RetrogeneDB ID: retro_rnor_2979

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: X:126070229..126071717(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Fh
• Ensembl ID: ENSRNOG00000003653
• Aliases: Fh, Fh1
• Description: fumarate hydratase, mitochondrial precursor [Source:RefSeq peptide;Acc:NP_058701]

Sequence

>retro_rnor_2979
ATGAAACAGTCACTCTGACTCTTTGCATGCTCACCATTGTCTCCTATGGGCCCTGTCTTCCAGTGTTGCAGTGCCAGGAA
GGAAGCCAGACAACCAAGGTATCCTCTGAAAGTCGCACCAATAGCAAGCCAAAATTCCTTCTGTATAGAATAAGACACAT
TTGGTGAACTGAAGTTCCTAATCGGTAAGTATAATGTTGCTCAGACTGTGAGATCAATTATGAACTTCAAGATTGGAGGT
ACAGTTGAACATATGCCAATCCCAGTTGTTAAAGCTTTTGGCATCTTGATGGGAGCTGCTGCTGAAGTAAACCAGGATAT
GGTCTTGATCCAAAAATTACAATAATGAAGGCAGAAGATGAGGTAGCTGAAAGTAAACTAAATGATCACTTTCCTCTACT
GCTGTGACAGACTGGATCAGGAACCCAGACAAACATAGACGTAAATGCGGTTATTAGCAACAGAGCAATTGAAATGTTAG
AAGGGGAACTTGGCAACAAAAACACTTTGTACCCCAATGACCATGTTAATAAAAGCCAGAGCTAGAATAACACCTTTCCC
ACAGCAATGTACTTTGCGGCTGCAGTGCAAGTTCAGAAGGTTCTCTTGCCAGGACTACAGAAGCTGCATGATGCTTCCAA
TACAAAATCCAGACTTTGTGCAGGTCATCAAAAATGGGTGAATTCACATGCAGAAGGCTGTCCCACTCTAGGGCAGAAAT
TCAGTGGTTATGTTCATCAAGTCCAGTATGTGATGGTGAGAATAAAATCTACCTTGCTTAGAATCTCTGAGCTCGCTGCT
GGAGACATTGCCAATGGAACAGGATTAAACACCAGGATCTATTTCACAGAAAAAGTGGCTACAAAAGTAGCAGCACTCAC
GGATTTGCCTTTTGTCACAGCTCAGGATGAGTTTGATGCTCTGGCAGCTCATGATGCTCTGGTGGAATTTAGTGAACCAC
GAACAGTACCGCCTGTAGTCTGATGAAGATTTCAAGTATTATTGCCTTTCCTTGGTTCAGGTTTCAGAGAGCTGATCTTG
CCTGAGGGTGAGCCAAGGAACAGTAGCATGCCAGAAAAAGTGAACCTTACTCAGTGTGAAGTGATAACCATAGTTACAGC
CCAAGTCATGGAGAATCATGCTGCTCTTACTGTTGGAGGCAGCAATGGACATTTGGAACTGAATGTTTTTAAACCAATGA
TTAAGAATGTGTTGTACTCAGCTAGGCTGCTGGGGGTGCATCAGGGTCCTTTATAGAGAACTGTGTGAAGGGTATCCAGG
CCAACACAGAGAGAAGCAACAAGCTAATGAATGAGTCTTTGATGTTGGTCATAGTTCTTAATCTGCATAAAGAGTATGAC
AAAGCAGCGAAGTTTGCCAAGACCACATTCACGAAAGGATCAATCTTGAAGGAAATGGCTGTTGAACTCGGCTCTCTCAA
AGCAGAGCAGTTTGATGAGTGAATCCCAAGAACATGCTCAGTCCAAAG

Alignment

ORF - retro_rnor_2979 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.21 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  MNRAFCLLARSRRFPRVPSAGAVLSGEAATLPRCAPNVVRMASQNSFRIEYDTFGELKVPTDKYYGAQTV
          M.....L.A.S...P..P..........A..PR....V...ASQNSF.IE.DTFGELK....KY..AQTV
Retrocopy MKQSL*LFACSPLSPMGPVFQCCSARKEARQPRYPLKVAPIASQNSFCIE*DTFGELKFLIGKYNVAQTV

