RetrogeneDB ID: retro_mmus_632

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 10:30780855..30781614(-)
• Located in intron of: ENSMUSG00000039697

Retrocopy information

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

Parental gene information

• Parental gene symbol: Nono
• Ensembl ID: ENSMUSG00000031311
• Aliases: Nono, AA407051, AV149256, NRB54, P54NRB, nonA
• Description: non-POU-domain-containing, octamer binding protein [Source:MGI Symbol;Acc:MGI:1855692]

Sequence

>retro_mmus_632
CCTCGGCCTGTGACTGTGGAGCCTATGGACCAGTGAGATGATGAAGAGGGACTTCCAGAGAAACTGGTTATAAAAACCAG
CAATTTCACAAGGAGAGAGAACAGCCACCCAGATTTGCACAACCTGGGTCCTTTGAGTATGAGTATGCCATGCGCTGGAA
GGCACTCATTGAGATGGAGAAGCAGCAGCAGGATCAAGTGGACCGGAACATCAAGGAGGCTCGTGAGAAGCTGGAGATGG
AAATGGAGGCAGCGCACCATGAGCACCAGGTTATGCTAATGAGGCAGGATTTGATGAGATGTCAAGAAGAGCTTCTGAGA
ATGGAGGAGCTGCATAACTAAGAGGTTCAGAAGCGAAAGCAGTTAGAACTCAGGCAGGAAGAGGAGTGCAGGCGCTGTGA
GGAAGTGAGGCGGGCCACAGCAAGAGGAAATGATGCGCCGACAGCAGGAAGGATTCAAGGGAACCTTCCCTGATGCGAGA
GAACAAGAGATACGGATGGGCCAAATGGCTATGGGAGGTGCTATGGGCATAAACAATAGAGGCGCGATGCCCCCTGCTCC
TGTGCCACCTGGTACTCCAGCTCCTCCAGGACCTGCCACTATGATGCCAGATGGAACCCTTGGATTGACCCCACCAACAA
CTGAACATTTTGGCCAAGCTGCAACAATGGAAGGAATTGGAGCAATTGGTGGAACTCCTCCTGCATTCAACAGTCCAGCT
CTGGGAGCTGAATTTGCTCCAAATAAACACCCCCGATAT

Alignment

ORF - retro_mmus_632 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.33 %
• Parental protein coverage: 53.49 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  PRPVTVEPMDQLDDEEGLPEKLVIK-NQQFHKEREQPPRFAQPGSFEYEYAMRWKALIEMEKQQQDQVDR
          PRPVTVEPMDQ.DDEEGLPEKLVIK.NQQFHKEREQPPRFAQPGSFEYEYAMRWKALIEMEKQQQDQVDR
Retrocopy PRPVTVEPMDQ*DDEEGLPEKLVIK<NQQFHKEREQPPRFAQPGSFEYEYAMRWKALIEMEKQQQDQVDR

Parental  NIKEAREKLEMEMEAARHEHQVMLMRQDLMRRQEELRRMEELHNQEVQKRKQLELRQEEERRRREEEMRR
          NIKEAREKLEMEMEAA.HEHQVMLMRQDLMR.QEEL.RMEELHN.EVQKRKQLELRQEEE.RR.EE..R.
Retrocopy NIKEAREKLEMEMEAAHHEHQVMLMRQDLMRCQEELLRMEELHN*EVQKRKQLELRQEEECRRCEEVRRA

Parental  -QQEEMMRRQQEGFKGTFPDAREQEIRMGQMAMGGAMGINNRGAMPPAPVPPGTPAPPGPATMMPDGTLG
          .QQEEMMRRQQEGFKGTFPDAREQEIRMGQMAMGGAMGINNRGAMPPAPVPPGTPAPPGPATMMPDGTLG
Retrocopy >QQEEMMRRQQEGFKGTFPDAREQEIRMGQMAMGGAMGINNRGAMPPAPVPPGTPAPPGPATMMPDGTLG

Parental  LTPPTTERFGQAATMEGIGAIGGTPPAFNRPAPGAEFAPNKRRRY
          LTPPTTE.FGQAATMEGIGAIGGTPPAFN.PA.GAEFAPNK..RY
Retrocopy LTPPTTEHFGQAATMEGIGAIGGTPPAFNSPALGAEFAPNKHPRY

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	0.09 RPM	77.12 RPM
SRP007412_cerebellum	0.22 RPM	100.30 RPM
SRP007412_heart	0.19 RPM	62.51 RPM
SRP007412_kidney	0.52 RPM	106.84 RPM
SRP007412_liver	0.03 RPM	73.60 RPM
SRP007412_testis	0.23 RPM	16.65 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_632 was not detected

EST

No EST(s) were mapped for retro_mmus_632 retrocopy.

TSS

No TSS is located nearby retro_mmus_632 retrocopy 5' end.

Lab

retro_mmus_632 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_632 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 21 parental genes, and 31 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016057	2 retrocopies	retro_amel_1438, retro_amel_795,
Bos taurus	ENSBTAG00000012152	2 retrocopies	retro_btau_1027, retro_btau_313,
Canis familiaris	ENSCAFG00000017071	1 retrocopy	retro_cfam_98,
Callithrix jacchus	ENSCJAG00000036744	1 retrocopy	retro_cjac_3990,
Equus caballus	ENSECAG00000008502	2 retrocopies	retro_ecab_357, retro_ecab_427,
Felis catus	ENSFCAG00000014807	2 retrocopies	retro_fcat_1219, retro_fcat_147,
Homo sapiens	ENSG00000147140	1 retrocopy	retro_hsap_1699,
Gorilla gorilla	ENSGGOG00000006194	1 retrocopy	retro_ggor_1273,
Microcebus murinus	ENSMICG00000000232	1 retrocopy	retro_mmur_569,
Myotis lucifugus	ENSMLUG00000002489	1 retrocopy	retro_mluc_622,
Mustela putorius furo	ENSMPUG00000004937	1 retrocopy	retro_mputfur_937,
Mus musculus	ENSMUSG00000031311	2 retrocopies	retro_mmus_3652, retro_mmus_632 ,
Nomascus leucogenys	ENSNLEG00000001278	1 retrocopy	retro_nleu_1344,
Oryctolagus cuniculus	ENSOCUG00000021848	2 retrocopies	retro_ocun_1317, retro_ocun_1804,
Otolemur garnettii	ENSOGAG00000004834	3 retrocopies	retro_ogar_1525, retro_ogar_546, retro_ogar_593,
Pongo abelii	ENSPPYG00000020451	1 retrocopy	retro_pabe_1398,
Pan troglodytes	ENSPTRG00000022010	1 retrocopy	retro_ptro_1150,
Pteropus vampyrus	ENSPVAG00000016503	1 retrocopy	retro_pvam_444,
Rattus norvegicus	ENSRNOG00000003689	2 retrocopies	retro_rnor_1178, retro_rnor_1503,
Sorex araneus	ENSSARG00000007959	2 retrocopies	retro_sara_661, retro_sara_663,
Drosophila melanogaster	FBgn0004227	1 retrocopy	retro_dmel_11,