RetrogeneDB ID: retro_mmus_950

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 12:77452646..77453282(-)
• Located in intron of: ENSMUSG00000021065

Retrocopy information

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

Parental gene information

• Parental gene symbol: Sbds
• Ensembl ID: ENSMUSG00000025337
• Aliases: Sbds, 4733401P19Rik, AI836084, CGI-97, SDS
• Description: Shwachman-Bodian-Diamond syndrome homolog (human) [Source:MGI Symbol;Acc:MGI:1913961]

Sequence

>retro_mmus_950
CGTGCGAAGTGGGAAAGGAAGCACTTTGAAATCGCCTGCTATAAAAACAAGGTCGTCTGCTGGCAGAGTGGCGTGGAAAA
AGACCTTGATGAAGTTCTGCAGACCAATTCAGTGTTTGTAAATGTTTCCAAAGGTCAGGTTGCCAAGAAGGAAGACCTTA
TCAGTGCATTTGGGACAGATGAACAGACTGAAATCTGCAAGCAGATTTTGACTAAAGGAGAAGTTCAAGTGTCTGATAAA
GAATGGCACACACAGCTGGAGCAGATGTTTAGGGATATTGCCACCATTGTGGCAGACAAGTGTGTGAACCCAGAAACAAA
GAGACCTTACACCGTTATCCTCATGGAGAGAGCCATGAAGGACATCCACTACTCCGTCAAACCCAACAAGAGCACAAAGA
AGCAGGCTTTGGAAGTGATAAAGCAGCTGAAAGAGAAGATGAAGATGGAGCGGGCCCACATGGGATTGCGCTTTATTTTG
CCAGTGAACAAAGGGAAGAAGCTGAAGGAAAAGCTGAAGCCACTGATGAAGGTGGTGGAGAGTGAGAACTACAGCCAGCA
GCTGCAGATCCTGTGCCTCATCGACTCAGGCTGCCTTAGAGACACTGATGAGCTAATAAAAAAGGAAAGGCAAGGG

Alignment

ORF - retro_mmus_950 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.68 %
• Parental protein coverage: 84.8 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RMKRGGKRFEIACYKNKVVGWRSGVEKDLDEVLQTHSVFVNVSKGQVAKKEDLISAFGTDDQTEICKQIL
          R.K...K.FEIACYKNKVV.W.SGVEKDLDEVLQT.SVFVNVSKGQVAKKEDLISAFGTD.QTEICKQIL
Retrocopy RAKWERKHFEIACYKNKVVCWQSGVEKDLDEVLQTNSVFVNVSKGQVAKKEDLISAFGTDEQTEICKQIL

Parental  TKGEVQVSDKERHTQLEQMFRDIATIVADKCVNPETKRPYTVILIERAMKDIHYSVKPNKSTKQQALEVI
          TKGEVQVSDKE.HTQLEQMFRDIATIVADKCVNPETKRPYTVIL.ERAMKDIHYSVKPNKSTK.QALEVI
Retrocopy TKGEVQVSDKEWHTQLEQMFRDIATIVADKCVNPETKRPYTVILMERAMKDIHYSVKPNKSTKKQALEVI

Parental  KQLKEKMKIERAHMRLRFILPVNEGKKLKEKLKPLMKVVESEDYSQQLEIVCLIDPGCFREIDELIKKET
          KQLKEKMK.ERAHM.LRFILPVN.GKKLKEKLKPLMKVVESE.YSQQL.I.CLID.GC.R..DELIKKE.
Retrocopy KQLKEKMKMERAHMGLRFILPVNKGKKLKEKLKPLMKVVESENYSQQLQILCLIDSGCLRDTDELIKKER

Parental  KG
          .G
Retrocopy QG

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	0.14 RPM	48.06 RPM
SRP007412_cerebellum	0.13 RPM	63.87 RPM
SRP007412_heart	0.06 RPM	40.56 RPM
SRP007412_kidney	0.04 RPM	79.21 RPM
SRP007412_liver	0.03 RPM	54.51 RPM
SRP007412_testis	0.05 RPM	123.50 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_950 was not detected

EST

No EST(s) were mapped for retro_mmus_950 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_24681	915 libraries	148 libraries	7 libraries	1 library	1 library

The graphical summary, for retro_mmus_950 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_950 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_950 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000003795	2 retrocopies	retro_chof_1999, retro_chof_623,
Callithrix jacchus	ENSCJAG00000004283	1 retrocopy	retro_cjac_3984,
Dasypus novemcinctus	ENSDNOG00000016904	1 retrocopy	retro_dnov_748,
Loxodonta africana	ENSLAFG00000008763	1 retrocopy	retro_lafr_920,
Monodelphis domestica	ENSMODG00000006644	1 retrocopy	retro_mdom_2004,
Mus musculus	ENSMUSG00000025337	1 retrocopy	retro_mmus_950 ,
Otolemur garnettii	ENSOGAG00000009011	1 retrocopy	retro_ogar_3368,
Ochotona princeps	ENSOPRG00000008721	6 retrocopies	retro_opri_1179, retro_opri_154, retro_opri_363, retro_opri_484, retro_opri_698, retro_opri_957,
Rattus norvegicus	ENSRNOG00000000888	1 retrocopy	retro_rnor_686,
Ictidomys tridecemlineatus	ENSSTOG00000022203	1 retrocopy	retro_itri_1763,