RetrogeneDB ID: retro_rnor_2027

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 4:248058533..248059368(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSRNOG00000036912
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Nsl1
• Ensembl ID: ENSRNOG00000042286
• Aliases: Nsl1, RGD1562052
• Description: kinetochore-associated protein NSL1 homolog [Source:RefSeq peptide;Acc:NP_001102553]

Sequence

>retro_rnor_2027
TTGGCGGGTGCCCCTGAAACAGTGCTTGTCTCCGCCCCGCAGGATCAAGATGCCCAGGCCGCCTTAGATTCCCAGGCCAT
GGCAGCAGTTTCTCCCCTAGAGGACTTCCGAGTGCGCTGCACCTTGAAGAGGGCCATGGTGGAAGTGATAGAGATGTGCG
ATTGCTTCATGCAGGAGCTCGAGCTGCGCTGCCAGAGGACATCCGCGAGCTCCTGCTGCGGGACGCGCAGTGGACTTTTG
AGTCGGCTGTGCAGGATAATGTCAGCATTAATGGACAGGCCTGGGAGGAAGCTACAGATCATTGTTTTGTGGATTCTGAC
ATCAAAGTGCTTGAAGATGAATTTGATGAGCTCATAGTAGATGTGACAACAAAGCGGAGGCAGTATCCCAGAAGGATCCT
GGAGAGCTAATCAAAACCTTGAAAGCACAGCATGCGAGTCTGAAGCAGTATCATCCTGTCGTGCCTCCTCTGGACCTGAA
ATGTGACCCTGACCCAGCTTCTCGTGTGGAAGATCTGAAAAGCCGTGGAGAAGTCATAGCTAAGGAAATGAGTGAGGCCC
TGAAGGCTTTACCTGTGTTAATTGAACAAGGAGACGGCTTTTTCCAGGTCTTAAAGATGCGGCCTGTCATCCAACTGCAG
AGGATCAGCCAGGAAGTCTTCTCCAGTCTTTGCAGGAGAGCAGATTCCAAGCCTGACAAGTGTGTAACACACGTAGAATC
CACACCAACTGAGACTGGAGCCAGGAAGGCCTCCAACATTGTGCTAAAGAGAAAGAAAACCCCAGATTGCGCCCAGAGAA
AGTGTTACCAACTGCGACTGAAGAGAATCTCGATA

Alignment

ORF - retro_rnor_2027 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.9 %
• Parental protein coverage: 99.29 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAGVPETVLVSAPQDQDAQAALDSQATAAASPLEDFRVRCTLKRAVVEVMEMCGRFVQELG-AALPEDVR
          .AG.PETVLVSAPQDQDAQAALDSQA.AA.SPLEDFRVRCTLKRA.VEV.EMC..F.QEL..AALPED.R
Retrocopy LAGAPETVLVSAPQDQDAQAALDSQAMAAVSPLEDFRVRCTLKRAMVEVIEMCDCFMQELE<AALPEDIR

Parental  ELAVRDAQWTFESAVQENVSINGQVWEEATDHCFMDSDIKVLEDEFDELIVDVSTKRRQYPRRILES-IV
          EL..RDAQWTFESAVQ.NVSINGQ.WEEATDHCF.DSDIKVLEDEFDELIVDV.TKRRQYPRRILES...
Retrocopy ELLLRDAQWTFESAVQDNVSINGQAWEEATDHCFVDSDIKVLEDEFDELIVDVTTKRRQYPRRILES<LI

Parental  KTLKAQHASLKQYHPVVPPLDLKCDPDPASHVEDLKCRGETIAKEMSEAMKALPVLIEQGDGFSQVLKMQ
          KTLKAQHASLKQYHPVVPPLDLKCDPDPAS.VEDLK.RGE.IAKEMSEA.KALPVLIEQGDGF.QVLKM.
Retrocopy KTLKAQHASLKQYHPVVPPLDLKCDPDPASRVEDLKSRGEVIAKEMSEALKALPVLIEQGDGFFQVLKMR

Parental  PVIQLQRISQEVFSSLCRRADFKPDKCGTHVESTPTETGARKASNIVLKRKKATDCAQRKCYPLRLKRIN
          PVIQLQRISQEVFSSLCRRAD.KPDKC.THVESTPTETGARKASNIVLKRKK..DCAQRKCY.LRLKRI.
Retrocopy PVIQLQRISQEVFSSLCRRADSKPDKCVTHVESTPTETGARKASNIVLKRKKTPDCAQRKCYQLRLKRIS

Parental  L
          .
Retrocopy I

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
SRP017611_brain	0.00 RPM	1.01 RPM
SRP017611_kidney	0.00 RPM	0.98 RPM
SRP017611_liver	0.00 RPM	0.47 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2027 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2027 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2027 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000001862	1 retrocopy	retro_chof_464,
Rattus norvegicus	ENSRNOG00000042286	1 retrocopy	retro_rnor_2027 ,
Tarsius syrichta	ENSTSYG00000003900	1 retrocopy	retro_tsyr_202,
Tursiops truncatus	ENSTTRG00000016584	1 retrocopy	retro_ttru_564,