Parental  RSTMNFKIGGATERMPIPVIKAFGILKRAAAEVNQE-YGLDPKIASAIMKAADEVAEGKLNDHFPLVVWQ
          RS.MNFKIGG..E.MPIPV.KAFGIL..AAAEVNQ..YGLDPKI...IMKA.DEVAE.KLNDHFPL...Q
Retrocopy RSIMNFKIGGTVEHMPIPVVKAFGILMGAAAEVNQD<YGLDPKIT--IMKAEDEVAESKLNDHFPLLL*Q

Parental  TGSGTQTNMNVNEVISNRAIEMLGGELGSKKPVHPNDHVNKSQSSNDTFPTAMHIAAALEVHQVLLPGLQ
          TGSGTQTN..VN.VISNRAIEML.GELG.K....PNDHVNKSQS.N.TFPTAM..AAA..V..VLLPGLQ
Retrocopy TGSGTQTNIDVNAVISNRAIEMLEGELGNKNTLYPNDHVNKSQS*NNTFPTAMYFAAAVQVQKVLLPGLQ

Parental  KLHDALSAKSKEFAQVIKIGRTHTQDAVPLTLGQEFSGYVQQVQYAMERIKAAMPRIYELAAGGTAVGTG
          KLHDA...KS...A...K....H.......TLGQ.FSGYV.QVQY.M.RIK....RI.ELAAG..A.GTG
Retrocopy KLHDASNTKSRLCAGHQKWVNSHAEGCP--TLGQKFSGYVHQVQYVMVRIKSTLLRISELAAGDIANGTG

Parental  LNTRIGFAEKVAAKVAALTGLPFVTAPNKFEALAAHDALVELSG-AMNTTACSLMKIANDIR-FLGSGPR
          LNTRI.F.EKVA.KVAALT.LPFVTA...F.ALAAHDALVE.S....N.TACSLMKI...I..FLGSG.R
Retrocopy LNTRIYFTEKVATKVAALTDLPFVTAQDEFDALAAHDALVEFSE<TTNSTACSLMKISSIIA>FLGSGFR

Parental  SGLGELILPENEPGSSIMPGKVNPTQCEAMTMVAAQVMGNHVAVTVGGSNGHFELNVFKPMMIKNVLHSA
          ....ELILPE.EP..S.MP.KVN.TQCE..T.V.AQVM.NH.A.TVGGSNGH.ELNVFKP.MIKNVL.SA
Retrocopy ----ELILPEGEPRNSSMPEKVNLTQCEVITIVTAQVMENHAALTVGGSNGHLELNVFKP-MIKNVLYSA

Parental  RLL-GDASVSFTENCVVGIQANTERINKLMNESLMLVTALNPHIGYDKAAKIAKTAHKNGSTLKETAIEL
          RLL.G.AS.SF.ENCV.GIQANTER.NKLMNESLMLV..LN.H..YDKAAK.AKT....GS.LKE.A.EL
Retrocopy RLL<GGASGSFIENCVKGIQANTERSNKLMNESLMLVIVLNLHKEYDKAAKFAKTTFTKGSILKEMAVEL

Parental  GYLTAEQFDEWVKPK-DMLGPK
          G.L.AEQFDE...P...ML.PK
Retrocopy GSLKAEQFDE*I-PR<NMLSPK

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	43.50 RPM
SRP017611_kidney	0.00 RPM	187.50 RPM
SRP017611_liver	0.00 RPM	114.77 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2979 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2979 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2979 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Mus musculus	retro_mmus_3600

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000017359	1 retrocopy	retro_cjac_2339,
Echinops telfairi	ENSETEG00000018721	2 retrocopies	retro_etel_1069, retro_etel_1457,
Microcebus murinus	ENSMICG00000003451	2 retrocopies	retro_mmur_1215, retro_mmur_720,
Mus musculus	ENSMUSG00000026526	1 retrocopy	retro_mmus_3600,
Oryctolagus cuniculus	ENSOCUG00000021494	1 retrocopy	retro_ocun_50,
Otolemur garnettii	ENSOGAG00000009936	1 retrocopy	retro_ogar_322,
Rattus norvegicus	ENSRNOG00000003653	1 retrocopy	retro_rnor_2979 ,
Xenopus tropicalis	ENSXETG00000032112	1 retrocopy	retro_xtro_55,