RetrogeneDB ID: retro_mmus_1778

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 18:57588007..57588811(-)
• Located in intron of: ENSMUSG00000058925

Retrocopy information

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

Parental gene information

• Parental gene symbol: Rnh1
• Ensembl ID: ENSMUSG00000038650
• Aliases: Rnh1, AW546468, C80305, RNH
• Description: ribonuclease/angiogenin inhibitor 1 [Source:MGI Symbol;Acc:MGI:1195456]

Sequence

>retro_mmus_1778
CTGAAGGACTCTGCCTGTCAACTGGAGTCACTCAAGCTGGAGAACTGTGGTATCACATCAGCCAGCTGCAAGGATCTGTG
TGATGTTGTGGCCTCCAACGCCTCACTGCAGGAACTGGACTTGGGCAGCAACAAGCTGGGTAATGCAGGCATTGCAGCAC
TGTGCCCAGGACTGCTGCTTCCCAGCTGTAAGCTCAGGACTCTGTTGCTCTGGGAGTGTGATGTCACTGCAGAGGGCTTC
GAGGACCTGTGCTGTGTCCTCAGGGCCAAGCAGAGCCTGAAGGAACTCAGCCTAGCTGCCAATGAGCTGAAGGATGAGGG
GGCCCGGCTGCTGTGTGAGAGCCTATTAGAGCCTGGCTATCAGCTAGAGTCACTGTGGGTAAAGACCTGTAGCCTCACAG
CTGCCTCTTGTCCCCACTTCTGCTCCGTGTTGACCAAAGACCGTTCTCTGCTGGAGCTGCAAATGAGCAGCAATCCACTG
GGAGACTTGGGAGTCCAGGAGCTTTGCACGGCCCTGGGCCAGCCAGACCCAGTGCCGCGTGTGCTTTGGCTGGGAGACTG
GGATGTGACAGATAGTGGTTGCAGTAGCCTTGCCACTGTCCTGCTGGCCAACCGCAGCCTGATTAATCTGGACCTCAGTA
GCAACTCTGTGGGGGGCTCAGGTGTCCTGCAACTGCTGGAGAGCCTCAAACAGCCCAGCTGTGCCCATCAGCAGCATGTC
CTGTGTGACATTTACTGGGCAGATGAGGTGGAAGACTATCTTTGGGCCCTGGAGGAGGAAAGGCCTTCCTGGAGGGTCAT
TTCC

Alignment

ORF - retro_mmus_1778 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.07 %
• Parental protein coverage: 58.77 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LKDSACQLESLKLENCGITAANCKDLCDVVASKASLQELDLSSNKLGNAGIAALCPGLLLPSCKLRTLWL
          LKDSACQLESLKLENCGIT.A.CKDLCDVVAS.ASLQELDL.SNKLGNAGIAALCPGLLLPSCKLRTL.L
Retrocopy LKDSACQLESLKLENCGITSASCKDLCDVVASNASLQELDLGSNKLGNAGIAALCPGLLLPSCKLRTLLL

Parental  WECDITAEGCKDLCRVLRAKQSLKELSLASNELKDEGARLLCESLLEPGCQLESLWIKTCSLTAASCPYF
          WECD.TAEG..DLC.VLRAKQSLKELSLA.NELKDEGARLLCESLLEPG.QLESLW.KTCSLTAASCP.F
Retrocopy WECDVTAEGFEDLCCVLRAKQSLKELSLAANELKDEGARLLCESLLEPGYQLESLWVKTCSLTAASCPHF

Parental  CSVLTKSRSLLELQMSSNPLGDEGVQELCKALSQPDTVLRELWLGDCDVTNSGCSSLANVLLANRSLREL
          CSVLTK.RSLLELQMSSNPLGD.GVQELC.AL.QPD.V.R.LWLGD.DVT.SGCSSLA.VLLANRSL..L
Retrocopy CSVLTKDRSLLELQMSSNPLGDLGVQELCTALGQPDPVPRVLWLGDWDVTDSGCSSLATVLLANRSLINL

Parental  DLSNNCMGGPGVLQLLESLKQPSCTLQQLVLYDIYWTNEVEEQLRALEEERPSLRIIS
          DLS.N..GG.GVLQLLESLKQPSC..QQ.VL.DIYW..EVE..L.ALEEERPS.R.IS
Retrocopy DLSSNSVGGSGVLQLLESLKQPSCAHQQHVLCDIYWADEVEDYLWALEEERPSWRVIS

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	0.02 RPM	27.12 RPM
SRP007412_cerebellum	0.00 RPM	33.48 RPM
SRP007412_heart	0.00 RPM	38.91 RPM
SRP007412_kidney	0.02 RPM	62.72 RPM
SRP007412_liver	0.00 RPM	81.98 RPM
SRP007412_testis	0.09 RPM	10.34 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_1778 was not detected

EST

No EST(s) were mapped for retro_mmus_1778 retrocopy.

TSS

No TSS is located nearby retro_mmus_1778 retrocopy 5' end.

Lab

retro_mmus_1778 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1778 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000010466	1 retrocopy	retro_amel_1537,
Felis catus	ENSFCAG00000007585	1 retrocopy	retro_fcat_1347,
Mus musculus	ENSMUSG00000038650	2 retrocopies	retro_mmus_1727, retro_mmus_1778 ,