RetrogeneDB ID: retro_mmur_861

Retrocopy location

• Organism: Mouse Lemur (Microcebus murinus)
• Coordinates: scaffold_1139:271607..272280(-)
• Located in intron of: ENSMICG00000015517

Retrocopy information

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

Parental gene information

• Parental gene symbol: SNRPB
• Ensembl ID: ENSMICG00000016519
• Aliases: None
• Description: small nuclear ribonucleoprotein polypeptides B and B1 [Source:HGNC Symbol;Acc:11153]

Sequence

>retro_mmur_861
ACTGTGGCCAAGAGCAGCAAGATGCTGTGGCACATCAACTGTAGAATGAGATGTATCCTGTGAGATGGCCAAGTGGTCAT
CAACACCTTTAAGGCTTTTGATAAGCATATGAATTTGAGCCTCTGAGTGGATAAATTCAGGAAGATCAACCAAAGAATTT
GGAGCAGACAGCGTGAAGAAAAGCAGGTTTGGGGGCTGGTCTTGCTGTGTTGGGAGAACTTGGTATCTATGGCTGTGGAG
GGACCACCCCCAAAGATACTGCATTGCTCAGGTACCACTTGCTGGAGCTGCAGGAGGCCCTGGAATTGGTAGGGCAGCTG
GCAGAGGAACACCAGATGTTGTACCAATTTCCCAAGCTCCTGCTGGGTTAGCAGGCCCTGTCCAAGGAGTTGGAGGATCA
TCCCAGCAGGTAATGACCTCATAGGGAAAGGGCACTGTAGCAGCTGCTGCCATTGCTACTGCTGCCACCATTGGTGAAGC
TCCAACACGTTACCCACCAGGACTCTACCCCCACCTGTAGGCAGAACAACCCCACCTCCAGGCATTATGGTTCCTCCATC
TGGTTTGAAGCCCACCAATTGGGCTTTTCCCTACTCAAGCAACTCCAATAGGCCTGCCCCCTGCAGGAACGAGGCCTCTT
TCACCAGGAATTGGAAGTCCACCTCCTCCAGGA

Alignment

ORF - retro_mmur_861 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.53 %
• Parental protein coverage: 78.67 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  TVGKSSKMLQHIDYRMRCILQDGRIFIGTFKAFDKHMNLILCDCDEFRKIKPKNSKQAEREEKRVLGLVL
          TV.KSSKML.HI..RMRCIL.DG...I.TFKAFDKHMNL.L...D.FRKI.........REEK.V.GLVL
Retrocopy TVAKSSKMLWHINCRMRCIL*DGQVVINTFKAFDKHMNLSL*-VDKFRKINQRIWSR-QREEKQVWGLVL

Parental  LRGENLVSMTVEGPPPK-DTG-IARVPLAGAAGGPGIGRAAGRGIPAGVPMPQAPAGLAGPVRGVGGPSQ
          L..ENLVSM.VEGPPPK.DT..IA.VPLAGAAGGPGIGRAAGRG.P..VP..QAPAGLAGPV.GVGG.SQ
Retrocopy LCWENLVSMAVEGPPPK<DTA<IAQVPLAGAAGGPGIGRAAGRGTPDVVPISQAPAGLAGPVQGVGGSSQ

Parental  QVMTPQGRGTVAAAAAAATASIAGAPTQYPPG-RAGPPPPMGRGAPPPGMMGPPPGMR-PPMG--PPMGI
          QVMT..G.GTVAAAA.A..A.I..APT.YPPG....PP...GR..PPPG.M.PP.G...PP.G..P....
Retrocopy QVMTS*GKGTVAAAAIATAATIGEAPTRYPPG<TLPPP--VGRTTPPPGIMVPPSGLK>PPIGLFPTQAT

Parental  PPGRGTPMGMPP--PGM-RPPPPG
          P.G...P.G..P..PG...PPPPG
Retrocopy PIGL-PPAGTRPLSPGIGSPPPPG

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Microcebus murinus was not studied using RNA-Seq expression data.

ChIP-Seq

Microcebus murinus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmur_861 retrocopy.

TSS

Microcebus murinus was not studied using FANTOM5 data.

Lab

retro_mmur_861 was not experimentally validated.

Homology

Retrocopy orthology:

Microcebus murinus does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 33 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000011353	1 retrocopy	retro_amel_1403,
Canis familiaris	ENSCAFG00000006693	3 retrocopies	retro_cfam_1268, retro_cfam_1773, retro_cfam_461,
Callithrix jacchus	ENSCJAG00000020971	2 retrocopies	retro_cjac_172, retro_cjac_1739,
Dasypus novemcinctus	ENSDNOG00000007896	2 retrocopies	retro_dnov_2060, retro_dnov_2471,
Erinaceus europaeus	ENSEEUG00000015568	3 retrocopies	retro_eeur_312, retro_eeur_434, retro_eeur_6,
Felis catus	ENSFCAG00000014447	2 retrocopies	retro_fcat_1788, retro_fcat_1960,
Microcebus murinus	ENSMICG00000016519	4 retrocopies	retro_mmur_1012, retro_mmur_1478, retro_mmur_546, retro_mmur_861 ,
Myotis lucifugus	ENSMLUG00000016951	1 retrocopy	retro_mluc_1725,
Mustela putorius furo	ENSMPUG00000009283	1 retrocopy	retro_mputfur_1153,
Nomascus leucogenys	ENSNLEG00000009206	1 retrocopy	retro_nleu_761,
Otolemur garnettii	ENSOGAG00000016149	4 retrocopies	retro_ogar_2197, retro_ogar_2841, retro_ogar_2918, retro_ogar_3236,
Ochotona princeps	ENSOPRG00000007459	2 retrocopies	retro_opri_697, retro_opri_72,
Pongo abelii	ENSPPYG00000010841	1 retrocopy	retro_pabe_2265,
Pteropus vampyrus	ENSPVAG00000017013	1 retrocopy	retro_pvam_289,
Tupaia belangeri	ENSTBEG00000010040	3 retrocopies	retro_tbel_1117, retro_tbel_1171, retro_tbel_2839,
Tarsius syrichta	ENSTSYG00000014498	2 retrocopies	retro_tsyr_45, retro_tsyr_719,