RetrogeneDB ID: retro_rnor_2228

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 5:84757030..84757849(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Eno3
• Ensembl ID: ENSRNOG00000004078
• Aliases: Eno3, BBE, MSE
• Description: Beta-enolase [Source:UniProtKB/Swiss-Prot;Acc:P15429]

Sequence

>retro_rnor_2228
AAGATTGACAAACTGATGGTTGCAATGGACAGCACTGAGAATAAATCTAAATTTGGTATAAATACCATTCTGGGAGTATC
CCTGGCTGTCTGTAAAACTGGTGCCATGGGAAAGGGGGGTGCCTCTTTACTATCACATTGCTGACTTGGCCGGCAACCCT
GAAGTCATCCTGATTGTCCCAGCTTTCAATGTGATCAACTGTGGCTCTCATCCCTGCAATAAGCTGGCCATGGAAGAGGT
CATGATCCTGCCTGTGTGGGCATACTATTTCCCAGAAGCCATGTGCATTGAAGTAGAGGTTTACCACAACCTAAAGAATG
TCATCAACAAGAAGTACCAGAAGGATGCCATTAATGAGGGTGATGAGGATAGATTTGTTCCTAACATCCTGGAGAACAAA
GAGGTCCTGGAACTGATGAAGACTGCAATTGCAAAGGCTGTCTACACTGACCAGGTTTTCATCAGCATGGATGTGGCTGC
CTCTGAGTTCTAAAGGTCTGGCAAGTATGACCTGGACTTTAAATCTTAGAATGATTCCAGCAGGTACATCAATCACACCA
GACCAGCTGGTGGCCCTTTACAAGTCTTCCATCCAGGAGTATCCAGTAGTGTCCATTGAGAACCTCTTTGACCAGGAGGA
CTGGGGAAACCTGGCAGAAGTACACAGCTAGTGCAGGCATCCAGGTGGTGGGAGATGACCTCACAGTAACCAATCCTACG
TGAATTGCCAAGGCTGTGGGTAAGAACTCCTGCAACTGCCTCATTCTCAAAGTGAACCAGATTGGTTCTATGGCCGAGTC
TATATAGGCAAGTAAGCTG

Alignment

ORF - retro_rnor_2228 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.91 %
• Parental protein coverage: 62.44 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  KVDKFMIELDGTENKSKFGANAILGVSLAVCKAGAA-EKGVPLYRHIADLAGNPDLVLPVPAFNVINGGS
          K.DK.M...D.TENKSKFG.N.ILGVSLAVCK.GA..E.GVPLY.HIADLAGNP...L.VPAFNVIN.GS
Retrocopy KIDKLMVAMDSTENKSKFGINTILGVSLAVCKTGAM>ERGVPLYYHIADLAGNPEVILIVPAFNVINCGS

Parental  HAGNKLAMQEFMILPVGASSFKEAMRIGAEVYHHLKGVIKAKYGKDATNVGDEGGFAPNILENNEALELL
          H..NKLAM.E.MILPV.A..F.EAM.I..EVYH.LK.VI..KY.KDA.N.GDE..F.PNILEN.E.LEL.
Retrocopy HPCNKLAMEEVMILPVWAYYFPEAMCIEVEVYHNLKNVINKKYQKDAINEGDEDRFVPNILENKEVLELM

Parental  KTAIQAAGYPDKVVIGMDVAASEFYRNGKYDLDFKSPDD-PA-RHISGEKLGELYKSFIKNYPVVSIEDP
          KTAI..A.Y.D.V.I.MDVAASEF.R.GKYDLDFKS..D.PA...I....L..LYKS.I..YPVVSIE..
Retrocopy KTAIAKAVYTDQVFISMDVAASEF*RSGKYDLDFKS*ND>PAGTSITPDQLVALYKSSIQEYPVVSIENL

Parental  FDQDDWA-TWTSFLSGVDIQIVGDDLTVTNPKRIAQAVEKKACNCLLLKVNQIGSVTESIQACKL
          FDQ.DW..TW........IQ.VGDDLTVTNP..IA.AV.K..CNCL.LKVNQIGS..ESI.A.KL
Retrocopy FDQEDWG>TWQKYTASAGIQVVGDDLTVTNPT*IAKAVGKNSCNCLILKVNQIGSMAESI*ASKL

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	5.61 RPM
SRP017611_kidney	0.00 RPM	2.93 RPM
SRP017611_liver	0.00 RPM	2.49 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2228 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2228 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2228 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 43 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000011679	2 retrocopies	retro_cjac_115, retro_cjac_177,
Dasypus novemcinctus	ENSDNOG00000011654	2 retrocopies	retro_dnov_1712, retro_dnov_75,
Macropus eugenii	ENSMEUG00000007915	25 retrocopies	retro_meug_1019, retro_meug_1341, retro_meug_1483, retro_meug_1540, retro_meug_1566, retro_meug_1605, retro_meug_170, retro_meug_1701, retro_meug_1743, retro_meug_1869, retro_meug_1905, retro_meug_1929, retro_meug_2026, retro_meug_2190, retro_meug_235, retro_meug_269, retro_meug_578, retro_meug_607, retro_meug_637, retro_meug_803, retro_meug_820, retro_meug_906, retro_meug_965, retro_meug_973, retro_meug_976,
Rattus norvegicus	ENSRNOG00000004078	1 retrocopy	retro_rnor_2228 ,
Rattus norvegicus	ENSRNOG00000017895	1 retrocopy	retro_rnor_112,
Tupaia belangeri	ENSTBEG00000002346	5 retrocopies	retro_tbel_1514, retro_tbel_3080, retro_tbel_3130, retro_tbel_4230, retro_tbel_4383,
Tarsius syrichta	ENSTSYG00000007066	7 retrocopies	retro_tsyr_1019, retro_tsyr_1157, retro_tsyr_1626, retro_tsyr_1917, retro_tsyr_2043, retro_tsyr_52, retro_tsyr_534,