RetrogeneDB ID: retro_mmus_409

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 1:8791925..8792162(-)
• Located in intron of: ENSMUSG00000025909

Retrocopy information

• Ensembl ID: ENSMUSG00000084353
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Cks2
• Ensembl ID: ENSMUSG00000062248
• Aliases: Cks2, 1110038L14Rik, CKSHS2
• Description: CDC28 protein kinase regulatory subunit 2 [Source:MGI Symbol;Acc:MGI:1913447]

Sequence

>retro_mmus_409
ATGGCCCACAAGCAGATCTACTACTCAGACAAGTACTTCGATGAGCACTACGAGTACCGGCATGTCATGTTACCCAGAGA
ACTCTCTAAACAAGTACCCAAAACTCATCTGATGTCCGAAGAGGAGTGGAGGAGACTTGGTGTCCAACAGAGTCTAGGAT
GGGTTCATTACATGATTCATGAGCCAGAACCGCATATTCTTCTCTTTAGACGACCTCTTCCAAAAGAACAACAAAAA

Alignment

ORF - retro_mmus_409 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

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

Retrocopy - Parental Gene Alignment:

Parental  MAHKQIYYSDKYFDEHYEYRHVMLPRELSKQVPKTHLMSEEEWRRLGVQQSLGWVHYMIHEPEPHILLFR
          MAHKQIYYSDKYFDEHYEYRHVMLPRELSKQVPKTHLMSEEEWRRLGVQQSLGWVHYMIHEPEPHILLFR
Retrocopy MAHKQIYYSDKYFDEHYEYRHVMLPRELSKQVPKTHLMSEEEWRRLGVQQSLGWVHYMIHEPEPHILLFR

Parental  RPLPKEQQK
          RPLPKEQQK
Retrocopy RPLPKEQQK

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	0.00 RPM	0.19 RPM
SRP007412_cerebellum	0.00 RPM	0.26 RPM
SRP007412_heart	0.00 RPM	0.16 RPM
SRP007412_kidney	0.02 RPM	2.29 RPM
SRP007412_liver	0.00 RPM	2.65 RPM
SRP007412_testis	0.14 RPM	13.81 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_409 was not detected

EST

No EST(s) were mapped for retro_mmus_409 retrocopy.

TSS

No TSS is located nearby retro_mmus_409 retrocopy 5' end.

Lab

retro_mmus_409 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_409 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 18 parental genes, and 49 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000007792	1 retrocopy	retro_cjac_261,
Dasypus novemcinctus	ENSDNOG00000009427	8 retrocopies	retro_dnov_1200, retro_dnov_1527, retro_dnov_195, retro_dnov_1984, retro_dnov_2530, retro_dnov_2532, retro_dnov_585, retro_dnov_755,
Erinaceus europaeus	ENSEEUG00000004384	7 retrocopies	retro_eeur_183, retro_eeur_255, retro_eeur_293, retro_eeur_551, retro_eeur_632, retro_eeur_639, retro_eeur_640,
Felis catus	ENSFCAG00000022286	1 retrocopy	retro_fcat_1875,
Homo sapiens	ENSG00000123975	1 retrocopy	retro_hsap_4183,
Macaca mulatta	ENSMMUG00000012534	1 retrocopy	retro_mmul_269,
Mus musculus	ENSMUSG00000028044	1 retrocopy	retro_mmus_280,
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,
Ochotona princeps	ENSOPRG00000007583	3 retrocopies	retro_opri_111, retro_opri_1122, retro_opri_912,
Pongo abelii	ENSPPYG00000025843	1 retrocopy	retro_pabe_57,
Pan troglodytes	ENSPTRG00000021093	1 retrocopy	retro_ptro_2837,
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,
Sorex araneus	ENSSARG00000002443	1 retrocopy	retro_sara_213,
Sus scrofa	ENSSSCG00000021161	2 retrocopies	retro_sscr_458, retro_sscr_675,
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,