RetrogeneDB ID: retro_mmus_82

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 8:95825363..95825882(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000061104
• Aliases: Gm10094, ENSMUSG00000061104
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: Sap18
• Ensembl ID: ENSMUSG00000021963
• Aliases: Sap18, C530046K05Rik, D11Ertd539e, EMegR4, Sinbp1
• Description: Sin3-associated polypeptide 18 [Source:MGI Symbol;Acc:MGI:1277978]

Sequence

>retro_mmus_82
ATGCTCGCCGCAGGGGTCGGAGGTCAGGGCGAGCGTCTCCCGGGCCGAAGGAGGAAGATGGCGGTGGAGTCGCGCGTTAC
CCAGGAGGAAATTAAGAAGGAGCCGGAGAAGCCGATCGACCGCGAGAAGACCTGCCCGCTCCTGCTGCGGGTCTTCACCA
CCAACAACGGCCGCCACCACCGAATGGACGAGTTCTCCCGCGGGAACGTGCCTTCGAGCGAGCTGCAGATCTACACCTGG
ATGGATGCAACCTTGAAAGAACTGACTAGTTTAGTGAAGGAAGTCTACCCAGAAGCCAGAAAGAAGGGCACACACTTCAA
TTTTGCAATTGTTTTTATGGATCTTAAAAGACCTGGATATCGAGTTAAGGAGATTGGCAGCACCATGTCTGGCAGGAAGG
GCACTGATGACTCCATGACCCTGCAGTCACAGAAGTTCCAAATAGGGGATTATCTGGACATAGCCATCACGCCTCCAAAT
CGGGCGCCGCCTTCGTCAGGGAGGATGAGACCCTACTGA

Alignment

ORF - retro_mmus_82 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  MLAAGVGGQGERLPGRRRKMAVESRVTQEEIKKEPEKPIDREKTCPLLLRVFTTNNGRHHRMDEFSRGNV
          MLAAGVGGQGERLPGRRRKMAVESRVTQEEIKKEPEKPIDREKTCPLLLRVFTTNNGRHHRMDEFSRGNV
Retrocopy MLAAGVGGQGERLPGRRRKMAVESRVTQEEIKKEPEKPIDREKTCPLLLRVFTTNNGRHHRMDEFSRGNV

Parental  PSSELQIYTWMDATLKELTSLVKEVYPEARKKGTHFNFAIVFMDLKRPGYRVKEIGSTMSGRKGTDDSMT
          PSSELQIYTWMDATLKELTSLVKEVYPEARKKGTHFNFAIVFMDLKRPGYRVKEIGSTMSGRKGTDDSMT
Retrocopy PSSELQIYTWMDATLKELTSLVKEVYPEARKKGTHFNFAIVFMDLKRPGYRVKEIGSTMSGRKGTDDSMT

Parental  LQSQKFQIGDYLDIAITPPNRAPPSSGRMRPY
          LQSQKFQIGDYLDIAITPPNRAPPSSGRMRPY
Retrocopy LQSQKFQIGDYLDIAITPPNRAPPSSGRMRPY

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	0.16 RPM	30.18 RPM
SRP007412_cerebellum	0.04 RPM	26.40 RPM
SRP007412_heart	0.31 RPM	25.28 RPM
SRP007412_kidney	0.17 RPM	30.05 RPM
SRP007412_liver	0.16 RPM	24.58 RPM
SRP007412_testis	0.37 RPM	33.12 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_82 was not detected

EST

No EST(s) were mapped for retro_mmus_82 retrocopy.

