RetrogeneDB ID: retro_sscr_458

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 15:67544196..67544469(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CKS2
• Ensembl ID: ENSSSCG00000021161
• Aliases: None
• Description: CDC28 protein kinase regulatory subunit 2 [Source:HGNC Symbol;Acc:2000]

Sequence

>retro_sscr_458
CCATCACTTCCTTCCAGCACTGCCTACCCGCCGGCTTGCAGGATGGCCCAGAAGCAGATCTGCTAATTGGATAAGTACTT
CAATGAGCACTATGAGTACTGGCGTGTCATGTTACCCAGAGACCTTTCCAAGCAAGTACCCAAAACCTATCTGATGTCTG
AAGAGGAGTGGAGGAGACTTGGTGTCCAACAGAGTGTAGGCTGAGTTCATTACATGATTCATGAGCCAGAACCACACATT
CTTCTCTTTAGACGACCTCTTCCAAAAGATCAG

Alignment

ORF - retro_sscr_458 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.42 %
• Parental protein coverage: 96.81 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PSLRFSAGYPPSCRMAHKQIYYSDKYFDEHYEYRHVMLPRELSKQVPKTHLMSEEEWRRLGVQQSLGWVH
          PSL..S..YPP.CRMA.KQI...DKYF.EHYEY..VMLPR.LSKQVPKT.LMSEEEWRRLGVQQS.G.VH
Retrocopy PSLPSSTAYPPACRMAQKQIC*LDKYFNEHYEYWRVMLPRDLSKQVPKTYLMSEEEWRRLGVQQSVG*VH

Parental  YMIHEPEPHILLFRRPLPKDQ
          YMIHEPEPHILLFRRPLPKDQ
Retrocopy YMIHEPEPHILLFRRPLPKDQ

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
SRP014902_placenta	0.00 RPM	9.95 RPM
SRP014902_testis	0.00 RPM	17.96 RPM
SRP018288_heart	0.00 RPM	5.58 RPM
SRP018288_kidney	0.00 RPM	18.91 RPM
SRP018288_liver	0.00 RPM	15.51 RPM
SRP018288_lung	0.00 RPM	6.31 RPM
SRP018856_adipose	0.00 RPM	3.59 RPM
SRP035408_brain	0.00 RPM	3.49 RPM
SRP035408_liver	0.00 RPM	22.87 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_458 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_458 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_458 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 40 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000002194	2 retrocopies	retro_cfam_1495, retro_cfam_472,
Callithrix jacchus	ENSCJAG00000007792	1 retrocopy	retro_cjac_261,
Echinops telfairi	ENSETEG00000001260	10 retrocopies	retro_etel_1194, retro_etel_1752, retro_etel_1839, retro_etel_229, retro_etel_590, retro_etel_704, retro_etel_717, retro_etel_721, retro_etel_838, retro_etel_979,
Felis catus	ENSFCAG00000022286	1 retrocopy	retro_fcat_1875,
Macaca mulatta	ENSMMUG00000012534	1 retrocopy	retro_mmul_269,
Mus musculus	ENSMUSG00000062248	4 retrocopies	retro_mmus_1356, retro_mmus_1470, retro_mmus_2392, retro_mmus_409,
Nomascus leucogenys	ENSNLEG00000008729	1 retrocopy	retro_nleu_1793,
Otolemur garnettii	ENSOGAG00000028843	1 retrocopy	retro_ogar_798,
Pongo abelii	ENSPPYG00000025843	1 retrocopy	retro_pabe_57,
Pteropus vampyrus	ENSPVAG00000011011	3 retrocopies	retro_pvam_1297, retro_pvam_1307, retro_pvam_605,
Rattus norvegicus	ENSRNOG00000014130	5 retrocopies	retro_rnor_1209, retro_rnor_1909, retro_rnor_2742, retro_rnor_279, retro_rnor_402,
Sus scrofa	ENSSSCG00000021161	2 retrocopies	retro_sscr_458 , retro_sscr_675,
Sus scrofa	ENSSSCG00000029737	1 retrocopy	retro_sscr_730,
Ictidomys tridecemlineatus	ENSSTOG00000000048	7 retrocopies	retro_itri_1058, retro_itri_1306, retro_itri_1429, retro_itri_1632, retro_itri_269, retro_itri_585, retro_itri_774,