RetrogeneDB ID: retro_mmus_2855

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 6:92564619..92565840(-)
• Located in intron of: ENSMUSG00000030020

Retrocopy information

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

Parental gene information

• Parental gene symbol: Rbm17
• Ensembl ID: ENSMUSG00000037197
• Aliases: Rbm17, 2700027J02Rik
• Description: RNA binding motif protein 17 [Source:MGI Symbol;Acc:MGI:1924188]

Sequence

>retro_mmus_2855
ATGTCCCTATAGGATGACCTGGGAGTGGAGACCAGTGACTCAAAAACTGAAGGCTGGTCCAAAAGCTTCAAGCTTCTGCA
GTTCCAGCTCCAGGTGAAGAAGGCAGCGCTCACTCAGGCCAAGAGCCAAAGGACCAAGCAAAGTAGGATGCTTGCTCAGG
TCATCAACCTAAAGCGAGGCGGCTCCTCAGATGACCGGCAGATTACAGACACACCACCTCACGTGACAGCTGGGCTGAAG
GACCCTGTGCCCAGTGGGTTTTCTGCAGGGGAAGTTCTGATCCCCTTAGCTGATGAATATGACCCTATGTTCTCTAATGA
CTATGAGAAAGTGGTGAAGCACCAGAGAGAACGGCAGAGGCAGCGGGAGCTGGAAAGACAGAAGGAAATAGAGGAAAGAG
AAAAGAGGCGTAAAGACAGACACGAAGCCAGTAGGCTTTTAAGACAACCAGACCCAGATTCTGATGAGGATAAAGATTAT
GAGCGAGAGCGGAGGAAAAGAAGTATGGGAGGAGCTGCCATCGCCCCACGGAAGTCTCTTGTAGAGAAAGACAAAGAGTT
ACCCTGGGATTTTCCTTATGAAGAGGACTCAAGACCTAGATCACAGTCTTCCAAAGCTGCTATTCCTTCCCCCCCCCCCC
CCATGTATGAGGAGCCAGACAGACCAAGATCTCCAACAGGCCCCAGCAACTCCTTCCTTGCTAACATGGGTGGCACAGTG
GCTCATAAGATTATGCAGAAGTATGGCTTCCGGGAAGGTCAGGGACTGGGGAAACACGAGCAAGGGCTGAGTACTGCATT
GTCTGTGGAGAAGACCAGCAAGCGTGGCGGCAAGATCATTGTGGGGGATGTGAAAGAGAAGGGCAAGGCTCAAGATGCAT
CCAAGAAGTCAGATTCAAATCCATTAACTGAAATTCTTAAGTGTCCTACTAAAGTGGTCTTGCTGAGGAACATGGTTGGT
GCAGGAGAGGTCGATAAAGACTTGGAAGTTGAAACCAAGGAAGAATGTGAAAAATATGGCAAGGTTGGGAAATGTGTGAT
ATTTGAGATTCCTGGTGCCCCTGATGATGAAGCAGTACGGATATTTTTAGAATTTGAGAGAGTAGAATCGGCAATTAAAG
CTGTTGTTGATCTGAATGGGAGGTATTTTGGTGGACAGGTGGTAAAAGCATGTTTCTACAATTTGGATAAATTCAGGGTC
TTGGATCTAGCAGAACAAGTT

Alignment

ORF - retro_mmus_2855 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.4 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSLYDDLGVETSDSKTEGWSKNFKLLQSQLQVKKAALTQAKSQRTKQSTVLAPVIDLKRGGSSDDRQIAD
          MSL.DDLGVETSDSKTEGWSK.FKLLQ.QLQVKKAALTQAKSQRTKQS..LA.VI.LKRGGSSDDRQI.D
Retrocopy MSL*DDLGVETSDSKTEGWSKSFKLLQFQLQVKKAALTQAKSQRTKQSRMLAQVINLKRGGSSDDRQITD

Parental  TPPHVAAGLKDPVPSGFSAGEVLIPLADEYDPMFPNDYEKVVKRQREERQRQRELERQKEIEEREKRRKD
          TPPHV.AGLKDPVPSGFSAGEVLIPLADEYDPMF.NDYEKVVK.QRE.RQRQRELERQKEIEEREKRRKD
Retrocopy TPPHVTAGLKDPVPSGFSAGEVLIPLADEYDPMFSNDYEKVVKHQRE-RQRQRELERQKEIEEREKRRKD

