RetrogeneDB ID: retro_mmus_1401

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 15:68715011..68715718(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Nfu1
• Ensembl ID: ENSMUSG00000029993
• Aliases: Nfu1, 0610006G17Rik, CGI-33, Hirip5
• Description: NFU1 iron-sulfur cluster scaffold homolog (S. cerevisiae) [Source:MGI Symbol;Acc:MGI:1913290]

Sequence

>retro_mmus_1401
CGGCTGTGCAGGTGGTTCTGTCATGTAGCGACTCCACACACCTTTAAGAAACAACCTCTGCACCAATATGTACGGAGACC
ACTTTTCCCGCTGCGCGCATCCTTGTGTAACATGTTTATTCAAACACAAGACACCCCAAATCCCAACAGCTTAAAGTTTA
TACCAGGAAAGCGGGTTCTTGAGACGAGGACCATGGATTTCTCCACCCCTGCTGCAGCTTTCCGCTCCCCTCTGGCCAGG
CAGTTATTCAGAATTGAAGGTGTGAAGAGCGTCTTCTTCGGCCCAGATTTCATCACAGTCACAAAGGAGAATGGAGAGTT
AGACTGGAATTTACTGAAACCAGACATTCATGCCACAATTATGGACTTCTTTGCATCTGGCTTACCCCTAGTGACCGAGG
AGACGCCTCCGCCTCCGGGAGAAGCAGGCTCTGAGGAAGATGACGGAGTCGTGGCAATGATTAAAGAACTGTTAGATACT
AGAATACGGCCAACTGTGCAGGAGGATGGGGGCGACGTGATCTACAGGGCCTTTGAAGATGGCATTGTGCGGCTGAAGCT
CCAGGGCTCCTGCCCCAGCTGCCCCAGCTCCATCATCACCCTGAAGAGCGGGATTCGAACATGCTGCAGTTTTATATTCC
AGAAGTGGAAGGTGTAGAGCAGGTGATGGATGATGACGAATCAGATGAAAAAGAAGCAAATTCATCT

Alignment

ORF - retro_mmus_1401 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.5 %
• Parental protein coverage: 94.14 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  RLCRRFCHVATPHTFKKQPLHQYVRRPLFPLRAPLCNTVRFMFIQTQDTPNPNSLKFIPGKPVLETRTMD
          RLCR.FCHVATPHTFKKQPLHQYVRRPLFPLRA.LCN....MFIQTQDTPNPNSLKFIPGK.VLETRTMD
Retrocopy RLCRWFCHVATPHTFKKQPLHQYVRRPLFPLRASLCN----MFIQTQDTPNPNSLKFIPGKRVLETRTMD

Parental  FPTPAAAFRSPLARQLFRIEGVKSVFFGPDFITVTKENEELDWNLLKPDIYATIMDFFASGLPLVTEETP
          F.TPAAAFRSPLARQLFRIEGVKSVFFGPDFITVTKEN.ELDWNLLKPDI.ATIMDFFASGLPLVTEETP
Retrocopy FSTPAAAFRSPLARQLFRIEGVKSVFFGPDFITVTKENGELDWNLLKPDIHATIMDFFASGLPLVTEETP

Parental  PPPGEAGSSEEDDEVVAMIKELLDTRIRPTVQEDGGDVIYRGFEDGIVRLKLQGSCTSCPSSIITLKSGI
          PPPGEAG.SEEDD.VVAMIKELLDTRIRPTVQEDGGDVIYR.FEDGIVRLKLQG........IITLKSGI
Retrocopy PPPGEAG-SEEDDGVVAMIKELLDTRIRPTVQEDGGDVIYRAFEDGIVRLKLQGXXXXXXXXIITLKSGI

Parental  Q-NMLQFYIPEVEGVEQVMDDDESDEKEANSS
          ..NMLQFYIPEVEGVEQVMDDDESDEKEANSS
Retrocopy R<NMLQFYIPEVEGVEQVMDDDESDEKEANSS

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	0.07 RPM	20.70 RPM
SRP007412_cerebellum	0.04 RPM	16.20 RPM
SRP007412_heart	0.06 RPM	35.05 RPM
SRP007412_kidney	0.27 RPM	28.43 RPM
SRP007412_liver	0.30 RPM	26.27 RPM
SRP007412_testis	0.82 RPM	31.97 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_1401 was not detected

EST

No EST(s) were mapped for retro_mmus_1401 retrocopy.

TSS

No TSS is located nearby retro_mmus_1401 retrocopy 5' end.

Lab

retro_mmus_1401 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1401 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000005978	1 retrocopy	retro_chof_456,
Callithrix jacchus	ENSCJAG00000019156	1 retrocopy	retro_cjac_1573,
Echinops telfairi	ENSETEG00000019002	1 retrocopy	retro_etel_1371,
Homo sapiens	ENSG00000169599	1 retrocopy	retro_hsap_2638,
Macaca mulatta	ENSMMUG00000000435	1 retrocopy	retro_mmul_1524,
Monodelphis domestica	ENSMODG00000011805	1 retrocopy	retro_mdom_1395,
Mustela putorius furo	ENSMPUG00000006663	1 retrocopy	retro_mputfur_67,
Mus musculus	ENSMUSG00000029993	1 retrocopy	retro_mmus_1401 ,
Nomascus leucogenys	ENSNLEG00000010101	1 retrocopy	retro_nleu_646,
Ochotona princeps	ENSOPRG00000016760	2 retrocopies	retro_opri_380, retro_opri_48,
Pongo abelii	ENSPPYG00000012339	1 retrocopy	retro_pabe_2329,
Pan troglodytes	ENSPTRG00000012016	1 retrocopy	retro_ptro_1778,
Tupaia belangeri	ENSTBEG00000008616	1 retrocopy	retro_tbel_525,
Tarsius syrichta	ENSTSYG00000013765	1 retrocopy	retro_tsyr_108,