TSS

TSS No.	TSS Name	TSS expression level (Expr) in TPM range:
		no expression	0 < Expr ≤ 1	1 < Expr ≤ 5	5 < Expr ≤ 10	Expr > 10
TSS #1	TSS_145714	155 libraries	413 libraries	462 libraries	36 libraries	6 libraries

The graphical summary, for retro_mmus_82 TSS expression levels > 0 TPM .
TSS expression levels were studied across 1072 TSS-CAGE libraries, based on FANTOM5 data.
The expression values were visualized using beanplot. If you have any doubts, how to read it, read more in Kampstra P (2008)

Lab

retro_mmus_82 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_82 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 27 parental genes, and 82 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000018631	1 retrocopy	retro_btau_1443,
Canis familiaris	ENSCAFG00000032070	3 retrocopies	retro_cfam_561, retro_cfam_733, retro_cfam_979,
Callithrix jacchus	ENSCJAG00000018645	3 retrocopies	retro_cjac_1601, retro_cjac_2804, retro_cjac_2935,
Cavia porcellus	ENSCPOG00000008598	1 retrocopy	retro_cpor_897,
Dasypus novemcinctus	ENSDNOG00000015204	3 retrocopies	retro_dnov_1027, retro_dnov_119, retro_dnov_1600,
Equus caballus	ENSECAG00000013508	1 retrocopy	retro_ecab_321,
Erinaceus europaeus	ENSEEUG00000006309	1 retrocopy	retro_eeur_674,
Echinops telfairi	ENSETEG00000005565	11 retrocopies	retro_etel_1176, retro_etel_1379, retro_etel_1411, retro_etel_1716, retro_etel_1811, retro_etel_262, retro_etel_456, retro_etel_708, retro_etel_879, retro_etel_891, retro_etel_98,
Felis catus	ENSFCAG00000007026	1 retrocopy	retro_fcat_1450,
Homo sapiens	ENSG00000150459	2 retrocopies	retro_hsap_2186, retro_hsap_2759,
Loxodonta africana	ENSLAFG00000030963	2 retrocopies	retro_lafr_338, retro_lafr_358,
Microcebus murinus	ENSMICG00000004309	2 retrocopies	retro_mmur_1092, retro_mmur_1312,
Myotis lucifugus	ENSMLUG00000002852	4 retrocopies	retro_mluc_1903, retro_mluc_2197, retro_mluc_2239, retro_mluc_407,
Macaca mulatta	ENSMMUG00000010416	2 retrocopies	retro_mmul_465, retro_mmul_914,
Mustela putorius furo	ENSMPUG00000000607	1 retrocopy	retro_mputfur_35,
Mus musculus	ENSMUSG00000021963	1 retrocopy	retro_mmus_82 ,
Nomascus leucogenys	ENSNLEG00000001995	2 retrocopies	retro_nleu_2922, retro_nleu_315,
Oryctolagus cuniculus	ENSOCUG00000012716	1 retrocopy	retro_ocun_915,
Otolemur garnettii	ENSOGAG00000010062	2 retrocopies	retro_ogar_2213, retro_ogar_650,
Pongo abelii	ENSPPYG00000005198	2 retrocopies	retro_pabe_2066, retro_pabe_2253,
Pan troglodytes	ENSPTRG00000005692	2 retrocopies	retro_ptro_1664, retro_ptro_1866,
Pteropus vampyrus	ENSPVAG00000016315	2 retrocopies	retro_pvam_1246, retro_pvam_43,
Rattus norvegicus	ENSRNOG00000010732	1 retrocopy	retro_rnor_163,
Sorex araneus	ENSSARG00000004923	3 retrocopies	retro_sara_232, retro_sara_471, retro_sara_743,
Ictidomys tridecemlineatus	ENSSTOG00000005735	3 retrocopies	retro_itri_1114, retro_itri_1382, retro_itri_1627,
Tarsius syrichta	ENSTSYG00000005454	22 retrocopies	retro_tsyr_1018, retro_tsyr_1117, retro_tsyr_1225, retro_tsyr_1342, retro_tsyr_1439, retro_tsyr_1490, retro_tsyr_1578, retro_tsyr_1708, retro_tsyr_1767, retro_tsyr_1851, retro_tsyr_1938, retro_tsyr_2118, retro_tsyr_2179, retro_tsyr_398, retro_tsyr_451, retro_tsyr_563, retro_tsyr_826, retro_tsyr_837, retro_tsyr_886, retro_tsyr_892, retro_tsyr_901, retro_tsyr_967,
Tursiops truncatus	ENSTTRG00000016912	3 retrocopies	retro_ttru_115, retro_ttru_1453, retro_ttru_381,