RetrogeneDB ID: retro_cpor_356

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_130:1158393..1158697(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ZBTB8OS
• Ensembl ID: ENSCPOG00000015349
• Aliases: None
• Description: None

Sequence

>retro_cpor_356
GGAGGGACCCTGGAGGAAGTGGGAGCGGCATGCATGGCCGCGTTTGCTTATGAGACAGACACTGGACCGCAGAACCCTGC
CCAACAGAAGTGGGAACCCAAGAGAGGCACTTAGTCTCTTCGATTTCAATTTTTTGGATGAATGGCTTTATAAATTTAGT
GCCAATGAATTCTTCATATCCCAGCAAGTGAAAGTACTTAGTACTGTTCAAAGAAATTTCAAATTACTTTCATTTAGGTG
GGGAGAAGAATCTTCACTTCCCAAGCATCCTCAGGGAGCAGAAATCAAAGCAATAACGTATTCA

Alignment

ORF - retro_cpor_356 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.09 %
• Parental protein coverage: 57.14 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  GETLEEAFEQCAMAMFAYMTDTE-TVEPLQTVEVEAQGDDLQSLL-FHFLDEWLYKFSADEFFIPREVKV
          G.TLEE....C.MA.FAY.TDT..T.EP..T.EV..Q...L.S...F.FLDEWLYKFSA.EFFI...VKV
Retrocopy GGTLEEVGAAC-MAAFAYETDTG<TAEPCPT-EVGTQERHLVSSI<FNFLDEWLYKFSANEFFISQQVKV

Parental  LSIDQRNFKLRSIGWGEEFSLSKHPQGTEVKAITYS
          LS..QRNFKL.S..WGEE.SL.KHPQG.E.KAITYS
Retrocopy LSTVQRNFKLLSFRWGEESSLPKHPQGAEIKAITYS

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	5.46 RPM
SRP017611_kidney	0.00 RPM	9.84 RPM
SRP017611_liver	0.00 RPM	10.66 RPM
SRP040447_lung	0.00 RPM	6.81 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_356 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_356 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 16 parental genes, and 27 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000010550	1 retrocopy	retro_cfam_2152,
Choloepus hoffmanni	ENSCHOG00000004061	2 retrocopies	retro_chof_1005, retro_chof_1158,
Cavia porcellus	ENSCPOG00000015349	2 retrocopies	retro_cpor_356 , retro_cpor_903,
Dasypus novemcinctus	ENSDNOG00000001861	2 retrocopies	retro_dnov_1056, retro_dnov_2193,
Equus caballus	ENSECAG00000020982	1 retrocopy	retro_ecab_610,
Felis catus	ENSFCAG00000000700	1 retrocopy	retro_fcat_703,
Homo sapiens	ENSG00000176261	2 retrocopies	retro_hsap_2396, retro_hsap_2992,
Gorilla gorilla	ENSGGOG00000007519	2 retrocopies	retro_ggor_2072, retro_ggor_231,
Myotis lucifugus	ENSMLUG00000000745	5 retrocopies	retro_mluc_1961, retro_mluc_2533, retro_mluc_2570, retro_mluc_2617, retro_mluc_2622,
Macaca mulatta	ENSMMUG00000009939	1 retrocopy	retro_mmul_1915,
Monodelphis domestica	ENSMODG00000017419	2 retrocopies	retro_mdom_400, retro_mdom_901,
Mus musculus	ENSMUSG00000057572	1 retrocopy	retro_mmus_2631,
Oryctolagus cuniculus	ENSOCUG00000000940	1 retrocopy	retro_ocun_492,
Otolemur garnettii	ENSOGAG00000011630	1 retrocopy	retro_ogar_3231,
Pongo abelii	ENSPPYG00000001589	2 retrocopies	retro_pabe_13, retro_pabe_2478,
Tursiops truncatus	ENSTTRG00000014968	1 retrocopy	retro_ttru_1200,