RetrogeneDB ID: retro_mmus_1782

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 18:62481492..62481906(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Xlr5b
• Ensembl ID: ENSMUSG00000072479
• Aliases: None
• Description: X-linked lymphocyte-regulated 5B [Source:MGI Symbol;Acc:MGI:3574109]

Sequence

>retro_mmus_1782
GGGTTTCTTATGAGAAAGAGGAAGCAGTTTGAAGAGGATGTAAATGCTTCTTCCAGACGCCTGAAAGAAAACCTCCAGGG
TATATTGAAAACTCAGCAGAAGTCAAAGCAGAAGCTTAAGTCTGTGTACTGTGAAGGTTTGGGTCCCCGTACCAGAAGCG
GCTGGATGAGGTGGGCAGCACAAGGGACCAGGAAAAACACCTCAGTTTTATAACTCAGCAGCAAATGAAGATTTTTACAG
ATGGCTATAGCGGATCATGAAACCAAGCTTGAAAACTCTGAAGATATGTGTGATGCATTTATGAAGAAAGCCAAGGACTT
GAGTACACATAGCAGCAAAACCTTTAGTGACAGTCAGCAAACTAATGTGGAGAAGGAAATCTCCAAGGGGCCGGACAGAG
TTAGCATGGGAACT

Alignment

ORF - retro_mmus_1782 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.86 %
• Parental protein coverage: 58.05 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  GLLMEKRKQFEEDVNASFRSLNENLQSILKAQQNSRQELKSLYCE-RFGSVYHNWLVEMDRTRDQEEYFS
          G.LM.KRKQFEEDVNAS.R.L.ENLQ.ILK.QQ.S.Q.LKS.YCE.RFGS.Y...L.E...TRDQE...S
Retrocopy GFLMRKRKQFEEDVNASSRRLKENLQGILKTQQKSKQKLKSVYCE<RFGSPYQKRLDEVGSTRDQEKHLS

Parental  FITQQQMKI-LQTAIEDHETKLKNAKDMCDTFLKKANDLSKR-QKTFIGGQQTIVEKEISKVQNRVIMET
          FITQQQMKI.LQ.AI.DHETKL.N..DMCD.F.KKA.DLS....KTF...QQT.VEKEISK...RV.M.T
Retrocopy FITQQQMKI>LQMAIADHETKLENSEDMCDAFMKKAKDLSTHSSKTFSDSQQTNVEKEISKGPDRVSMGT

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	0.00 RPM
SRP007412_cerebellum	0.00 RPM	0.00 RPM
SRP007412_heart	0.00 RPM	0.00 RPM
SRP007412_kidney	0.00 RPM	0.00 RPM
SRP007412_liver	0.00 RPM	0.00 RPM
SRP007412_testis	0.00 RPM	0.05 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_1782 was not detected

EST

No EST(s) were mapped for retro_mmus_1782 retrocopy.

TSS

No TSS is located nearby retro_mmus_1782 retrocopy 5' end.

Lab

retro_mmus_1782 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1782 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,