RetrogeneDB ID: retro_rnor_2876

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: X:144257150..144258073(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Esrrb
• Ensembl ID: ENSRNOG00000010259
• Aliases: Esrrb, Err2, Errb
• Description: Steroid hormone receptor ERR2 [Source:UniProtKB/Swiss-Prot;Acc:P11475]

Sequence

>retro_rnor_2876
GGTATCATAGAGCACTCGGCCGTCAAGGGCTAGTACATGCTAAACACCATCCACAAGCCCCTGTACATCATGTGCCAGGA
CATTGCCTCTGGCTACCATTACAGAGTGGCCTCCTACAAGGCTTGCAAGACGTTCTTCAAGAGAACCATTCAAGGAAACA
TCAAATACAGCTGCCCAGCCACCAACAAGTGTGAGATCACCAAACAGAGGTAAAAGTTTTGTCAGGTCTGCCAATTCAGG
AAATGCCTCAAAGTGGGATGCTGAAGAAAAGTGTGCATGCTGACCAGGTGCTTGGAGGCGGCCAGAAGTACAAGGGACAG
CTAGATTTGGAGAAGAGTCCCTACCTGAGCTTACAGATTTCCCTACCTGCTAAAAAGTCATTGACTAAGATTGTCTCCTA
TTTACTGGTGGCTGAGCTTGACAAGTGTAGGCTATGCCTCCAGGTGATATACCTGAGGGAGATATCAAGGCCCTGCCCAT
TACTCTGTGACTTGGCAGCTCAGGAGCTTGTGGTCCTCATTAGCTGAGCCAAGAACATCGTAGACTTCTCCAGTCTGTCA
CTTGGGGACCAGATGAGCCTGCTGCAGAGTGCCGGGATGGGGAGTCTCATCCTGGGCACCGTGAACCACTCACTGCCCTA
CAATGACAAACAGGCATATGCAGAGGACTATATGATGGATGAGGAGCATTCTCCACTGGTGGGGATGCTGGAGCTTTGCT
GAGCCACCCTTCAGCTGGTACATAGGTACAAGAAGCTCAAGGTAGAAGAGGAAGAGCTTGTGATGTTCAAGGCCCTGACC
CTTGCCAAATCAGATTCAGTGTACATTGAGGACCTGGAGGCTGTGCAGAAGCTTCAGGACCTTCTGCATAAGGCATTATA
GGACTGTGAGCTGAGCTAGTACCATGAGGAGCCATGGAGGTCC

Alignment

ORF - retro_rnor_2876 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.67 %
• Parental protein coverage: 71.13 %
• Number of stop codons detected: 7
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  GIMEDSAIKCEYMLNAIPKRLCLVCGDIASGYHYGVASCEACKAFFKRTIQGNIEYSCPATNECEITKRR
          GI.E.SA.K..YMLN.I.K.L...C.DIASGYHY.VAS..ACK.FFKRTIQGNI.YSCPATN.CEITK.R
Retrocopy GIIEHSAVKG*YMLNTIHKPLYIMCQDIASGYHYRVASYKACKTFFKRTIQGNIKYSCPATNKCEITKQR

Parental  RKSCQACRFMKCLKV-GMLKEGVRLDRVRGGRQKYKRRLDSENSPYLSLQISPPAKKPLTKIVSYLLVAE
          .K.CQ.C.F.KCLKV.GMLK..V..D.V.GG.QKYK..LD.E.SPYLSLQIS.PAKK.LTKIVSYLLVAE
Retrocopy *KFCQVCQFRKCLKV<GMLKKSVHADQVLGGGQKYKGQLDLEKSPYLSLQISLPAKKSLTKIVSYLLVAE

Parental  PDK-LYAMPPDDVPEGDIKAL-TTLCDLADRELVFLISWAKHIPGFSNLTLGDQMSLLQSAWMEILILGI
          .DK...AMPP.D.PEGDIKAL...LCDLA..ELV.LIS.AK.I..FS.L.LGDQMSLLQSA.M..LILG.
Retrocopy LDK<V*AMPPGDIPEGDIKAL>PLLCDLAAQELVVLIS*AKNIVDFSSLSLGDQMSLLQSAGMGSLILGT

Parental  VYRSLPYDDKLAYAEDYIMDEEHSRLVGLLELYRAILQLVRRYKKLKVEKEEFVMLKALALANSDSMYIE
          V..SLPY.DK.AYAEDY.MDEEHS.LVG.LEL..A.LQLV.RYKKLKVE.EE.VM.KAL.LA.SDS.YIE
Retrocopy VNHSLPYNDKQAYAEDYMMDEEHSPLVGMLELC*ATLQLVHRYKKLKVEEEELVMFKALTLAKSDSVYIE

Parental  NLEAVQKLQDLLHEALQDYELSQRHEEPRRA
          .LEAVQKLQDLLH.AL.D.ELS..HEEP.R.
Retrocopy DLEAVQKLQDLLHKAL*DCELS*YHEEPWRS

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
SRP017611_brain	0.00 RPM	0.22 RPM
SRP017611_kidney	0.00 RPM	12.84 RPM
SRP017611_liver	0.00 RPM	0.00 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2876 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2876 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2876 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Mus musculus	retro_mmus_3461

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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,