RetrogeneDB ID: retro_rnor_499

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 1:172918509..172919295(+)
• 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_499
TCAAAGTCCAAGATGGCAACCCTCAAGAATCTTCTTAAGGAAGAACAGGTCCCCCAGAACAAGATTACAGTTGTTGGGGT
TGGTGCAGTTGGCATGGCTGTGCCATCCGTATCTTAATGAAGGACTTGGCCGATGAGCTTGCCCTTGTTGATGTCATGGA
AGACAAGCTAAAGGGAGAGATGATGGCTCTCCAGCATGGCAGCCTTTTCCTTGAAACACCAAAAATAGTCTCCAGCAAAG
ACTATAGAGTGACTGCAAACTCCACGCTGGTCATTATCACGGCGGGGGCTGGTCAGCAAGAGGGAGAGAGCCGACTTGAT
TTGGTCCAGCGAAACGTGAACATCTTCAGGTTCATAGTTCTGAACATTGTGAAGTAGAGTTCACACTTCAAGCTGCTCAT
TGTCTCAAATCCAGTGGGAATCTTAACCTACGTGGTTTGGCAAATCAACGGCTTTCCCCAAAGCAGAGTTATTGGAAGTG
GTTGCGGTCTGGACTCAGCTCGGTTCGGTTACCTGAGAAAGGCTGGGGGTTCGAGTGCTGAACTGTCACGGGTGGGTCCT
GGGAGAGCATGGCGACTCCAGTGTGCCTGTGTGGAGTGGTGTGAACATTGGCGGCGTCTCCCTGAAATCTCTGAACCCAG
AGCTGGGCACGGATGCAGATACGGGGCAGTGGAAGGATGTTCACAGGCAGGTGGTTGACAGTGCATATGAGGTGATCAAA
CTGAAAGGTTGCACATCCTGGGCCATTGACCTCTCGGTGGCAGACTTGGCCGAGAGCATAATGAAG

Alignment

ORF - retro_rnor_499 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.04 %
• Parental protein coverage: 79.52 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  STVKEQLIQNLAPDEKQSRCKITVVGVGNVGMA-CAISILLKGLADELALVDADENKLKGEALDLLHGSL
          S..K.....NL...E.....KITVVGVG.VGMA.CAI.IL.K.LADELALVD..E.KLKGE...L.HGSL
Retrocopy SKSKMATLKNLLKEEQVPQNKITVVGVGAVGMA<CAIRILMKDLADELALVDVMEDKLKGEMMALQHGSL

Parental  FLSTPKIVFGKDYSVSANSKLVIITAGARMVSGESRLALLQRNVTIMKAIVPGVIQNSPDCKIMIVTNPV
          FL.TPKIV..KDY.V.ANS.LVIITAGA....GESRL.L.QRNV.I...IV......S...K..IV.NPV
Retrocopy FLETPKIVSSKDYRVTANSTLVIITAGAGQQEGESRLDLVQRNVNIFRFIVLNIVK*SSHFKLLIVSNPV

Parental  DILTYVVWKISGLPVSSVIGSGCNLDSARFRYLIGEKLG-VNPSSCHGWVLGEHGDSSVPIWSGVNIAGV
          .ILTYVVW.I.G.P.S.VIGSGC.LDSARF.YL...K.G.V....CHGWVLGEHGDSSVP.WSGVNI.GV
Retrocopy GILTYVVWQINGFPQSRVIGSGCGLDSARFGYL--RKAG>VRVLNCHGWVLGEHGDSSVPVWSGVNIGGV

Parental  TLKSLNPAIGSDSDKEQWKTVHKQVVDGGYEVLNLKGYTSWAIALSVTDIAASILK
          .LKSLNP..G.D.D..QWK.VH.QVVD..YEV..LKG.TSWAI.LSV.D.A.SI.K
Retrocopy SLKSLNPELGTDADTGQWKDVHRQVVDSAYEVIKLKGCTSWAIDLSVADLAESIMK

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_499 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_499 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_499 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,