RetrogeneDB ID: retro_mmus_1085

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 13:24598360..24599052(-)
• Located in intron of: ENSMUSG00000036006

Retrocopy information

• Ensembl ID: ENSMUSG00000085603
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Xlr5c
• Ensembl ID: ENSMUSG00000067764
• Aliases: Xlr5c, Xlr5
• Description: X-linked lymphocyte-regulated 5C [Source:MGI Symbol;Acc:MGI:1350981]

Sequence

>retro_mmus_1085
ATGTCAAGCAAGGAACAGAAGGCCATGAAGTAAAGTGCCAAGTGCCCGAGGGTAGATAAGACCCTCCATCAGAAGACTCC
AAGAACCGAGATGCAGTCAACCCTGCGGACAATCCAGTAGTTGGTACCAGTGAGATGGGCAGTCATTGCTCAGATTCAGA
TGTGCAAGAGGCCCCGAGCCTGTTCAGAAGAGGATGCAGGATTTCTAAGGTGATGCTACTTAGTTTCTTATGGAAAAGAG
GAAGCAGTTTGAAAAGGATGTAAATGCCTCTTTCAGAAACCTGAATGAAAGCCTCCAGGGTATTCTGAAAGCTCAGCAGA
AGTCAAGGCAGGAGCTTGAGTCTGTGTACTGTGAAAGGTATGGGTCCCTATACCAGAAGTGTCTAGATGAGGTGGGCAGC
ACAAGGGGCCAAGAAGAACACCTCGGTTTTATAACAGCAGCAAATGAAGATTTTACAGACAGGTATAGCAGATCATGAAA
CCAAGCTTGAAAATACTGAAGATATGTCTGACACATTTTTGAAGAAAGCCAACGACTTGAGTAAACATCGCAGACCCCTT
TTTGGCAGTCAGCAAACAAATGTAGAGAAGGAAATCTCGAAGGTACAGGGCAGAGTTACCATGGAAACTCAAGAACAAGA
TGTATCTGTTGTTGAAAGGTACCTTCAGTCCCTGATCCTTGACCACTCTGAA

Alignment

ORF - retro_mmus_1085 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.34 %
• Parental protein coverage: 98.73 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MSNKEQKDMKKSGKHQRVHKTL-PSDDFKNSDAVNPADKPAVGTSGMGSHSSGSDMQEAR-EPVQKKMQD
          MS.KEQK.MK.S.K..RV.KTL.PS.D.KN.DAVNPAD.P.VGTS.MGSH.S.SD.QEA..EPVQK.MQD
Retrocopy MSSKEQKAMK*SAKCPRVDKTL<PSEDSKNRDAVNPADNPVVGTSEMGSHCSDSDVQEAP<EPVQKRMQD

Parental  FKGDDGTGLLMEKRKQFEEDVNASFRSLNENLQSILKAQQNSRQELKSLYCERFGSVYHNWLVEMDRTRD
          F.GD..T..LMEKRKQFE.DVNASFR.LNE.LQ.ILKAQQ.SRQEL.S.YCER.GS.Y...L.E...TR.
Retrocopy F*GD-AT*FLMEKRKQFEKDVNASFRNLNESLQGILKAQQKSRQELESVYCERYGSLYQKCLDEVGSTRG

Parental  QEEYFSFIT-QQQMKILQTAIEDHETKLKNAKDMCDTFLKKANDLSKRQKTFIGGQQTIVEKEISKVQNR
          QEE...FIT.QQ.MKILQT.I.DHETKL.N..DM.DTFLKKANDLSK......G.QQT.VEKEISKVQ.R
Retrocopy QEEHLGFIT>QQ-MKILQTGIADHETKLENTEDMSDTFLKKANDLSKHRRPLFGSQQTNVEKEISKVQGR

Parental  VIMETQDQDISMVETYLQSLIHESSE
          V.METQ.QD.S.VE.YLQSLI...SE
Retrocopy VTMETQEQDVSVVERYLQSLILDHSE

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	0.00 RPM
SRP007412_cerebellum	0.00 RPM	0.00 RPM
SRP007412_heart	0.25 RPM	0.00 RPM
SRP007412_kidney	0.08 RPM	0.04 RPM
SRP007412_liver	0.00 RPM	0.00 RPM
SRP007412_testis	0.37 RPM	0.14 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_1085 was not detected

EST

No EST(s) were mapped for retro_mmus_1085 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_27996	1047 libraries	19 libraries	2 libraries	3 libraries	1 library

The graphical summary, for retro_mmus_1085 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_1085 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1085 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000013389	2 retrocopies	retro_chof_1384, retro_chof_2693,
Callithrix jacchus	ENSCJAG00000001658	1 retrocopy	retro_cjac_2710,
Cavia porcellus	ENSCPOG00000001202	1 retrocopy	retro_cpor_686,
Dasypus novemcinctus	ENSDNOG00000017387	2 retrocopies	retro_dnov_2623, retro_dnov_739,
Dasypus novemcinctus	ENSDNOG00000017624	3 retrocopies	retro_dnov_2294, retro_dnov_2402, retro_dnov_420,
Echinops telfairi	ENSETEG00000007664	1 retrocopy	retro_etel_1510,
Myotis lucifugus	ENSMLUG00000010711	2 retrocopies	retro_mluc_1098, retro_mluc_1839,
Mus musculus	ENSMUSG00000067764	1 retrocopy	retro_mmus_1085 ,
Mus musculus	ENSMUSG00000072479	1 retrocopy	retro_mmus_1782,
Otolemur garnettii	ENSOGAG00000024543	1 retrocopy	retro_ogar_633,
Ictidomys tridecemlineatus	ENSSTOG00000001853	1 retrocopy	retro_itri_931,