RetrogeneDB ID: retro_rnor_2081

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 4:176197337..176198325(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Ldhc
• Ensembl ID: ENSRNOG00000013103
• Aliases: Ldhc, Ldh3
• Description: L-lactate dehydrogenase C chain [Source:RefSeq peptide;Acc:NP_058962]

Sequence

>retro_rnor_2081
TCAACCCTCAAGGACCAGCTAATTGTAAATCTTCTTAAGGAGAAACAGGTCCCCCAGAACAAGACTGCAGTTGTTGGGGT
CGGTGCTTTTGACATGGCTAGTGCCATCAGTATCTTAATGAAGGATTTGTCATATGAGCTTGCCTTTGTTGATGTCATGG
AAGAGAAGCTGAAGGGAGAGATGATAAATCTCCAGCATGGCAACCTTTTCCTTAAAACACCAAATATTGTCTTTAGCAAA
GACTATACTGTGACTGCAAACTCCAAGCTGGTCATTATCATAACCGGGGCCCGTCAGCAAGAGGGAGAGAGCTAACTCAA
TTTGGTCCAGCAAAACATGAACCCCATCTTCAAGTTCATCATTCCCTACATTGTGAATGCTCACATTGCAAGTTGTTCAT
TGTCTCAAAGCCAGTGGATATCTTGACCTACAAGGTTTGGAAAATCAACGTCTTTCCCAAAAGCAGAGTTATTGGAAGTG
GTTGCAATCTGGATTCAGCTTGGTTCCATTACCTGATGGGAGAAAGGCTGGGAGTTCACCCAATGAACTGTCATGGGTGG
GTCCTAGGAGAGCCTGGTGATTCCAGTGTGCCTGTGTGGAGTAGTGTAAACATCGCTGGCATCTCCCTAAAGTCTCTGAA
CTCAGAACTGGGCACAGATACAGACAAGGAGTAGTGGAAGGATGTTCACAAGCATGTATTGACAGTGCATACGAGGTGAT
CAAGCTGAAAGTTTACACGTCCTAGGCCATTGACCTCTCTTTGGCACACTTGGCTGAGAGCATAATGAAGAACCTTAGGC
GGGGGCATCCCATTTCCATCATGACTAAGGGTCTCTATGGAATCAAAGATGATGTCTTCCTCATTGCCCCTTGTATCAAT
GGACAAAATAGAATCTCCGATATTGTGAAGGTGACACTGACTCCTGAGGAGGAGGCCCGACTGAAGAAGAGTGCAGATAC
CCTCTGGGGAATCCAGAAGGAGTTGCAA

Alignment

ORF - retro_rnor_2081 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.34 %
• Parental protein coverage: 99.4 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  STVKEQLIQNLAPDEKQSRCKITVVGVGNVGMACAISILLKGLADELALVDADENKLKGEALDLLHGSLF
          ST.K.QLI.NL.........K..VVGVG...MA.AISIL.K.L..ELA.VD..E.KLKGE...L.HG.LF
Retrocopy STLKDQLIVNLLKEKQVPQNKTAVVGVGAFDMASAISILMKDLSYELAFVDVMEEKLKGEMINLQHGNLF

Parental  LSTPKIVFGKDYSVSANSKLVIITAGARMVSGESRLALLQRNVTIMKAIVPGVIQNS-PDCKIMIVTNPV
          L.TP.IVF.KDY.V.ANSKLVII..GAR...GES.L.L.Q.N...........I.N....CK..IV..PV
Retrocopy LKTPNIVFSKDYTVTANSKLVIIITGARQQEGES*LNLVQQNMNPIFKFIIPYIVNA<SHCKLFIVSKPV

Parental  DILTYVVWKISGLPVSSVIGSGCNLDSARFRYLIGEKLGVNPSSCHGWVLGEHGDSSVPIWSGVNIAGVT
          DILTY.VWKI...P.S.VIGSGCNLDSA.F.YL.GE.LGV.P..CHGWVLGE.GDSSVP.WS.VNIAG..
Retrocopy DILTYKVWKINVFPKSRVIGSGCNLDSAWFHYLMGERLGVHPMNCHGWVLGEPGDSSVPVWSSVNIAGIS

Parental  LKSLNPAIGSDSDKEQWKTVHKQV-VDGGYEVLNLKGYTSWAIALSVTDIAASILKNLKRVHAVTTLVKG
          LKSLN...G.D.DKE.WK.VHK.V..D..YEV..LK.YTS.AI.LS....A.SI.KNL.R.H......KG
Retrocopy LKSLNSELGTDTDKE*WKDVHKHV<IDSAYEVIKLKVYTS*AIDLSLAHLAESIMKNLRRGHPISIMTKG

Parental  LYGIKEEIFLSIPCVLGQSGITDLVKVNMNTEEEALFKKSCDILWNIQKDLQ
          LYGIK...FL..PC..GQ..I.D.VKV....EEEA..KKS.D.LW.IQK.LQ
Retrocopy LYGIKDDVFLIAPCINGQNRISDIVKVTLTPEEEARLKKSADTLWGIQKELQ

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	0.00 RPM
SRP017611_kidney	0.00 RPM	1.05 RPM
SRP017611_liver	0.00 RPM	0.07 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2081 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2081 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2081 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 50 retrocopies.

Species	Parental gene accession	Retrocopies number
Rattus norvegicus	ENSRNOG00000013000	3 retrocopies	retro_rnor_2697, retro_rnor_2749, retro_rnor_2834,
Rattus norvegicus	ENSRNOG00000013009	17 retrocopies	retro_rnor_1131, retro_rnor_1336, retro_rnor_1738, retro_rnor_1769, retro_rnor_1881, retro_rnor_2146, retro_rnor_2377, retro_rnor_2560, retro_rnor_2830, retro_rnor_2950, retro_rnor_2957, retro_rnor_2984, retro_rnor_490, retro_rnor_491, retro_rnor_563, retro_rnor_578, retro_rnor_843,
Rattus norvegicus	ENSRNOG00000013103	2 retrocopies	retro_rnor_2081 , retro_rnor_499,
Tupaia belangeri	ENSTBEG00000011741	24 retrocopies	retro_tbel_1130, retro_tbel_1300, retro_tbel_1344, retro_tbel_1657, retro_tbel_2072, retro_tbel_2125, retro_tbel_2227, retro_tbel_2254, retro_tbel_2367, retro_tbel_2433, retro_tbel_2640, retro_tbel_2775, retro_tbel_2859, retro_tbel_2877, retro_tbel_2960, retro_tbel_3042, retro_tbel_3188, retro_tbel_3468, retro_tbel_3683, retro_tbel_4189, retro_tbel_4323, retro_tbel_4557, retro_tbel_499, retro_tbel_676,
Tarsius syrichta	ENSTSYG00000008062	4 retrocopies	retro_tsyr_1811, retro_tsyr_2064, retro_tsyr_2071, retro_tsyr_731,