RetrogeneDB ID: retro_rnor_371

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 2:140165789..140167400(-)
• Located in intron of: ENSRNOG00000049819

Retrocopy information

• Ensembl ID: ENSRNOG00000047902
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: Fxr2
• Ensembl ID: ENSRNOG00000011876
• Aliases: Fxr2, Fxr2h
• Description: fragile X mental retardation syndrome-related protein 2 [Source:RefSeq peptide;Acc:NP_001094117]

Sequence

>retro_rnor_371
NNGCTGACGGTGGAGGTTCGCGGCTCCAACGGGGCTCTCTACAAGGGATTTATCAAAGATGTCCACGAAGACTCCCTCAC
AGTTGTTTTTGAAAATAATTGGCAACCAGAACGCCAGGTTCCGTTTAATGAAGTTCGATTACCACCACCACCTGATATAA
AGAAAGAAATTAGTGAAGGAGATGAAGTAGAGGTATATTCAAGAGCAAATGACCAAGAACCATGTGGATGGTGGCTGGCT
AAAGTTCGGATGATGAAAGGCGAGTTTTATGTCATTGAATATGCTGCTTGTGATGCCACTTACAATGAAATAGTCACATT
TGAACGACTTCGGCCTGTCAATCAAAATAAAACTGTCAAAAAAAATACCTTCTTTAAGTGCACAGTGGATGTTCCTGAGG
ATTTGAGAGAAGCGTGTGCTAATGAAAATGCCCATAAAGATTTCAAGAAAGCAGTAGGAGCGTGCAGAATTTTCTATCAT
CCTGAAACTACCCAGCTAATGATACTGTCGGCCAGTGAAGCAACTGTGAAGAGAGTAAATATCTTAAGTGATATGCATTT
GCGAAGTATTCGGACGAAGTTGATGCTTATGTCCAGAAATGAAGAGGCCACTAAGCATTTAGAATGCACAAAACAGCTTG
CAGCAGCTTTTCATGAAGAATTTGTTGTGAGAGAAGATCTAATGGGCCTGGCAATAGGAACGCATGGTAGTAACATACAG
CAAGCTAGGAAGGTCCCTGGAGTTACTGCCATTGAGTTAGATGAAGATACTGGAACGTTTAGAATCTACGGAGAGAGTGC
TGAGGCTGTAAAGAAAGCAAGAGGTTTCTTGGAATTTGTGGAAGATTTTATTCAAGTTCCCAGGAATCTTGTTGGAAAAG
TTATTGGAAAAAATGGCAAAGTTATTCAAGAAATAGTGGATAAATCTGGTGTGGTTCGAGTAAGAATTGAAGGAGACAAT
GAAAATAAACTACCTAGAGAAGATGGAATGGTTCCATTTGTATTTGTTGGCACTAAAGAAAGTATTGGAAATGTGCAAGT
TCTTCTAGAGTATCACATTGCTTACTTAAAGGAAGTGGAACAACTAAGAATGGAACGCCTGCAGATCGATGAACAGCTGC
GACAGATTGGTTCTAGGTCTTATAGTGGAAGAGGCAGAGGTCGTCGGGGCCCTAATTACACCACCGGTTATGGTACAAAT
TCTGAGCTGTCTAACCCCTCCGAAACAGAATCTGAGCGTAAAGATGAGCTGAGTGATTGGTCATTGGCAGGAGAAGATGA
TCGAGAGACTCGACATCAGCGAGACAGCAGGAGACGCCCAGGAGGAAGAGGCAGAAGTGTTTCTGGGGGACGAGGTCGTG
GTGGACCACGTGGTGGCAAATCCTCCATCAGTTCTGTGCTCAAAGATCCAGACAGCAATCCATACAGCTTACTTGATAAT
ACAGAATCAGATCAGACTGCAGACACTGACGCCAGCGAATCTCACCACAGTACTAACCGTCGTAGGCGGTCTCGTAGACG
AAGGACTGATGAAGATGCTGTTCTGATGGATGGAATGACTGAATCTGATACAGCCTCAGTTAATGAGAATGGGCTAGTCA
CAGTTGCAGAT

