RetrogeneDB ID: retro_mmur_534

Retrocopy location

• Organism: Mouse Lemur (Microcebus murinus)
• Coordinates: GeneScaffold_3710:227835..228847(-)
• Located in intron of: ENSMICG00000007046

Retrocopy information

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

Parental gene information

• Parental gene symbol: NUP50
• Ensembl ID: ENSMICG00000006840
• Aliases: None
• Description: nucleoporin 50kDa [Source:HGNC Symbol;Acc:8065]

Sequence

>retro_mmur_534
ATGGCCAAAAGAACTGCCCAGAAGGAACCGACAGACAGGAACTGGGATCAGGAAGATGAAGCCGAAGAGGTGGGAACATT
CTCAGTGGCCAGTGAGGAAGTCTTGAAGAACAGAGATACAAAGAAAGAGAAGCGCAGAAATGTTGGATTTGAATCTGATA
GTGGAGGTGCCTTTAAAGCTCTGGTCGTAGATCCTGGAGGAGGAGGGTTTTCTGGATTTGGTAGTGGTGCTGGAGAGAAG
CCTCTGGAAGGAATGTCAAATGGAAACAGCATAACCAGCACCACTCCCCTCACCAGTGCAGGGGTGGCCACAGGGACCAA
GGCGGCCTCTGGTCGTGTTGCTGCAGGCGGCTCTACCACCTCGGTTGATAAAACGATTTCAAATGCCAAAACTAACAGGG
ACAGTCAGCAGCCTTCCTCCTCTGGCCTTGCTTCCAGCGAAGCCTATGCCAACAATCCTTGGAACAAGCAGCTGACTATC
TTGAACTGCTGCGTTCGGGACTGGATAGCGAAGCATGTGAACGCAAGCCCGCTCTGTGATCTAACGCCTGTCTTTAAATA
CTATGAGAAATATCTGGAGATATTATACAGCACCACAGAAACTATGTCAGTGGCCATTATCAAGGTGAAACTAACAAGAT
GGTGGTTGAAAAGCAGTCTCCTTCCCTACTTGGTTCAACAAAATTACAGGAAGAGTCAGCATATTTGTTCCACGGCAACA
AAACTGAAGATACATCCGAAAAGAAGACTGAGGTTGTGTCTGAAAAAGAAAAACGGACCCATCCACTAGGAGCAAAAAGT
GCCCCATTTAATTTTGGCAAGAAAAACCGATAGCTCCTGCTTTGGGCTCATTAAGCTCTGGCCCCCTGGCTGGACTTGCA
TTTTCCTCTGGAAACTCCAGTTTATTTGGCAAAGGTATTGCCCAGAATAAACCAGTTTCTCTGCCATTTTCCACTAAAAC
ACTGAGAGCCAAGCAGAGGGTGCAGTAATGAATGGAAAGTGGAGATGAGGAG

Alignment

ORF - retro_mmur_534 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.49 %
• Parental protein coverage: 72.49 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  MAKRIAEKELTDRNWDQEDEAEEVGTFSVASEEVLKNRAIKKAKRRNVGFESDSGGAFKGFKGLVVPSGG
          MAKR.A.KE.TDRNWDQEDEAEEVGTFSVASEEVLKNR..KK.KRRNVGFESDSGGA...FK.LVV..GG
Retrocopy MAKRTAQKEPTDRNWDQEDEAEEVGTFSVASEEVLKNRDTKKEKRRNVGFESDSGGA---FKALVVDPGG

Parental  GGFSGFGSSTGGKPLEGLSNGNSTAITPPFTSARVATETKAAFGSMAANGPTTLVDKKISNPKTNGDSQQ
          GGFSGFGS..G.KPLEG.SNGNS...T.P.TSA.VAT.TKAA.G..AA.G.TT.VDK.ISN.KTN.DSQQ
Retrocopy GGFSGFGSGAGEKPLEGMSNGNSITSTTPLTSAGVATGTKAASGRVAAGGSTTSVDKTISNAKTNRDSQQ

Parental  PSSSGFASSKAYASNTYNKQLAALNCSVRDWIVKHVNANPLCDLTPIFKDYEKYL-ANIEQQHGNSVSNN
          PSSSG.ASS.AYA.N..NKQL..LNC.VRDWI.KHVNA.PLCDLTP.FK.YEKYL...I.Q.H.N.VS..
Retrocopy PSSSGLASSEAYANNPWNKQLTILNCCVRDWIAKHVNASPLCDLTPVFKYYEKYL<GDIIQHHRNYVSGH

Parental  SQSEADKTLVETQSPSLCGSTKLQQESSFLFSGNKTEDTSEKKTEVVSEK-KMDPSLGATSASFNFGK-K
          .Q.E..K..VE.QSPSL.GSTKLQ.ES..LF.GNKTEDTSEKKTEVVSEK.K....LGA.SA.FNFGK.K
Retrocopy YQGETNKMVVEKQSPSLLGSTKLQEESAYLFHGNKTEDTSEKKTEVVSEKEKRTHPLGAKSAPFNFGK>K

Parental  IDSS-VLGSLSSGPVAGFSFSSGNSSLFGKDTTQSNPVSSPLSTKTL-ESQAEGG-SNECK-GGDEE
          .DSS..LGSLSSGP.AG..FSSGNSSLFGK...Q..PVS.P.STKTL.ESQAEG..SNE.K..GDEE
Retrocopy TDSS>ALGSLSSGPLAGLAFSSGNSSLFGKGIAQNKPVSLPFSTKTL<ESQAEGA<SNEWK<SGDEE

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_534 retrocopy.

TSS

Microcebus murinus was not studied using FANTOM5 data.

Lab

retro_mmur_534 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 7 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000016242	1 retrocopy	retro_cjac_4080,
Homo sapiens	ENSG00000093000	3 retrocopies	retro_hsap_1429, retro_hsap_3301, retro_hsap_3434,
Microcebus murinus	ENSMICG00000006840	1 retrocopy	retro_mmur_534 ,
Mus musculus	ENSMUSG00000016619	1 retrocopy	retro_mmus_1905,
Nomascus leucogenys	ENSNLEG00000013154	2 retrocopies	retro_nleu_1359, retro_nleu_1844,
Otolemur garnettii	ENSOGAG00000002320	1 retrocopy	retro_ogar_942,
Pongo abelii	ENSPPYG00000011928	1 retrocopy	retro_pabe_2723,