007553	1 retrocopy	retro_eeur_612,
Homo sapiens	ENSG00000089157	7 retrocopies	retro_hsap_1403, retro_hsap_1553, retro_hsap_1889, retro_hsap_2095, retro_hsap_2334, retro_hsap_512, retro_hsap_784,
Gorilla gorilla	ENSGGOG00000026582	5 retrocopies	retro_ggor_1088, retro_ggor_1771, retro_ggor_472, retro_ggor_649, retro_ggor_650,
Macropus eugenii	ENSMEUG00000016409	12 retrocopies	retro_meug_1211, retro_meug_1245, retro_meug_1339, retro_meug_1410, retro_meug_1672, retro_meug_1689, retro_meug_1789, retro_meug_1800, retro_meug_1943, retro_meug_2166, retro_meug_294, retro_meug_772,
Macaca mulatta	ENSMMUG00000009157	2 retrocopies	retro_mmul_2245, retro_mmul_939,
Mus musculus	ENSMUSG00000067274	2 retrocopies	retro_mmus_143, retro_mmus_2249,
Oryctolagus cuniculus	ENSOCUG00000005749	2 retrocopies	retro_ocun_293, retro_ocun_376,
Otolemur garnettii	ENSOGAG00000003843	4 retrocopies	retro_ogar_2184, retro_ogar_2294, retro_ogar_556, retro_ogar_713,
Procavia capensis	ENSPCAG00000016429	6 retrocopies	retro_pcap_232, retro_pcap_314, retro_pcap_339, retro_pcap_353, retro_pcap_408, retro_pcap_67,
Petromyzon marinus	ENSPMAG00000001339	1 retrocopy	retro_pmar_6,
Pongo abelii	ENSPPYG00000005022	5 retrocopies	retro_pabe_2113, retro_pabe_3035, retro_pabe_568, retro_pabe_66, retro_pabe_749,
Rattus norvegicus	ENSRNOG00000001148	3 retrocopies	retro_rnor_1350, retro_rnor_2092, retro_rnor_2970,
Sarcophilus harrisii	ENSSHAG00000001623	2 retrocopies	retro_shar_286, retro_shar_413,
Tupaia belangeri	ENSTBEG00000005498	1 retrocopy	retro_tbel_3323,
Tursiops truncatus	ENSTTRG00000005658	1 retrocopy	retro_ttru_965,