RetrogeneDB ID: retro_rnor_2749

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: AABR06109393.1:11004..11711(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Ldhb
• Ensembl ID: ENSRNOG00000013000
• Aliases: Ldhb, Ldh2
• Description: L-lactate dehydrogenase B chain [Source:UniProtKB/Swiss-Prot;Acc:P42123]

Sequence

>retro_rnor_2749
TATGCAAAGACTGCAAACTCCAAACTAGTCATTATCACAGCACAGGCCTGTCAGCAAGAGGGAGATAACCAATTTAATTT
GGTCCAGCAAAACATGAACATCTTAAATTTTATCATTACCAACATTGTGAACAAGAGTTCATACTGCAAGCTGCTTAATG
GCTCAAATCCAGTGGATATCTGGACCTACATAGCTTAGAATATTAATGTTTTCCCAAAAGCTGAGTTATTGGAAGTGGTT
GCAATCTGGATTCAGCTAAACACTGTTACCCGAGAAAGGCTGGGTGTTTGCCTACTGAGCTTACATTAGTGGGTCCTGAG
AGAGTGTGGTGACTCCAGTGCACTAAAGTGTAGTTGTGTGAATGTTGCTGGCGTCTCCCTGAAGTCTCTGAACCCAGAAA
TGAGCACTGATCGAGAAACAGAAAAGTGGAATGATGTTTACAAGGTAGTTTACAGTGAATATGAGGTCATTGAGCTGAAA
GGTTACACATCATGGGCCATTGACCGCTCTGTGACAGACTTGGCTGAGCATGTGATGAAGAACCTTAGGTGGTTGCATCT
CATTTCCACCAAAATAATGCTCTATATATAATCAGTGAAGATGTCTTCCTCAGTGTTCCACATATCTGGGAACAAAATGG
AATCTCAAATGTTGTGAAAGTGATACTGACTCCTAAGGAAGAAGCCCACCTGAAAAAGAGTAGAGAT

Alignment

ORF - retro_rnor_2749 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 50.83 %
• Parental protein coverage: 71.56 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  YSVTANSKIVVVTAGVRQQEGESRLNLVQRNVNVFKFIIPQIVKYSPDCTIIVVSNPVDILTYVTWKLSG
          Y..TANSK.V..TA...QQEG....NLVQ.N.N...FII..IV..S..C.....SNPVDI.TY.......
Retrocopy YAKTANSKLVIITAQACQQEGDNQFNLVQQNMNILNFIITNIVNKSSYCKLLNGSNPVDIWTYIA*NINV

Parental  LPKHR-VIGSGCNLDSARFRYLMAEKLGIHPS-SCHGWILGEHGDSSVAVWSGVNVAGVSLQELNPEMGT
          .PK...VIGSGCNLDSA...Y....K.G..P..S.H.W.L.E.GDSS....S.VNVAGVSL..LNPEM.T
Retrocopy FPKAE<VIGSGCNLDSAKHCY--PRKAGCLPT>SLH*WVLRECGDSSALKCSCVNVAGVSLKSLNPEMST

Parental  DNDSENWKEVHKMVVDSAYEVIKLKGYTNWAIGLSVADLIESMLKNLSRIHPVSTMV-KGMYGIENEVFL
          D...E.W..V.K.VV.S.YEVI.LKGYT.WAI..SV.DL.E...KNL...H..ST......Y.I...VFL
Retrocopy DRETEKWNDVYK-VVYSEYEVIELKGYTSWAIDRSVTDLAEHVMKNLRWLHLISTKI<NALYIISEDVFL

Parental  SLPCILNARGLTSVINQKLKDDEVAQLRKSAD
          S.P.I....G...V....L...E.A.L.KS.D
Retrocopy SVPHIWEQNGISNVVKVILTPKEEAHLKKSRD

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	330.44 RPM
SRP017611_kidney	0.00 RPM	514.78 RPM
SRP017611_liver	0.00 RPM	1.61 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2749 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2749 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2749 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 19 parental genes, and 70 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016175	4 retrocopies	retro_amel_1316, retro_amel_814, retro_amel_882, retro_amel_977,
Canis familiaris	ENSCAFG00000012195	9 retrocopies	retro_cfam_1068, retro_cfam_111, retro_cfam_1674, retro_cfam_17, retro_cfam_1700, retro_cfam_174, retro_cfam_1836, retro_cfam_701, retro_cfam_93,
Cavia porcellus	ENSCPOG00000007138	1 retrocopy	retro_cpor_762,
Dasypus novemcinctus	ENSDNOG00000013620	4 retrocopies	retro_dnov_1161, retro_dnov_1511, retro_dnov_1570, retro_dnov_529,
Felis catus	ENSFCAG00000012639	1 retrocopy	retro_fcat_462,
Gorilla gorilla	ENSGGOG00000015758	1 retrocopy	retro_ggor_3033,
Loxodonta africana	ENSLAFG00000000972	2 retrocopies	retro_lafr_197, retro_lafr_315,
Macropus eugenii	ENSMEUG00000004825	1 retrocopy	retro_meug_311,
Microcebus murinus	ENSMICG00000017183	2 retrocopies	retro_mmur_275, retro_mmur_300,
Myotis lucifugus	ENSMLUG00000012155	1 retrocopy	retro_mluc_202,
Macaca mulatta	ENSMMUG00000002679	4 retrocopies	retro_mmul_212, retro_mmul_303, retro_mmul_308, retro_mmul_315,
Monodelphis domestica	ENSMODG00000017786	1 retrocopy	retro_mdom_1484,
Mus musculus	ENSMUSG00000030246	4 retrocopies	retro_mmus_1817, retro_mmus_2035, retro_mmus_2509, retro_mmus_335,
Otolemur garnettii	ENSOGAG00000004763	9 retrocopies	retro_ogar_1469, retro_ogar_2093, retro_ogar_2344, retro_ogar_2459, retro_ogar_3288, retro_ogar_3342, retro_ogar_3383, retro_ogar_689, retro_ogar_721,
Pteropus vampyrus	ENSPVAG00000002462	3 retrocopies	retro_pvam_1487, retro_pvam_320, retro_pvam_673,
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,
Sus scrofa	ENSSSCG00000000576	1 retrocopy	retro_sscr_37,