RetrogeneDB ID: retro_cpor_261

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_11:30030612..30030945(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPL11
• Ensembl ID: ENSCPOG00000008432
• Aliases: None
• Description: None

Sequence

>retro_cpor_261
CTCGTGGAGTATCAAGCTGAAGAGGTGAACTCCCATGTGGAAACTGGGCATCCACAAGCTGTGTCTCAACATCTGTGTGG
GGCAAAGTGGAGCCACACTGAGCTGGACGGTCAAGGTGCTACAGCGGTTCATACAACAGACATCACGTTTCCCAGAGCTA
AATAAATTGCCAGATCCTTAGGCTTTGGGAGAAATGAAAAGATTGCTGCCCACTGCACATCTGTGGGGCGCCAGCAGAAG
AAACCTGGATAGAGACCTAAAGTTGCAGAGTATAACTTAAGAAAAAATAATAACTTCTCAGTTACCAGAAGCTTTGATTT
GGGGATCCAGGAT

Alignment

ORF - retro_cpor_261 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 52.99 %
• Parental protein coverage: 62.36 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  LQQDQGEKEN-PMRELRIRKLCLNICVGESGDRLTRAAKVLEQLTGQTP-VFSKARYTVRSFGIRRNEKI
          L...Q.E..N.PM..L.I.KLCLNICVG.SG..L....KVL.....QT...F..A....RS.G..RNEKI
Retrocopy LVEYQAEEVN>PMWKLGIHKLCLNICVGQSGATLSWTVKVLQRFIQQTS<TFPRAK*IARSLGFGRNEKI

Parental  AVHCT-VRGAKAEEI-LEKGL-KVREYELRK-NNFSDTGNFGFGIQE
          A.HCT...GA.AEE..L...L.KV.EY.LRK.NNFS.T..F..GIQ.
Retrocopy AAHCT<ICGAPAEET<LDRDL<KVAEYNLRKNNNFSVTRSFDLGIQD

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	89.44 RPM
SRP017611_kidney	0.00 RPM	127.61 RPM
SRP017611_liver	0.00 RPM	112.08 RPM
SRP040447_lung	0.00 RPM	187.90 RPM
SRP040447_skeletal_muscle	0.00 RPM	159.72 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_261 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_261 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 17 parental genes, and 53 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000005058	1 retrocopy	retro_acar_165,
Ailuropoda melanoleuca	ENSAMEG00000009704	3 retrocopies	retro_amel_1123, retro_amel_1754, retro_amel_234,
Canis familiaris	ENSCAFG00000013232	2 retrocopies	retro_cfam_1059, retro_cfam_543,
Cavia porcellus	ENSCPOG00000008432	2 retrocopies	retro_cpor_261 , retro_cpor_788,
Equus caballus	ENSECAG00000021136	3 retrocopies	retro_ecab_471, retro_ecab_669, retro_ecab_926,
Felis catus	ENSFCAG00000028651	2 retrocopies	retro_fcat_1069, retro_fcat_1877,
Gorilla gorilla	ENSGGOG00000014628	6 retrocopies	retro_ggor_1192, retro_ggor_1325, retro_ggor_1690, retro_ggor_2204, retro_ggor_533, retro_ggor_603,
Macropus eugenii	ENSMEUG00000013738	3 retrocopies	retro_meug_488, retro_meug_517, retro_meug_633,
Myotis lucifugus	ENSMLUG00000008868	3 retrocopies	retro_mluc_1271, retro_mluc_1345, retro_mluc_2321,
Macaca mulatta	ENSMMUG00000002445	3 retrocopies	retro_mmul_2039, retro_mmul_2415, retro_mmul_2462,
Monodelphis domestica	ENSMODG00000012828	1 retrocopy	retro_mdom_641,
Mus musculus	ENSMUSG00000059291	3 retrocopies	retro_mmus_144, retro_mmus_146, retro_mmus_78,
Ornithorhynchus anatinus	ENSOANG00000000321	1 retrocopy	retro_oana_49,
Otolemur garnettii	ENSOGAG00000032741	6 retrocopies	retro_ogar_1325, retro_ogar_1935, retro_ogar_1963, retro_ogar_2322, retro_ogar_2630, retro_ogar_569,
Rattus norvegicus	ENSRNOG00000026260	9 retrocopies	retro_rnor_1735, retro_rnor_2287, retro_rnor_2314, retro_rnor_2690, retro_rnor_271, retro_rnor_2725, retro_rnor_668, retro_rnor_795, retro_rnor_919,
Sarcophilus harrisii	ENSSHAG00000006767	1 retrocopy	retro_shar_638,
Tursiops truncatus	ENSTTRG00000016115	4 retrocopies	retro_ttru_1525, retro_ttru_1779, retro_ttru_476, retro_ttru_911,