RetrogeneDB ID: retro_mmus_2208

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 3:144779304..144780219(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Nr5a2
• Ensembl ID: ENSMUSG00000026398
• Aliases: Nr5a2, AU020803, D1Ertd308e, Ftf, LRH-1, UF2-H3B
• Description: nuclear receptor subfamily 5, group A, member 2 [Source:MGI Symbol;Acc:MGI:1346834]

Sequence

>retro_mmus_2208
TCACAGGAAGTGTCTCAATTTAAATGGTGAATTACTCCTATGATGAAGATCTGGAATTGCTTTGTCCTGTGTGTGATGAT
AAAGTACCTGGGTATCATTACGGTCTCCTTGCCTTTGAAAACTTCCAGGGTTTTTTTTAATTGAACTGTCCAAAACCAAA
AAAGGTACATGTGCATAGAGAACCAGAATTGCCAAATTGCCAAAATACAGAGAAAACACTGTCCTTACTGTCATTAAAAA
AAATGTATTGATGTTGGAATGAAGCTGTAAGCTGTAAGTGCTGACTGCATGCAAGGAGGCAGAAATAAGTTTGGGTCAAT
GTACATGAGAGACAGGGCCCCGAAGAAACAGAAGAAAGCCCTCATTTGATTCAACAAACTTAAACTGGAAGTCATGTCTC
AGGTGATCCAAATAATGCCCTCAGACCTGACCTCTGCAATTCAGAACATTCATTCTACCTTCAAAGGCCTACCTCTGAGT
CATGTAGCCTTGCCTCCAACAGACTATGACAGAAGTCCCTTTGTCACATCTTCCATTAGCATGACAATGCCACCTCATGG
CAGCCTGCATGGTTACCAACCATATGGTCACTTTCCTAGTTTGGCCATCAAGACTGAGTAGCCAGACCCCTACCCCAGCT
GTCCTGAGTCAGTGATGGGCTACTCCTACATGGATGGTTACCAGACAAGCTCCCCAGCCAGCATCCCACACCTGAGACTG
GAACTTTTGAAGTGTGAACCAGACGAGCCTCGAATTCAAGCAAAGATCATGACTTACCTCCAGCAAGAGCAGAGTAACAG
GCAGGAAAAGCTGAGCACATTTGGACTCTTGTGCAAAATGGTAGACCAGATCCTGTTCTCCATTGTTGACTGGGCCAGGA
GTAGTATCTTCTTCAGGGAACTGAAGGTTGATGAA

Alignment

ORF - retro_mmus_2208 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.26 %
• Parental protein coverage: 54.82 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  NMQVSQFK-MVNYSYDEDLEELCPVCGDKVSGYHYGLLTCE-SCKGFFKRTVQNQKRYTCIENQNCQIDK
          ...VSQFK.MVNYSYDEDLE.LCPVC.DKV.GYHYGLL..E.........TVQNQKRY.CIENQNCQI.K
Retrocopy SQEVSQFK<MVNYSYDEDLELLCPVCDDKVPGYHYGLLAFE>TSRXXXN*TVQNQKRYMCIENQNCQIAK

Parental  TQRKRCPYCRFKKCIDVGMKLEAVRADRMRGGRNKFGPMYKRDRALKQQKKALIRANGLKLEAMSQVIQA
          .QRK.CPYC....CIDVGMKL.AV.AD.M.GGRNKFG.MY.RDRA.K.QKKALI..N.LKLE.MSQVIQ.
Retrocopy IQRKHCPYCHXXXCIDVGMKL*AVSADCMQGGRNKFGSMYMRDRAPKKQKKALI*FNKLKLEVMSQVIQI

Parental  MPSDLTSAIQNIHSASKGLPLSHVALPPTDYDRSPFVTSPISMTMPPHSSLHGYQPYGHFPSRAIKSEYP
          MPSDLTSAIQNIHS..KGLPLSHVALPPTDYDRSPFVTS.ISMTMPPH.SLHGYQPYGHFPS.AIK.E.P
Retrocopy MPSDLTSAIQNIHSTFKGLPLSHVALPPTDYDRSPFVTSSISMTMPPHGSLHGYQPYGHFPSLAIKTE*P

Parental  DPYSSSPESMMGYSYMDGYQTNSPASIPHLILELLKCEPDEPQVQAKIMAYLQQEQSNRNRQEKLSAFGL
          DPY.S.PES.MGYSYMDGYQT.SPASIPHL.LELLKCEPDEP..QAKIM.YLQQEQS..NRQEKLS.FGL
Retrocopy DPYPSCPESVMGYSYMDGYQTSSPASIPHLRLELLKCEPDEPRIQAKIMTYLQQEQS--NRQEKLSTFGL

Parental  LCKMADQTLFSIVEWARSSIFFRELKVDD
          LCKM.DQ.LFSIV.WARSSIFFRELKVD.
Retrocopy LCKMVDQILFSIVDWARSSIFFRELKVDE

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	0.05 RPM
SRP007412_cerebellum	0.00 RPM	0.04 RPM
SRP007412_heart	0.00 RPM	1.00 RPM
SRP007412_kidney	0.04 RPM	0.31 RPM
SRP007412_liver	0.05 RPM	48.64 RPM
SRP007412_testis	0.09 RPM	0.23 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_2208 was not detected

EST

No EST(s) were mapped for retro_mmus_2208 retrocopy.

TSS

No TSS is located nearby retro_mmus_2208 retrocopy 5' end.

Lab

retro_mmus_2208 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2208 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Mus musculus	ENSMUSG00000026398	1 retrocopy	retro_mmus_2208 ,
Oryctolagus cuniculus	ENSOCUG00000006240	1 retrocopy	retro_ocun_811,
Otolemur garnettii	ENSOGAG00000025622	1 retrocopy	retro_ogar_2546,