Parental  RHEASGFSRRPDPDSDEDEDYERERRKRSMGGAAIAPPTSLVEKDKELPRDFPYEEDSRPRSQSSKAAIP
          RHEAS...R.PDPDSDED.DYERERRKRSMGGAAIAP..SLVEKDKELP.DFPYEEDSRPRSQSSKAAIP
Retrocopy RHEASRLLRQPDPDSDEDKDYERERRKRSMGGAAIAPRKSLVEKDKELPWDFPYEEDSRPRSQSSKAAIP

Parental  PP---VYEEPDRPRSPTGPSNSFLANMGGTVAHKIMQKYGFREGQGLGKHEQGLSTALSVEKTSKRGGKI
          ......YEEPDRPRSPTGPSNSFLANMGGTVAHKIMQKYGFREGQGLGKHEQGLSTALSVEKTSKRGGKI
Retrocopy XXXXXMYEEPDRPRSPTGPSNSFLANMGGTVAHKIMQKYGFREGQGLGKHEQGLSTALSVEKTSKRGGKI

Parental  IVGDATEKGEAQDASKKSDSNPLTEILKCPTKVVLLRNMVGAGEVDEDLEVETKEECEKYGKVGKCVIFE
          IVGD..EKG.AQDASKKSDSNPLTEILKCPTKVVLLRNMVGAGEVD.DLEVETKEECEKYGKVGKCVIFE
Retrocopy IVGDVKEKGKAQDASKKSDSNPLTEILKCPTKVVLLRNMVGAGEVDKDLEVETKEECEKYGKVGKCVIFE

Parental  IPGAPDDEAVRIFLEFERVESAIKAVVDLNGRYFGGRVVKACFYNLDKFRVLDLAEQV
          IPGAPDDEAVRIFLEFERVESAIKAVVDLNGRYFGG.VVKACFYNLDKFRVLDLAEQV
Retrocopy IPGAPDDEAVRIFLEFERVESAIKAVVDLNGRYFGGQVVKACFYNLDKFRVLDLAEQV

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	0.12 RPM	30.96 RPM
SRP007412_cerebellum	0.26 RPM	61.27 RPM
SRP007412_heart	0.00 RPM	31.01 RPM
SRP007412_kidney	0.29 RPM	48.51 RPM
SRP007412_liver	0.16 RPM	48.58 RPM
SRP007412_testis	2.93 RPM	46.20 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_2855 was not detected

EST

No EST(s) were mapped for retro_mmus_2855 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_125940	385 libraries	551 libraries	131 libraries	1 library	4 libraries

The graphical summary, for retro_mmus_2855 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_2855 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2855 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000021951	2 retrocopies	retro_btau_1057, retro_btau_530,
Canis familiaris	ENSCAFG00000005206	1 retrocopy	retro_cfam_844,
Callithrix jacchus	ENSCJAG00000020573	1 retrocopy	retro_cjac_432,
Equus caballus	ENSECAG00000008939	1 retrocopy	retro_ecab_547,
Erinaceus europaeus	ENSEEUG00000013077	1 retrocopy	retro_eeur_390,
Homo sapiens	ENSG00000134453	1 retrocopy	retro_hsap_1551,
Macropus eugenii	ENSMEUG00000011347	1 retrocopy	retro_meug_438,
Macaca mulatta	ENSMMUG00000015152	2 retrocopies	retro_mmul_1209, retro_mmul_771,
Mus musculus	ENSMUSG00000037197	1 retrocopy	retro_mmus_2855 ,
Otolemur garnettii	ENSOGAG00000015687	1 retrocopy	retro_ogar_1119,
Pongo abelii	ENSPPYG00000002067	1 retrocopy	retro_pabe_1284,
Pan troglodytes	ENSPTRG00000002265	1 retrocopy	retro_ptro_1044,
Ictidomys tridecemlineatus	ENSSTOG00000013591	1 retrocopy	retro_itri_1376,
Tursiops truncatus	ENSTTRG00000001344	1 retrocopy	retro_ttru_1758,