RetrogeneDB ID: retro_mmus_1169

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 14:7801209..7802029(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000049460
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Slbp
• Ensembl ID: ENSMUSG00000004642
• Aliases: None
• Description: stem-loop binding protein [Source:MGI Symbol;Acc:MGI:108402]

Sequence

>retro_mmus_1169
ATGGCCTGCAGACCTAGAAGCCCACCTGGTTATGGGAGTCGCCGCGACGGTGGTGTGAGCCCGCGGTCCCCTGCGAGATG
GAGTCTCGGATGGAAGCGCAGAGCAGACAGAGGGGACCAGAAGCCCGAGGACTCCGAGGAAGGCGAGCTCCAGACTTCGG
ACCACGGACCTGAAAGCTTTACAACTCCTGAAGGTCATAAGCCCCGTTCTAGATGTTCTGACTGGGCCAGTGCAATTGAA
GAAGATGAAATGAGGGCCAGAGTTAACAAAGAGATTGCAAGGTACGAAAGAAAACTACTCATAAATGACTTTGGAAGAGA
TAGAAAATCATCATCGGGAAGTTCTGATTCAAAGGAGTCTATGTGTTCAGTGCCTGCTGATGTGGAGACGGATGAGAGTG
TCTTGATGAGAAAGCAGAAGCAGATCAACTATGGGAAGAACACTATTGCCTATGATCGATACATTAAAGAGGTCCCCAGA
CACCTGCGACAACCTGGAATCCATCCCAGGTCCCCCAACAAATTTAAGAAGTACAGCCGGCGGTCATGGGACCAACAGAT
TAAACTCTGGAAGGTGGCTTTGCATTTTGGGGATCCTCCTGCTGAAGAACGATGTGATTTGCAAGAAATACAACCTGTAG
ATCTTGGGGAAATGGAGACAGAATTCACAGAAAGCAGCTCTGAGTCTCAGACAAGTTCACAGGATAACTTTGGTGGCTGG
CACACCCACCAAAGTCAGACACGTGGACTGCCAAGTGGAGGGTGAGTTTGATTTGAAAGCTTGTTTAACTGAACCTTTGA
AAGACTTCTCTGCCATGAGT

Alignment

ORF - retro_mmus_1169 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.04 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MACRPRSPPGYGSRRDGGASPRSPARWSLGRKRRADGRDRKPEDSEEGELQTADHRPESFTTPEGHKPRS
          MACRPRSPPGYGSRRDGG.SPRSPARWSLG.KRRAD..D.KPEDSEEGELQT.DH.PESFTTPEGHKPRS
Retrocopy MACRPRSPPGYGSRRDGGVSPRSPARWSLGWKRRADRGDQKPEDSEEGELQTSDHGPESFTTPEGHKPRS

Parental  RCSDWASAVEEDEMRTRVNKEIARYKRKLLINDFGRERKSSSGSSDSKESMSSVPADVETDESVLMRRQK
          RCSDWASA.EEDEMR.RVNKEIARY.RKLLINDFGR.RKSSSGSSDSKESM.SVPADVETDESVLMR.QK
Retrocopy RCSDWASAIEEDEMRARVNKEIARYERKLLINDFGRDRKSSSGSSDSKESMCSVPADVETDESVLMRKQK

Parental  QINYGKNTIAYDRYIKEVPRHLRQPGIHPRTPNKFKKYSRRSWDQQIKLWKVALHFWDPPAEEGCDLQEI
          QINYGKNTIAYDRYIKEVPRHLRQPGIHPR.PNKFKKYSRRSWDQQIKLWKVALHF.DPPAEE.CDLQEI
Retrocopy QINYGKNTIAYDRYIKEVPRHLRQPGIHPRSPNKFKKYSRRSWDQQIKLWKVALHFGDPPAEERCDLQEI

Parental  QPVDLGEMETEFTESSSESQTSSQDN-FDVYAGTPTKVRHVDCQVEDEFDLEACLTEPLKDFSAMS
          QPVDLGEMETEFTE..S.S............AGTPTKVRHVDCQVE.EFDL.ACLTEPLKDFSAMS
Retrocopy QPVDLGEMETEFTE--SSSESQTSSQ>ITLVAGTPTKVRHVDCQVEGEFDLKACLTEPLKDFSAMS

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	13.18 RPM
SRP007412_cerebellum	0.00 RPM	14.03 RPM
SRP007412_heart	0.00 RPM	6.44 RPM
SRP007412_kidney	0.02 RPM	11.55 RPM
SRP007412_liver	0.00 RPM	7.62 RPM
SRP007412_testis	0.00 RPM	57.27 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_1169 was not detected

EST

No EST(s) were mapped for retro_mmus_1169 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_37988	551 libraries	370 libraries	151 libraries	0 libraries	0 libraries

The graphical summary, for retro_mmus_1169 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_1169 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1169 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000001328	1 retrocopy	retro_btau_1456,
Cavia porcellus	ENSCPOG00000000031	1 retrocopy	retro_cpor_364,
Mus musculus	ENSMUSG00000004642	1 retrocopy	retro_mmus_1169 ,
Otolemur garnettii	ENSOGAG00000009750	1 retrocopy	retro_ogar_1463,
Pteropus vampyrus	ENSPVAG00000002807	2 retrocopies	retro_pvam_490, retro_pvam_941,
Rattus norvegicus	ENSRNOG00000037162	2 retrocopies	retro_rnor_1864, retro_rnor_2016,
Tarsius syrichta	ENSTSYG00000000376	2 retrocopies	retro_tsyr_1595, retro_tsyr_482,
Tursiops truncatus	ENSTTRG00000010901	1 retrocopy	retro_ttru_10,