RetrogeneDB ID: retro_cpor_332

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_129:1875776..1876392(+)
• Located in intron of: ENSCPOG00000001178

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPF2
• Ensembl ID: ENSCPOG00000006797
• Aliases: None
• Description: None

Sequence

>retro_cpor_332
CCCAAAACAAAAAGGGCCAAGAGATTCCTGGAGAAGACAGAACCGAAACTTAAGTGAAAATATTAAAAGTGCCATGCTGA
TTAAGGGGGGAAATGCAAATGCAACAGTGACACAAGTCCTGAAAGACGTGCATGCACTGAAAAACCATACCAAGTACTCT
ACAAAACAAAACCGCTACAAGACCATTTGAGGAGCAGACCTCACTGGAATTCTTTTCAAGTAAGTTAGCTTGCTCTTCGT
TCATATTTGGATTGAGTAAGAAGCATCCCAATAACCCAGCAATAGGTTACTGGGTATATGGCTACTATGTGCTAGACATG
ACTGAATTGGATATTGAGAAATTTGTGTCTCTAAAAGATATTATGAACAGTAAATGTCCTGAGGGAACAGAACCCATGTT
AACAATTGCTAGTGATGATCCTGATGTAATAGAAGACTACAGAAGACTAAATGTCTTCTTACTGATTATTTCAGAGGCCC
CACGGTAGTAAACACACGCCGGGCTGGGTTAGAGTATGTTCTGCACGCCACTGCTCCGAAGGGTAACGTTTACTCTTGCA
GCTGTAAGTTGCTCTTGAAGAAATCCAGTTGCAGAACACCACGGATTGAATTAGAA

Alignment

ORF - retro_cpor_332 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.83 %
• Parental protein coverage: 69.13 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  PKTKRAKRFLEKREPKL-SENIKNAMLIKGGNANATVTQVLKDVYALK-KPYGVLYKKKNI-TRPFEDQT
          PKTKRAKRFLEK.EPKL.SENIK.AMLIKGGNANATVTQVLKDV.ALK.KPY.VLYK.K...TRPFE.QT
Retrocopy PKTKRAKRFLEKTEPKL>SENIKSAMLIKGGNANATVTQVLKDVHALK<KPYQVLYKTKPL<TRPFEEQT

Parental  SLEFFSKKSDCSLFMFGSHNKKRPNNLVIGR-MYDYHVLDMIELGIEKFVSLKDIKNSKCPEGTKPMLIF
          SLEFFS.K..CS.F.FG...KK.PNN..IG...Y.Y.VLDM.EL.IEKFVSLKDI.NSKCPEGT.PML..
Retrocopy SLEFFSSKLACSSFIFGL-SKKHPNNPAIGYWVYGYYVLDMTELDIEKFVSLKDIMNSKCPEGTEPMLTI

Parental  AGDDFDVTEDYRRL-KSLLIDFFRGPTVANVRLAGLEYVLHFTALQGKVYFRSYKLLLKKSGCRTPRIEL
          A.DD.DV.EDYRRL.K.LL.D.FRGPTV.N.R.AGLEYVLH.TA..G.VY..S.KLLLKKS.CRTPRIEL
Retrocopy ASDDPDVIEDYRRL<KCLLTDYFRGPTVVNTRRAGLEYVLHATAPKGNVYSCSCKLLLKKSSCRTPRIEL

Parental  E
          E
Retrocopy E

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	0.29 RPM	11.27 RPM
SRP017611_kidney	0.31 RPM	11.10 RPM
SRP017611_liver	0.65 RPM	7.57 RPM
SRP040447_lung	0.38 RPM	9.86 RPM
SRP040447_skeletal_muscle	0.07 RPM	6.42 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_332 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_332 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.

---

Parental genes homology:

Parental genes homology involve 17 parental genes, and 37 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000003918	2 retrocopies	retro_cfam_1611, retro_cfam_903,
Callithrix jacchus	ENSCJAG00000005212	6 retrocopies	retro_cjac_1675, retro_cjac_1768, retro_cjac_2244, retro_cjac_2473, retro_cjac_606, retro_cjac_933,
Cavia porcellus	ENSCPOG00000006797	2 retrocopies	retro_cpor_332 , retro_cpor_582,
Equus caballus	ENSECAG00000017121	1 retrocopy	retro_ecab_782,
Erinaceus europaeus	ENSEEUG00000006169	2 retrocopies	retro_eeur_454, retro_eeur_584,
Felis catus	ENSFCAG00000001527	1 retrocopy	retro_fcat_1584,
Homo sapiens	ENSG00000197498	1 retrocopy	retro_hsap_2425,
Gorilla gorilla	ENSGGOG00000001469	1 retrocopy	retro_ggor_83,
Myotis lucifugus	ENSMLUG00000005676	2 retrocopies	retro_mluc_485, retro_mluc_921,
Macaca mulatta	ENSMMUG00000021532	1 retrocopy	retro_mmul_1903,
Mus musculus	ENSMUSG00000038510	1 retrocopy	retro_mmus_2234,
Nomascus leucogenys	ENSNLEG00000012854	3 retrocopies	retro_nleu_2024, retro_nleu_2434, retro_nleu_2445,
Oryctolagus cuniculus	ENSOCUG00000016028	1 retrocopy	retro_ocun_831,
Pongo abelii	ENSPPYG00000016925	2 retrocopies	retro_pabe_1788, retro_pabe_2464,
Pan troglodytes	ENSPTRG00000018503	1 retrocopy	retro_ptro_1398,
Rattus norvegicus	ENSRNOG00000000587	1 retrocopy	retro_rnor_2336,
Tupaia belangeri	ENSTBEG00000017151	9 retrocopies	retro_tbel_1824, retro_tbel_2243, retro_tbel_2376, retro_tbel_2576, retro_tbel_3547, retro_tbel_3635, retro_tbel_3803, retro_tbel_3876, retro_tbel_4509,