RetrogeneDB ID: retro_cpor_998

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_39:10074931..10075283(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCPOG00000011748
• Aliases: None
• Description: None

Sequence

>retro_cpor_998
ATGGTGGACATGATGGAGTTGCCCACGTCAGACATCAACGCCAGGGTATTACCTCAGTTCATTGGCTAGCCAGTCTGCTT
TGCAGGGAGGGCAAAAAAGATTCATCCCACTGGAAAAATTTTTATCCTTTCAGATGGAGAAGGAAAAAGTGGAACAGGTG
AATTAATGGAGCCACTTGATGAAGAAATAACTGGATTCATGGAAGTAGTTGGAAGAGTAACAGCCAAGGCAATCATCGTG
TGTGCCTCTTATGTCCAGTTTAGAGAAGATAATGATTCTTTTGATCTCAAACTTTACAATGAAGCAGTGAAAATTATCCA
TGAGTTCCCTCAGCTTTTTTCCTTTCAGTGTG

Alignment

ORF - retro_cpor_998 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.81 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MVDVMELPKSRINASMLSQFIDRPVCFVGRLEKIHPTGKMFILSDGEGKNGTVELMEPLDEEISGIVEVV
          MVD.MELP.S.INA..L.QFI..PVCF.GR..KIHPTGK.FILSDGEGK.GT.ELMEPLDEEI.G..EVV
Retrocopy MVDMMELPTSDINARVLPQFIG*PVCFAGRAKKIHPTGKIFILSDGEGKSGTGELMEPLDEEITGFMEVV

Parental  GRVTAKATIMCSSYVQFREDNNPFDLGLYNEAVKIIHEFPQ-FFPFRV
          GRVTAKA.I.C.SYVQFREDN..FDL.LYNEAVKIIHEFPQ.FFPF.V
Retrocopy GRVTAKAIIVCASYVQFREDNDSFDLKLYNEAVKIIHEFPQ>FFPFSV

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	4.43 RPM
SRP017611_kidney	0.00 RPM	5.97 RPM
SRP017611_liver	0.00 RPM	8.62 RPM
SRP040447_lung	0.00 RPM	9.21 RPM
SRP040447_skeletal_muscle	0.00 RPM	4.10 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_998 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_998 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 20 parental genes, and 35 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016401	1 retrocopy	retro_amel_1031,
Callithrix jacchus	ENSCJAG00000000705	1 retrocopy	retro_cjac_3111,
Cavia porcellus	ENSCPOG00000011748	2 retrocopies	retro_cpor_855, retro_cpor_998 ,
Dasypus novemcinctus	ENSDNOG00000011718	3 retrocopies	retro_dnov_1044, retro_dnov_1824, retro_dnov_2045,
Equus caballus	ENSECAG00000007680	2 retrocopies	retro_ecab_212, retro_ecab_819,
Felis catus	ENSFCAG00000025369	1 retrocopy	retro_fcat_1287,
Homo sapiens	ENSG00000106399	2 retrocopies	retro_hsap_2179, retro_hsap_3473,
Gorilla gorilla	ENSGGOG00000022464	2 retrocopies	retro_ggor_1727, retro_ggor_2342,
Microcebus murinus	ENSMICG00000000741	1 retrocopy	retro_mmur_934,
Myotis lucifugus	ENSMLUG00000007421	1 retrocopy	retro_mluc_852,
Macaca mulatta	ENSMMUG00000000854	2 retrocopies	retro_mmul_131, retro_mmul_909,
Mus musculus	ENSMUSG00000012483	1 retrocopy	retro_mmus_413,
Nomascus leucogenys	ENSNLEG00000016151	2 retrocopies	retro_nleu_308, retro_nleu_340,
Oryctolagus cuniculus	ENSOCUG00000000467	1 retrocopy	retro_ocun_1097,
Otolemur garnettii	ENSOGAG00000001018	1 retrocopy	retro_ogar_113,
Pongo abelii	ENSPPYG00000017787	2 retrocopies	retro_pabe_2062, retro_pabe_2868,
Pan troglodytes	ENSPTRG00000018927	1 retrocopy	retro_ptro_2354,
Rattus norvegicus	ENSRNOG00000008309	2 retrocopies	retro_rnor_2803, retro_rnor_53,
Sus scrofa	ENSSSCG00000023886	1 retrocopy	retro_sscr_297,
Tupaia belangeri	ENSTBEG00000010930	6 retrocopies	retro_tbel_1347, retro_tbel_1876, retro_tbel_2736, retro_tbel_4029, retro_tbel_87, retro_tbel_917,