RetrogeneDB ID: retro_cpor_859

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_3:42102446..42102696(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CKS1B
• Ensembl ID: ENSCPOG00000024061
• Aliases: None
• Description: None

Sequence

>retro_cpor_859
GCGACCATGTCTCATAAACAAATTTATTATTCGGACAAATACGACGACGAGGAGTTTGAATACAGCCATGTCATGTTTGC
CCAAGGATATAGCCAAGCTGGTCCCTAAAACCCACTTGATGTCTGAATCTGAATGGAAGAATCTTGGGGGTTCAGCAGAG
TCAAGGATGGGTCCATTATATGATCCATGGAACCAAGAGCCGCACAATCTTGGTTGTTCGCGACGGCCACTACCCAAGAA
ACCAAACAAA

Alignment

ORF - retro_cpor_859 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.37 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  ATMSHKQIYYSDKYDDEEFEYRHVM-LPKDIAKLVPKTHLMSESEWRN-LGVQQSQGWVHYMIH-EP-EP
          ATMSHKQIYYSDKYDDEEFEY.HVM.LPKDIAKLVPKTHLMSESEW.N.LGVQQSQGWVHYMIH.EP.EP
Retrocopy ATMSHKQIYYSDKYDDEEFEYSHVM>LPKDIAKLVPKTHLMSESEWKN>LGVQQSQGWVHYMIH>EP>EP

Parental  HIL-LFRRPLPKKPNK
          H.L...RRPLPKKPNK
Retrocopy HNLGCSRRPLPKKPNK

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	0.06 RPM	1.67 RPM
SRP017611_kidney	0.10 RPM	7.43 RPM
SRP017611_liver	0.04 RPM	7.79 RPM
SRP040447_lung	0.03 RPM	7.19 RPM
SRP040447_skeletal_muscle	0.01 RPM	3.26 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_859 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_859 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 9 parental genes, and 36 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000033635	10 retrocopies	retro_cjac_13, retro_cjac_1441, retro_cjac_1478, retro_cjac_1779, retro_cjac_2040, retro_cjac_2212, retro_cjac_2649, retro_cjac_276, retro_cjac_57, retro_cjac_876,
Cavia porcellus	ENSCPOG00000024061	2 retrocopies	retro_cpor_859 , retro_cpor_941,
Dipodomys ordii	ENSDORG00000003764	6 retrocopies	retro_dord_25, retro_dord_290, retro_dord_599, retro_dord_64, retro_dord_647, retro_dord_739,
Homo sapiens	ENSG00000173207	1 retrocopy	retro_hsap_27,
Gorilla gorilla	ENSGGOG00000013419	4 retrocopies	retro_ggor_10, retro_ggor_1070, retro_ggor_2739, retro_ggor_659,
Myotis lucifugus	ENSMLUG00000002408	1 retrocopy	retro_mluc_1303,
Otolemur garnettii	ENSOGAG00000006384	10 retrocopies	retro_ogar_1673, retro_ogar_1703, retro_ogar_1713, retro_ogar_1983, retro_ogar_2317, retro_ogar_245, retro_ogar_3310, retro_ogar_450, retro_ogar_530, retro_ogar_877,
Rattus norvegicus	ENSRNOG00000042561	1 retrocopy	retro_rnor_97,
Sarcophilus harrisii	ENSSHAG00000004796	1 retrocopy	retro_shar_786,