RetrogeneDB ID: retro_ptro_558

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 11:81124023..81124260(+)
• Located in intron of: ENSPTRG00000004128

Retrocopy information

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

Parental gene information

• Parental gene symbol: CKS1B
• Ensembl ID: ENSPTRG00000001398
• Aliases: None
• Description: Pan troglodytes cyclin-dependent kinases regulatory subunit 1 (CKS1B), mRNA. [Source:RefSeq mRNA;Acc:NM_001252546]

Sequence

>retro_ptro_558
ATGTCGCACAAACAAATTTACTATTCAGACAAATACGACGACGAGGAGTTTGAGTATCGACATGTCGTGCTGCCCAAGGA
CATAGCCAAGCTGGTCCGTAAAACCCATTTGATGTCTGAATCTGAATGGAGGAATCTTGGCGTTCAGCAGAGTCAGGGAT
GGGTCTATTATATGATCCATGAACCAGAACCTCACATTTTGCTGTTCCGGTGCCCACTACCCAAGAAGCCAAAGAAA

Alignment

ORF - retro_ptro_558 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.94 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSHKQIYYSDKYDDEEFEYRHVMLPKDIAKLVPKTHLMSESEWRNLGVQQSQGWVHYMIHEPEPHILLFR
          MSHKQIYYSDKYDDEEFEYRHV.LPKDIAKLV.KTHLMSESEWRNLGVQQSQGWV.YMIHEPEPHILLFR
Retrocopy MSHKQIYYSDKYDDEEFEYRHVVLPKDIAKLVRKTHLMSESEWRNLGVQQSQGWVYYMIHEPEPHILLFR

Parental  RPLPKKPKK
          .PLPKKPKK
Retrocopy CPLPKKPKK

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
SRP007412_brain_prefrontal_cortex	0.00 RPM	3.65 RPM
SRP007412_cerebellum	0.00 RPM	3.23 RPM
SRP007412_heart	0.00 RPM	4.23 RPM
SRP007412_kidney	0.03 RPM	8.16 RPM
SRP007412_liver	0.00 RPM	14.44 RPM
SRP007412_testis	0.00 RPM	15.70 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_558 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_558 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_558 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Gorilla gorilla	retro_ggor_659
Pongo abelii	retro_pabe_717

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Parental genes homology:

Parental genes homology involve 17 parental genes, and 43 retrocopies.

Species	Parental gene accession	Retrocopies number
Dipodomys ordii	ENSDORG00000003764	6 retrocopies	retro_dord_25, retro_dord_290, retro_dord_599, retro_dord_64, retro_dord_647, retro_dord_739,
Equus caballus	ENSECAG00000003460	1 retrocopy	retro_ecab_975,
Echinops telfairi	ENSETEG00000003337	4 retrocopies	retro_etel_1246, retro_etel_1938, retro_etel_239, retro_etel_497,
Felis catus	ENSFCAG00000001347	1 retrocopy	retro_fcat_1041,
Homo sapiens	ENSG00000173207	1 retrocopy	retro_hsap_27,
Loxodonta africana	ENSLAFG00000032213	1 retrocopy	retro_lafr_243,
Mus musculus	ENSMUSG00000028044	1 retrocopy	retro_mmus_280,
Nomascus leucogenys	ENSNLEG00000011532	3 retrocopies	retro_nleu_1098, retro_nleu_2592, retro_nleu_411,
Oryctolagus cuniculus	ENSOCUG00000016204	2 retrocopies	retro_ocun_1389, retro_ocun_18,
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,
Pongo abelii	ENSPPYG00000000768	3 retrocopies	retro_pabe_1143, retro_pabe_3625, retro_pabe_717,
Pan troglodytes	ENSPTRG00000001398	4 retrocopies	retro_ptro_2769, retro_ptro_3100, retro_ptro_558 , retro_ptro_944,
Pan troglodytes	ENSPTRG00000021093	1 retrocopy	retro_ptro_2837,
Rattus norvegicus	ENSRNOG00000042561	1 retrocopy	retro_rnor_97,
Sorex araneus	ENSSARG00000012383	2 retrocopies	retro_sara_667, retro_sara_77,
Sus scrofa	ENSSSCG00000029737	1 retrocopy	retro_sscr_730,
Vicugna pacos	ENSVPAG00000012182	1 retrocopy	retro_vpac_532,