RetrogeneDB ID: retro_cpor_584

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_2:41836738..41836936(+)
• Located in intron of: ENSCPOG00000004935

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPS21
• Ensembl ID: ENSCPOG00000001965
• Aliases: None
• Description: 40S ribosomal protein S21 [Source:UniProtKB/TrEMBL;Acc:H0UXF6]

Sequence

>retro_cpor_584
TCTGCCAGCAGCTGCATCAGTGGTGCTAAGGACCAGGCATCCTTCAGATGAAAGTGGCTGAGGCTGACAAAATCACAGGC
AGGTTTAGTGGCCGGTTTAAAACCTATGCTGTCTGCGAAACCATTCGCAGGATGGGCTGAATCAGATGACTACATTTTAC
AATTGGCCAAAGCTTATGGCGTCGTCTGAAAGAACTTT

Alignment

ORF - retro_cpor_584 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.59 %
• Parental protein coverage: 79.52 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  SASNRIIGAKDHAS-IQMNVAEVDKVTGRFNGQFKTYAICGAIRRMG-ESDDSILRLAKADGIVSKNF
          SAS..I.GAKD.AS..QM.VAE.DK.TGRF.G.FKTYA.C..IRRMG.ESDD.IL.LAKA.G.V.KNF
Retrocopy SASSCISGAKDQAS<LQMKVAEADKITGRFSGRFKTYAVCETIRRMG>ESDDYILQLAKAYGVV*KNF

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	57.00 RPM
SRP017611_kidney	0.00 RPM	62.39 RPM
SRP017611_liver	0.00 RPM	50.01 RPM
SRP040447_lung	0.00 RPM	157.00 RPM
SRP040447_skeletal_muscle	0.00 RPM	154.97 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_584 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_584 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 14 parental genes, and 45 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017399	2 retrocopies	retro_amel_1783, retro_amel_87,
Bos taurus	ENSBTAG00000020795	2 retrocopies	retro_btau_174, retro_btau_1780,
Canis familiaris	ENSCAFG00000012676	4 retrocopies	retro_cfam_1055, retro_cfam_1687, retro_cfam_1896, retro_cfam_28,
Callithrix jacchus	ENSCJAG00000014195	5 retrocopies	retro_cjac_2266, retro_cjac_2572, retro_cjac_629, retro_cjac_82, retro_cjac_884,
Cavia porcellus	ENSCPOG00000001965	4 retrocopies	retro_cpor_1156, retro_cpor_1268, retro_cpor_262, retro_cpor_584 ,
Gorilla gorilla	ENSGGOG00000023745	7 retrocopies	retro_ggor_131, retro_ggor_1380, retro_ggor_1647, retro_ggor_2043, retro_ggor_2089, retro_ggor_2875, retro_ggor_917,
Latimeria chalumnae	ENSLACG00000012753	1 retrocopy	retro_lcha_124,
Monodelphis domestica	ENSMODG00000016769	1 retrocopy	retro_mdom_464,
Ornithorhynchus anatinus	ENSOANG00000003361	2 retrocopies	retro_oana_102, retro_oana_107,
Pongo abelii	ENSPPYG00000011205	8 retrocopies	retro_pabe_1562, retro_pabe_157, retro_pabe_2446, retro_pabe_2505, retro_pabe_3503, retro_pabe_365, retro_pabe_710, retro_pabe_986,
Pan troglodytes	ENSPTRG00000013708	1 retrocopy	retro_ptro_42,
Rattus norvegicus	ENSRNOG00000006325	2 retrocopies	retro_rnor_128, retro_rnor_172,
Sus scrofa	ENSSSCG00000021825	1 retrocopy	retro_sscr_7,
Ictidomys tridecemlineatus	ENSSTOG00000001029	5 retrocopies	retro_itri_1027, retro_itri_1487, retro_itri_637, retro_itri_82, retro_itri_849,