RetrogeneDB ID: retro_cpor_1333

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_7:18044151..18044495(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPS24
• Ensembl ID: ENSCPOG00000020096
• Aliases: None
• Description: ribosomal protein S24 [Source:HGNC Symbol;Acc:10411]

Sequence

>retro_cpor_1333
ACTGTCTGGACGAGGAAGGTCGGGGCCAACCGCCGGGCACTTGAGGGGAAGTAAATGGCCATCGATGTCCTGCATCCCGG
GAAGGCAGCTGTGCCTATGGCAGAAATTCAGGAAAAAGTCATCCAAGTGGACGGCACCACACTGATGCCTTCTTTGTATT
TGGATGCAGGACCCATTTTGGAGGTGGCAAGAGGATTGGTTTTGGACTGATCTATGAATCCTTGAATTATGCAAAGACAA
ATGACCTGGAACACAGATTTGCCACACGTGGGCCATGTGAGAAGAAAAAGACCTCAAGGAAACAAGGAAAAGAACAGAGT
AACAGAGTGAAGAGCATCACAGGG

Alignment

ORF - retro_cpor_1333 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.48 %
• Parental protein coverage: 85.07 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  TIRTRKFMTNR-LLQRKQMVIDVLHPGKATVPKTEIREKLAKMYKTT-PDVIFVFGFRTHFGGGKTTGFG
          T..TRK...NR..L..K.M.IDVLHPGKA.VP..EI.EK......TT..D..FVFG.RTHFGGGK..GFG
Retrocopy TVWTRKVGANRRALEGK*MAIDVLHPGKAAVPMAEIQEKVIQVDGTT<TDAFFVFGCRTHFGGGKRIGFG

Parental  MIYDSLDYAKKNEPKHRLARHGLYEKKKTSRKQRKERKNRMKKVRG
          .IY.SL.YAK.N...HR.A..G..EKKKTSRKQ.KE..NR.K...G
Retrocopy LIYESLNYAKTNDLEHRFATRGPCEKKKTSRKQGKEQSNRVKSITG

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	228.23 RPM
SRP017611_kidney	0.00 RPM	255.33 RPM
SRP017611_liver	0.04 RPM	152.39 RPM
SRP040447_lung	0.00 RPM	260.66 RPM
SRP040447_skeletal_muscle	0.00 RPM	206.26 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1333 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1333 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 12 parental genes, and 56 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017818	17 retrocopies	retro_amel_1043, retro_amel_1258, retro_amel_1303, retro_amel_1397, retro_amel_145, retro_amel_1814, retro_amel_1832, retro_amel_225, retro_amel_24, retro_amel_251, retro_amel_328, retro_amel_331, retro_amel_515, retro_amel_718, retro_amel_768, retro_amel_81, retro_amel_886,
Cavia porcellus	ENSCPOG00000020096	3 retrocopies	retro_cpor_1333 , retro_cpor_14, retro_cpor_923,
Dipodomys ordii	ENSDORG00000000189	4 retrocopies	retro_dord_248, retro_dord_498, retro_dord_717, retro_dord_766,
Felis catus	ENSFCAG00000000849	3 retrocopies	retro_fcat_19, retro_fcat_772, retro_fcat_85,
Gadus morhua	ENSGMOG00000012595	1 retrocopy	retro_gmor_15,
Loxodonta africana	ENSLAFG00000027878	10 retrocopies	retro_lafr_1017, retro_lafr_190, retro_lafr_303, retro_lafr_340, retro_lafr_439, retro_lafr_558, retro_lafr_596, retro_lafr_669, retro_lafr_854, retro_lafr_995,
Myotis lucifugus	ENSMLUG00000024102	1 retrocopy	retro_mluc_260,
Mustela putorius furo	ENSMPUG00000003778	1 retrocopy	retro_mputfur_10,
Mus musculus	ENSMUSG00000025290	13 retrocopies	retro_mmus_1101, retro_mmus_1462, retro_mmus_1589, retro_mmus_1592, retro_mmus_1599, retro_mmus_2134, retro_mmus_2332, retro_mmus_2497, retro_mmus_2984, retro_mmus_3162, retro_mmus_321, retro_mmus_3233, retro_mmus_602,
Oryctolagus cuniculus	ENSOCUG00000012472	1 retrocopy	retro_ocun_16,
Rattus norvegicus	ENSRNOG00000010189	1 retrocopy	retro_rnor_206,
Tarsius syrichta	ENSTSYG00000006715	1 retrocopy	retro_tsyr_1919,