RetrogeneDB ID: retro_mmus_3461

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: X:61090998..61091704(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000083543
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Esrrb
• Ensembl ID: ENSMUSG00000021255
• Aliases: Esrrb, Err2, Errb, Estrrb, Nr3b2
• Description: estrogen related receptor, beta [Source:MGI Symbol;Acc:MGI:1346832]

Sequence

>retro_mmus_3461
AAGTGTGACCGGGTATGTAGAGGCCAACAGAAGTACAAGGGATGGCTGGATTCAAAGAACAGCCCCTACCTGAGCCTACA
GATTTCCCCACCTGCTAAAAAGCCATCGACTAAGATTGTCTCATATCTACTGGTGGCTGAGCCAGACAAGTTTTATGTTA
TGCCTCCCAGTAATATACCTGAGGGAGATACCAAGGCCCTGGCTACTCTCTGTGTAGCCAGTTCACAAGCTTGTGGTCTT
TATTAGTTGGGCCAAGTACATCCCAGCCTTCTCCAGTCTGTCACCTGGGGACCAGATGAGTGCCTGGATGGAGATCCTCA
TCTTGGACATCATGTACCGCTTGCTGCCCTATGATGACAAACTGGCATATGCTGAGGACTGTATCATGGATAAGGAGCAC
ATGATGGGACTGCTGGAGCTTTACTGAGCTATCCTGCAACTGTTACACAGGTACAAGAAGCTCAAAGTAGAGAAGGAAGA
GTTTGGAATGCTCAAGGCCTTGGCCCTCACCAACTCAGATTCAGTGTACATTGAGGACCTGGAGGCTATGCAGAAGCTTC
AGGACCTGCTGCATGAGGCACTGCAGGACTATAAGCTGAGCCAACACCATGGGGAGCCATGGAGGACCAGCAAGCTGCTG
CTGATATTGCCCCTGCTGCCACAGACAGCAGCCAAAGTCTTGCAGCATTTCTACAGTGTAAAACTC

Alignment

ORF - retro_mmus_3461 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.6 %
• Parental protein coverage: 53.3 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  RLDRVRGGRQKYKRRLDSENSPYLNLPISPPAKKPLTKIVSNLLGVEQDKLYAMPPNDIPEGDIKALTTL
          ..DRV..G.QKYK..LDS.NSPYL.L.ISPPAKKP.TKIVS.LL..E.DK.Y.MPP..IPEGD.KAL.TL
Retrocopy KCDRVCRGQQKYKGWLDSKNSPYLSLQISPPAKKPSTKIVSYLLVAEPDKFYVMPPSNIPEGDTKALATL

Parental  CELADRE-LVFLINWAKHIPGFPSLTLGDQMSLLQSAWMEILILGIVYRSLPYDDKLAYAEDYIMDEEHS
          C........VF.I.WAK.IP.F.SL..GDQMS....AWMEILIL.I.YR.LPYDDKLAYAED.IMD.EH.
Retrocopy CVASSQA>VVF-ISWAKYIPAFSSLSPGDQMS----AWMEILILDIMYRLLPYDDKLAYAEDCIMDKEH-

Parental  RLVGLLDLYRAILQLVRRYKKLKVEKEEFMILKALALANSDSMYIENLEAVQKLQDLLHEALQDYELSQR
          ...GLL.LY.AILQL..RYKKLKVEKEEF..LKALAL.NSDS.YIE.LEA.QKLQDLLHEALQDY.LSQ.
Retrocopy -MMGLLELY*AILQLLHRYKKLKVEKEEFGMLKALALTNSDSVYIEDLEAMQKLQDLLHEALQDYKLSQH

Parental  HEEPRRAGKLLLTLPLLRQTAAKAVQHFYSVKL
          H.EP.R..KLLL.LPLL.QTAAK..QHFYSVKL
Retrocopy HGEPWRTSKLLLILPLLPQTAAKVLQHFYSVKL

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	0.00 RPM	2.73 RPM
SRP007412_cerebellum	0.00 RPM	15.41 RPM
SRP007412_heart	0.00 RPM	26.96 RPM
SRP007412_kidney	0.00 RPM	45.16 RPM
SRP007412_liver	0.00 RPM	0.90 RPM
SRP007412_testis	0.00 RPM	2.84 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_3461 was not detected

EST

No EST(s) were mapped for retro_mmus_3461 retrocopy.

TSS

No TSS is located nearby retro_mmus_3461 retrocopy 5' end.

Lab

retro_mmus_3461 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3461 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Rattus norvegicus	retro_rnor_2876

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000020709	1 retrocopy	retro_cjac_3190,
Mus musculus	ENSMUSG00000021255	1 retrocopy	retro_mmus_3461 ,
Rattus norvegicus	ENSRNOG00000010259	1 retrocopy	retro_rnor_2876,
Tursiops truncatus	ENSTTRG00000001302	1 retrocopy	retro_ttru_139,