Alignment

ORF - retro_rnor_371 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.84 %
• Parental protein coverage: 57.48 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LPVEVRGSNGAFYKGFVKDVHEDSVTIFFENNWQSERQIPFGDVRLPPPADYNKEITEGDEVEVYSRANE
          L.VEVRGSNGA.YKGF.KDVHEDS.T..FENNWQ.ERQ.PF..VRLPPP.D..KEI.EGDEVEVYSRAN.
Retrocopy LTVEVRGSNGALYKGFIKDVHEDSLTVVFENNWQPERQVPFNEVRLPPPPDIKKEISEGDEVEVYSRAND

Parental  QEPCGWWLARVRMMKGDFYVIEYAACDATYNEIVTLERLRPVNPNPLATKGSFFKVTMAVPEDLREACSN
          QEPCGWWLA.VRMMKG.FYVIEYAACDATYNEIVT.ERLRPVN.N....K..FFK.T..VPEDLREAC.N
Retrocopy QEPCGWWLAKVRMMKGEFYVIEYAACDATYNEIVTFERLRPVNQNKTVKKNTFFKCTVDVPEDLREACAN

Parental  ENVHKEFKKALGANCIFLNITDSELFILSTTEAPVKRASLLGDMHFRSLRTKLLLMSRNEEATKHLETSK
          EN.HK.FKKA.GA..IF.......L.ILS..EA.VKR...L.DMH.RS.RTKL.LMSRNEEATKHLE..K
Retrocopy ENAHKDFKKAVGACRIFYHPETTQLMILSASEATVKRVNILSDMHLRSIRTKLMLMSRNEEATKHLECTK

Parental  QLAAAFQEEFTVREDLMGLAIGTHGANIQQARKVPGVTAIELGEETCTFRIYGETPEACRQARSYLEFSE
          QLAAAF.EEF.VREDLMGLAIGTHG.NIQQARKVPGVTAIEL.E.T.TFRIYGE..EA...AR..LEF.E
Retrocopy QLAAAFHEEFVVREDLMGLAIGTHGSNIQQARKVPGVTAIELDEDTGTFRIYGESAEAVKKARGFLEFVE

Parental  DSVQVPRNLVGKVIGKNGKVIQEIVDKSGVVRVRVEGDNDKKNPREEGMVPFIFVGTRENISNAQALLEY
          D..QVPRNLVGKVIGKNGKVIQEIVDKSGVVRVR.EGDN..K.PRE.GMVPF.FVGT.E.I.N.Q.LLEY
Retrocopy DFIQVPRNLVGKVIGKNGKVIQEIVDKSGVVRVRIEGDNENKLPREDGMVPFVFVGTKESIGNVQVLLEY

Parental  HLSYLQEVEQLRLERLQIDEQLRQIG-LGFRPPGSGRGG
          H..YL.EVEQLR.ERLQIDEQLRQIG.......G.GR.G
Retrocopy HIAYLKEVEQLRMERLQIDEQLRQIGSRSYSGRGRGRRG

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	11.65 RPM	82.97 RPM
SRP017611_kidney	15.49 RPM	43.61 RPM
SRP017611_liver	10.02 RPM	26.96 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_371 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_371 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_371 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Echinops telfairi	ENSETEG00000018613	1 retrocopy	retro_etel_1220,
Monodelphis domestica	ENSMODG00000007179	1 retrocopy	retro_mdom_2009,
Rattus norvegicus	ENSRNOG00000011876	1 retrocopy	retro_rnor_371 ,
Sarcophilus harrisii	ENSSHAG00000015678	1 retrocopy	retro_shar_400,