RetrogeneDB ID: retro_mmus_1457

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 16:31924911..31925750(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000083890
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Rnaseh2a
• Ensembl ID: ENSMUSG00000052926
• Aliases: Rnaseh2a, 2400006P09Rik, RNASEHI, RNHIA, RNHL
• Description: ribonuclease H2, large subunit [Source:MGI Symbol;Acc:MGI:1916974]

Sequence

>retro_mmus_1457
AGTTTTTGTGGAAAACGCGCGCTGGGACTTGCGCTTGCAGTGTTTTTTTCTACAACTGTTGGCTGTCGCAGAGGCAGCAT
GGATCTCAGCGAGCTGGAGAGGGACAATATGAATCGTTGTTGTCTGAGTTCTCCTGTACCTTCTGTGTGTCTCAAGGAGC
CGTGCGTTCTGGGCGTGGATGAAGCGGGCCGAGCCCCTGTGCTTGGTCCCATGGTCTATGCCATCTGTTACTGCCCCCTG
TCTCGCTTGGCAGATCCGGAGGCCCTGAAAGTAGCAGACTCAAAGACCTTGACAGAGAATGAGCGGGAGAGGCTCTTTAC
GAAAATGGAGGAAGATGGAGACTTTGTGGGTTGGTCTTTGGACGTCCTGTCTCCAAACCTGATCTCTATCAGCATGCTTG
GGCGAGTCAAGTACAACCTCAACTCCCTGTCACACGATACAGCTGCGGAGCTGATATGGTATGCACTGGACCAGAATGTG
AATGTCACTCAGGTATTTGTGGACACTGTAGGAATGCCAGAGACATACCAGGCTCTATTATAACAGCGCTTTCCGGGATA
GAGGTGACAGTCAAGGCCAAAGCTGACTCCCTGTTCCCTGTGGTCAGTGCTGCCAGCATCTTTGCCAAGGTAACCAGAGA
CAAGGCTGTGAAGAACTGGCAGTTTGTGGAAATTTTACAGGATCTGGACTCCGATTATGGCTCAGGCTATCCCAGTGATC
CCAAGACCAAAGCCTGGCTGAGGAGACATGTGGACCCTGTGTTTGGCTTCCCCCAGTTTGTACGGTTCAGTTGGAGCACA
GCCCAAGCCATCTTGGAGAAGGAGGCAGATGTCACTTGG

Alignment

ORF - retro_mmus_1457 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.13 %
• Parental protein coverage: 98.94 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SFRGKRALGPALAVLFSTIVGCRRGSMDLSELERDNTGRCRLSSPVPAVCLKEPCVLGVDEAGRGPVLGP
          SF.GKRALG.ALAV.FST.VGCRRGSMDLSELERDN..RC.LSSPVP.VCLKEPCVLGVDEAGR.PVLGP
Retrocopy SFCGKRALGLALAVFFSTTVGCRRGSMDLSELERDNMNRCCLSSPVPSVCLKEPCVLGVDEAGRAPVLGP

Parental  MVYAICYCPLSRLADLEALKVADSKTLTENERERLFAKMEEDGDFVGWALDVLSPNLISTSMLGRVKYNL
          MVYAICYCPLSRLAD.EALKVADSKTLTENERERLF.KMEEDGDFVGW.LDVLSPNLIS.SMLGRVKYNL
Retrocopy MVYAICYCPLSRLADPEALKVADSKTLTENERERLFTKMEEDGDFVGWSLDVLSPNLISISMLGRVKYNL

Parental  NSLSHDTAAGLIQYALDQNVNVTQVFVDTVGMPETYQARLQQHFP-GIEVTVKAKADSLFPVVSAASIFA
          NSLSHDTAA.LI.YALDQNVNVTQVFVDTVGMPETYQA.L.Q.FP.GIEVTVKAKADSLFPVVSAASIFA
Retrocopy NSLSHDTAAELIWYALDQNVNVTQVFVDTVGMPETYQALL*QRFP<GIEVTVKAKADSLFPVVSAASIFA

Parental  KVARDKAVKNWQFVENLQDLDSDYGSGYPNDPKTKAWLRKHVDPVFGFPQFVRFSWSTAQAILEKEAEDV
          KV.RDKAVKNWQFVE.LQDLDSDYGSGYP.DPKTKAWLR.HVDPVFGFPQFVRFSWSTAQAILEKEA.DV
Retrocopy KVTRDKAVKNWQFVEILQDLDSDYGSGYPSDPKTKAWLRRHVDPVFGFPQFVRFSWSTAQAILEKEA-DV

Parental  IW
          .W
Retrocopy TW

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	0.12 RPM	12.99 RPM
SRP007412_cerebellum	0.09 RPM	18.63 RPM
SRP007412_heart	0.00 RPM	13.11 RPM
SRP007412_kidney	0.02 RPM	13.11 RPM
SRP007412_liver	0.00 RPM	13.85 RPM
SRP007412_testis	0.73 RPM	516.21 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_1457 was not detected

EST

No EST(s) were mapped for retro_mmus_1457 retrocopy.

TSS

No TSS is located nearby retro_mmus_1457 retrocopy 5' end.

Lab

retro_mmus_1457 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1457 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Mus musculus	ENSMUSG00000052926	1 retrocopy	retro_mmus_1457 ,