RetrogeneDB ID: retro_mmus_2305

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 3:135525963..135526532(-)
• Located in intron of: ENSMUSG00000028164

Retrocopy information

• Ensembl ID: ENSMUSG00000083610
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Oaz2
• Ensembl ID: ENSMUSG00000040652
• Aliases: Oaz2, AZ-2, AZ2, Oaz2-ps, Sez15
• Description: ornithine decarboxylase antizyme 2 [Source:MGI Symbol;Acc:MGI:109492]

Sequence

>retro_mmus_2305
ATGATAAACACCCAGGACAGTAGTATTTTGCCGTTGAGTAACTGTACCCAGCTCCAGTGCTGCAAGGCACATGGTTCCAG
GGCCTCTGTGGTGCTCCTGATGCCCCTCACCCACTGTCGAAGATCCCCGGTGGGCGAGGGGGCGGCAGGGATCCTTCTCT
CTCAGCTCTAATATATAAGGACGAGAAGCTCACTGTAACCCAGGACCTCCCCGTGAACGATGGGAAACCTCACATCGTCC
ACTTCCAGTATGAGGTCACCCAGGTGAAGGTCTCTTCCTGGGATGCAGTCCTGTCCAGCGAGAGCCTGTTTGTAGAAATC
CCAGATGGATTATTAGCTGATGGGAGCAAAGAAGGATTATTAACACTGCTAGAGTTTGCTGAGGAGAAGATGAAAGTGAA
CTACGTCTTCATCTGCTTCAGGAAGAGCCGGGAAGACAGAGCTCCACTCCTGAAGACGTTCAGCTTCTTGGGCTTTGAGA
TTGTGCGTCCAGGTCATCCCTGTGTCCCCTCTCGGCCAGATGTGATGTTTATGGTTTACCCCCTGGACCAGAACTTGTCT
GATGAGGAC

Alignment

ORF - retro_mmus_2305 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.29 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MINTQDSSILPLSKCPQLQCC-RHIVPGPLWCS-DAPHPLSKIPGGRGGGRDPSLSALIYKDEKLTVTQD
          MINTQDSSILPLS.C.QLQCC.RH.VPGPLWCS.DAPHPLSKIPGGRGGGRDPSLSALIYKDEKLTVTQD
Retrocopy MINTQDSSILPLSNCTQLQCC>RHMVPGPLWCS>DAPHPLSKIPGGRGGGRDPSLSALIYKDEKLTVTQD

Parental  LPVNDGKPHIVHFQYEVTEVKVSSWDAVLSSQSLFVEIPDGLLADGSKEGLLALLEFAEEKMKVNYVFIC
          LPVNDGKPHIVHFQYEVT.VKVSSWDAVLSS.SLFVEIPDGLLADGSKEGLL.LLEFAEEKMKVNYVFIC
Retrocopy LPVNDGKPHIVHFQYEVTQVKVSSWDAVLSSESLFVEIPDGLLADGSKEGLLTLLEFAEEKMKVNYVFIC

Parental  FRKGREDRAPLLKTFSFLGFEIVRPGHPCVPSRPDVMFMVYPLDQNLSDED
          FRK.REDRAPLLKTFSFLGFEIVRPGHPCVPSRPDVMFMVYPLDQNLSDED
Retrocopy FRKSREDRAPLLKTFSFLGFEIVRPGHPCVPSRPDVMFMVYPLDQNLSDED

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	63.41 RPM
SRP007412_cerebellum	0.13 RPM	44.55 RPM
SRP007412_heart	0.47 RPM	67.33 RPM
SRP007412_kidney	0.23 RPM	50.76 RPM
SRP007412_liver	0.08 RPM	11.96 RPM
SRP007412_testis	0.18 RPM	65.86 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_2305 was not detected

EST

No EST(s) were mapped for retro_mmus_2305 retrocopy.

TSS

No TSS is located nearby retro_mmus_2305 retrocopy 5' end.

Lab

retro_mmus_2305 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2305 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 8 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Microcebus murinus	ENSMICG00000007344	1 retrocopy	retro_mmur_1013,
Myotis lucifugus	ENSMLUG00000022795	2 retrocopies	retro_mluc_1003, retro_mluc_2416,
Mus musculus	ENSMUSG00000035242	1 retrocopy	retro_mmus_1622,
Mus musculus	ENSMUSG00000040652	2 retrocopies	retro_mmus_1343, retro_mmus_2305 ,
Oryctolagus cuniculus	ENSOCUG00000017341	1 retrocopy	retro_ocun_1612,
Ochotona princeps	ENSOPRG00000009548	2 retrocopies	retro_opri_1184, retro_opri_145,
Tupaia belangeri	ENSTBEG00000008091	1 retrocopy	retro_tbel_2493,
Tursiops truncatus	ENSTTRG00000011834	1 retrocopy	retro_ttru_502,