RetrogeneDB ID: retro_cpor_607

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_2:41229649..41229832(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: LSM5
• Ensembl ID: ENSCPOG00000010421
• Aliases: None
• Description: None

Sequence

>retro_cpor_607
CAGCTGTGGTTGCTAGAAGTTGCGGACCGGTGTATAGAATCAAGAACTCATATCGTGATGAGTAGTAAGAAGAAAATTGT
GTGTATTACTCTAGGGTTTGATGCCTTCGTCAGTCTGGTGCTGGAAGATGTCACCAAGGTGGAAATCCTACCAGAAGGAA
GAAGTAGACCAGATTTTGATAAA

Alignment

ORF - retro_cpor_607 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.02 %
• Parental protein coverage: 67.03 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  QLLPLELVDKCIGSRIHIVMKSDKEIVGTLLGFDDFVNMVLEDVTEFEITPEGRRITKLDQ
          QL..LE..D.CI.SR.HIVM.S.K.IV...LGFD.FV..VLEDVT..EI.PEGR.....D.
Retrocopy QLWLLEVADRCIESRTHIVMSSKKKIVCITLGFDAFVSLVLEDVTKVEILPEGRSRPDFDK

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	4.66 RPM
SRP017611_kidney	0.00 RPM	10.89 RPM
SRP017611_liver	0.00 RPM	7.92 RPM
SRP040447_lung	0.00 RPM	5.75 RPM
SRP040447_skeletal_muscle	0.00 RPM	5.30 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_607 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_607 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 14 parental genes, and 42 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006700	1 retrocopy	retro_amel_453,
Callithrix jacchus	ENSCJAG00000009185	3 retrocopies	retro_cjac_1883, retro_cjac_2760, retro_cjac_3068,
Cavia porcellus	ENSCPOG00000010421	1 retrocopy	retro_cpor_607 ,
Equus caballus	ENSECAG00000018445	1 retrocopy	retro_ecab_809,
Echinops telfairi	ENSETEG00000018068	8 retrocopies	retro_etel_1305, retro_etel_1502, retro_etel_1907, retro_etel_198, retro_etel_2054, retro_etel_2193, retro_etel_454, retro_etel_964,
Mus musculus	ENSMUSG00000091625	4 retrocopies	retro_mmus_1568, retro_mmus_423, retro_mmus_826, retro_mmus_837,
Nomascus leucogenys	ENSNLEG00000015268	1 retrocopy	retro_nleu_179,
Otolemur garnettii	ENSOGAG00000013892	3 retrocopies	retro_ogar_2727, retro_ogar_3062, retro_ogar_881,
Pongo abelii	ENSPPYG00000017661	1 retrocopy	retro_pabe_3449,
Pan troglodytes	ENSPTRG00000019057	1 retrocopy	retro_ptro_2862,
Pteropus vampyrus	ENSPVAG00000009786	1 retrocopy	retro_pvam_1410,
Rattus norvegicus	ENSRNOG00000042126	3 retrocopies	retro_rnor_1171, retro_rnor_567, retro_rnor_694,
Tupaia belangeri	ENSTBEG00000004876	11 retrocopies	retro_tbel_1043, retro_tbel_1107, retro_tbel_1217, retro_tbel_1323, retro_tbel_1549, retro_tbel_1865, retro_tbel_2203, retro_tbel_2908, retro_tbel_2956, retro_tbel_3330, retro_tbel_4335,
Tursiops truncatus	ENSTTRG00000004237	3 retrocopies	retro_ttru_1521, retro_ttru_1585, retro_ttru_874,