RetrogeneDB ID: retro_cpor_788

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_28:2622911..2623431(-)
• 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_788
GAGCAGGATCGATATGAACAGAACCCCATACAAGAACTTGGCGTCCATGAGCTCTATCTCAACGTCTGCATTGGGGGAGT
GGAGACAACACCAGGGCACCCAAGGTGTTGGAGCAGCTACAAGCCAGACCTATGCTTTATAATACTAGATACACTGTCAG
ATTCTCTGGCATCAGGAAAAGTGAGAAGATTGCGGTCCATTGCACAGTCTGTGGGGCTGAGATGAAAGAAATCCTGGAGA
AAAGTCTAATGATGCAAGAGTACATATTAAAGAAAAATAACTTCTCTGATACTGGAGGCTTTGGTTTGGGGATACAGCAA
CACATCAATCTGGGCATGAAATATGACCCAAACATTTGTATCTATGACCTGGACTTCTATGTGGTGATGTGCAGGCCAAG
TTCTAGCATTACAGACAAGCAGTGCAGGGCAGGGACATTTGGCCCAAACACAGAATCAGCAAAGAAGAGGCCACGTGCTG
GTTCAAGCAGAAGGATGGTGGACTTTTCTTTCCTGGCAAA

Alignment

ORF - retro_cpor_788 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.89 %
• Parental protein coverage: 99.44 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  QQDQGEKENPMRELRIRKLCLNICVGE-SGDRLTRAAKVLEQLTGQTPVFSKARYTVRSFGIRRNEKIAV
          .QD..E..NP..EL....L.LN.C.G..SGD..TRA.KVLEQL....P.....RYTVR..GIR..EKIAV
Retrocopy EQDRYE-QNPIQELGVHELYLNVCIGG<SGDN-TRAPKVLEQLQAR-PMLYNTRYTVRFSGIRKSEKIAV

Parental  HCTVRGAKAEEILEKGLKVREYELRKNNFSDTGNFGFGIQEHIDLGIKYDPSIGIYGLDFYVVLGRPGFS
          HCTV.GA...EILEK.L...EY.L.KNNFSDTG.FG.GIQ.HI.LG.KYDP.I.IY.LDFYVV..RP..S
Retrocopy HCTVCGAEMKEILEKSLMMQEYILKKNNFSDTGGFGLGIQQHINLGMKYDPNICIYDLDFYVVMCRPSSS

Parental  IADKKRRTGCIG-AKHRISKEEAMRWFQQKYDGIILPGK
          I.DK..R.G..G..KHRISKEEA..WF.QK..G...PGK
Retrocopy ITDKQCRAGTFG<PKHRISKEEATCWFKQKDGGLFFPGK

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_788 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_788 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,