RetrogeneDB ID: retro_mmus_173

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 6:7982537..7983386(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000096403
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: Rnps1
• Ensembl ID: ENSMUSG00000034681
• Aliases: None
• Description: ribonucleic acid binding protein S1 [Source:MGI Symbol;Acc:MGI:97960]

Sequence

>retro_mmus_173
ATGGCTCCTTCTCCTACCAAACGCAAGGACCGATCTGATGAGAAGTCCAAGGATCGATCTAAAGATAAAGGGGCCACTAA
AGAGTCAAGTGAGAAGGATCGTGGCAGAGATAAGACTCGGAAGAGACGCAGTGCTTCAAGCGGAAGCAGCAGTACCAGGT
CTAGGTCCAGCTCAACCTCCAGCTCGGGCTCCAGCACCAGCACAGGCTCAAGCAGTGGCTCCAGCTCGTCCTCTGCATCC
AGCCGCTCAGGAAGCTCCAGCATGTCCCGGAGCTCCAGTTCTAGCAGCTCCTCCGGCTCCCCAAGCCCTTCTCGGCGCAG
GCATGACAACAGGCGGCGCTCCCGCTCCAAATCCAAACCACCTAAAAGAGATGAAAAAGAGAGGAAAAGGCGGAGCCCTT
CACCTAAACCAACCAAAGTGCACATTGGGAGGCTCACCAGGAATGTGACCAAGGATCATATCATGGAAATATTTTCTACT
TACGGGAAAATCAAAATGATTGACATGCCTGTCGAGAGGATGCATCCTCACCTCTCCAAAGGCTATGCATATGTGGAGTT
TGAGAATCCCGATGAAGCAGAGAAGGCTCTGAAACACATGGATGGAGGACAAATTGATGGCCAAGAGATCACTGCTACTG
CTGTGTTGGCACCCTGGCCTCGGCCACCACCTCGGCGATTCAGCCCTCCTAGGAGGATGCTTCCACCACCTCCCATGTGG
CGTAGGTCACCCCCACGGATGAGGAGAAGGTCTCGATCCCCAAGACGCAGGTCCCCTGTGCGTAGGAGGTCTCGCTCTCC
TGGCCGCCGCCGCCACAGGAGCCGATCCAGCTCCAACTCCTCCCGATAA

Alignment

ORF - retro_mmus_173 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.65 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAPSPTKRKDRSDEKSKDRSKDKGATKESSEKDRGRDKTRKRRSASSGSSSTRSRSSSTSSSGSSTSTGS
          MAPSPTKRKDRSDEKSKDRSKDKGATKESSEKDRGRDKTRKRRSASSGSSSTRSRSSSTSSSGSSTSTGS
Retrocopy MAPSPTKRKDRSDEKSKDRSKDKGATKESSEKDRGRDKTRKRRSASSGSSSTRSRSSSTSSSGSSTSTGS

Parental  SSGSSSSSASSRSGSSSTSRSSSSSSSSGSPSPSRRRHDNRRRSRSKSKPPKRDEKERKRRSPSPKPTKV
          SSGSSSSSASSRSGSSS.SRSSSSSSSSGSPSPSRRRHDNRRRSRSKSKPPKRDEKERKRRSPSPKPTKV
Retrocopy SSGSSSSSASSRSGSSSMSRSSSSSSSSGSPSPSRRRHDNRRRSRSKSKPPKRDEKERKRRSPSPKPTKV

Parental  HIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALKHMDGGQIDGQEI
          HIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALKHMDGGQIDGQEI
Retrocopy HIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALKHMDGGQIDGQEI

Parental  TATAVLAPWPRPPPRRFSPPRRMLPPPPMWRRSPPRMRRRSRSPRRRSPVRRRSRSPGRRRHRSRSSSNS
          TATAVLAPWPRPPPRRFSPPRRMLPPPPMWRRSPPRMRRRSRSPRRRSPVRRRSRSPGRRRHRSRSSSNS
Retrocopy TATAVLAPWPRPPPRRFSPPRRMLPPPPMWRRSPPRMRRRSRSPRRRSPVRRRSRSPGRRRHRSRSSSNS

Parental  SR
          SR
Retrocopy SR

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	1.21 RPM	33.46 RPM
SRP007412_cerebellum	6.38 RPM	25.62 RPM
SRP007412_heart	0.28 RPM	21.08 RPM
SRP007412_kidney	3.25 RPM	11.28 RPM
SRP007412_liver	1.01 RPM	5.11 RPM
SRP007412_testis	4.30 RPM	15.83 RPM

ChIP-Seq

RNA Polymerase II actvity may be related with retro_mmus_173 in 1 libraries

ENCODE library ID	Target	ChIP-Seq Peak coordinates
ENCFF001YKA	POLR2A	6:7983229..7983438

EST

No EST(s) were mapped for retro_mmus_173 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_124766	427 libraries	138 libraries	231 libraries	212 libraries	64 libraries

The graphical summary, for retro_mmus_173 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_173 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_173 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 21 parental genes, and 47 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017861	1 retrocopy	retro_amel_194,
Bos taurus	ENSBTAG00000009969	7 retrocopies	retro_btau_1187, retro_btau_1239, retro_btau_1283, retro_btau_1515, retro_btau_764, retro_btau_776, retro_btau_85,
Canis familiaris	ENSCAFG00000019397	1 retrocopy	retro_cfam_449,
Callithrix jacchus	ENSCJAG00000014969	2 retrocopies	retro_cjac_2127, retro_cjac_3377,
Equus caballus	ENSECAG00000023288	1 retrocopy	retro_ecab_524,
Felis catus	ENSFCAG00000007690	1 retrocopy	retro_fcat_248,
Homo sapiens	ENSG00000205937	1 retrocopy	retro_hsap_2911,
Gorilla gorilla	ENSGGOG00000014275	1 retrocopy	retro_ggor_2016,
Macropus eugenii	ENSMEUG00000008882	1 retrocopy	retro_meug_1996,
Myotis lucifugus	ENSMLUG00000016808	3 retrocopies	retro_mluc_2237, retro_mluc_2618, retro_mluc_643,
Macaca mulatta	ENSMMUG00000019238	1 retrocopy	retro_mmul_794,
Monodelphis domestica	ENSMODG00000015891	1 retrocopy	retro_mdom_1171,
Mus musculus	ENSMUSG00000034681	1 retrocopy	retro_mmus_173 ,
Oryctolagus cuniculus	ENSOCUG00000004387	2 retrocopies	retro_ocun_1544, retro_ocun_1745,
Otolemur garnettii	ENSOGAG00000031582	1 retrocopy	retro_ogar_3241,
Rattus norvegicus	ENSRNOG00000008703	4 retrocopies	retro_rnor_1537, retro_rnor_2135, retro_rnor_2988, retro_rnor_649,
Sarcophilus harrisii	ENSSHAG00000016951	1 retrocopy	retro_shar_390,
Ictidomys tridecemlineatus	ENSSTOG00000013200	1 retrocopy	retro_itri_1160,
Tupaia belangeri	ENSTBEG00000009098	8 retrocopies	retro_tbel_1262, retro_tbel_1851, retro_tbel_2132, retro_tbel_2154, retro_tbel_2216, retro_tbel_3193, retro_tbel_3286, retro_tbel_4688,
Tarsius syrichta	ENSTSYG00000001629	1 retrocopy	retro_tsyr_957,
Tursiops truncatus	ENSTTRG00000008220	7 retrocopies	retro_ttru_1010, retro_ttru_1033, retro_ttru_1558, retro_ttru_1808, retro_ttru_1809, retro_ttru_203, retro_ttru_986,