RetrogeneDB ID: retro_mmus_335

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 1:73512045..73512981(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Ldhb
• Ensembl ID: ENSMUSG00000030246
• Aliases: Ldhb, AI790582, H-Ldh, LDH-B, LDH-H, Ldh-2, Ldh2
• Description: lactate dehydrogenase B [Source:MGI Symbol;Acc:MGI:96763]

Sequence

>retro_mmus_335
CAAGAAAAGCTCATCGCCCCTGTTGCGGAAGAGGAGGCAGCCACGCCACACAATAAGTTCACCACGGGGGCAGGTTTTCA
GACAAGTTGGTATGGCATATGCTACCAGCATTCTGGGCAACTCTCTGGCTAATGAACTTGCCCTTGTAGACATCTTAGAA
GACAAACTCAAAGGAGGAATGCTGAATCAGCAGCATGGGGGCTTCTTTTTTCATGTCCATAAAACTGTGGCAATAAAGAT
CACTCTGAGATAGCCAATTCATCGGTGGTGGTGCTGGTTGAAGGAATCCACCACCAGAAGGAAAAGGTTCACTCAACCAG
TACAAAGAAAGCCAGTGTGTTCAAGTCCAGTTTTCCTCAGACCATCCAGTACAGCTCTGACTGCACCATCACTATGGTTT
CTAACTCAGTGGATAATCCTACTTAGATGACCTGAAAACCCAGTGTGTTACCTAAAGGCCATGTGATTAGAAGTGTCTGC
AATCTGGGTTCTGCGAAGTTTTGGTATGTGGTGGCTGAGAAAGTTGCCCTTCATCCCCGTGGCTGTCAGGGGTGGATTCT
GGGAGAATATGGTGACTCCAGTGTGACTGTGTGGAGTAGAGTAAAGATGGTAGGCATTTCTCTCCAGGAATTGAACCCAG
AAATGGAAATGGACAGTCAGAGAGAGCCGGAAGGAAGTGTATGATATGGTGGTGGAAAGTGCCTATGAAATAATTAAACT
AAAAAGATATGCCACTATGTTGTTGGGTTATATGTGGCTGTCTTCCCTAAATCCATGCTGGAAAACCCACCTTGGATTCA
GCCCATGTCGTCAACAGCGGTGAAGGAAACACACAGCACTGAGAACAAAGTCTTCCTCAGTCTCCCAGAATTCTTGGTTT
TCAAAGATTAACCAGCACCATCAAACCAGACACTGAAGGTTGTCAAGGTTGCAGAA

Alignment

ORF - retro_mmus_335 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.01 %
• Parental protein coverage: 93.41 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 10

Retrocopy - Parental Gene Alignment:

Parental  KEKLIASVAD-DEAAVPNNKITVVGVG-QVGMACAISILGKSLADELALVDVLEDKLKGEMMDLQHGSLF
          .EKLIA.VA....A...N...T..G...QVGMA.A.SILG.SLA.ELALVD.LEDKLKG.M...QHG..F
Retrocopy QEKLIAPVAEEEAATPHNKFTTGAGFQ>QVGMAYATSILGNSLANELALVDILEDKLKGGMLNQQHGGFF

Parental  LQTPKIVA-DKDYSVTANSKIVVVTAGVRQQ-EGESRLNL-VQRN-VNVFKFIIPQIVKYSPDCTIIVVS
          ....K.VA..KD.S..ANS..VV...G...Q.EG...LN..VQR....VFK...PQ...YS.DCTI..VS
Retrocopy FHVHKTVA<NKDHSEIANSSVVVLVEGIHHQ<EGKGSLNQ<VQRK<ASVFKSSFPQTIQYSSDCTITMVS

Parental  NPVDILTYVTWKLSGLPKHRVIGSGCNLDSARFRYLMAEKLGIHPSSCHGWILGEHGDSSVAVWSGVNVA
          N.VD..T..T.K.S.LPK..VI.S.CNL.SA.F.Y..AEK...HP..C.GWILGE.GDSSV.VWS.V...
Retrocopy NSVDNPT*MT*KPSVLPKGHVIRSVCNLGSAKFWYVVAEKVALHPRGCQGWILGEYGDSSVTVWSRVKMV

Parental  GVSLQELN-PEMGTDNDS-ENWKEVHKMVVDSAYEVIKLKGYT-NWAIGLSVADLIESMLKNLSRIHPVS
          G.SLQELN.P..G......E..KEV..MVV.SAYE.IKLK.Y......GL.VA....SML.N...I.P.S
Retrocopy GISLQELN<PRNGNGQSE<ESRKEVYDMVVESAYEIIKLKRYA<HYVVGLYVAVFPKSMLENPPWIQPMS

Parental  -TMVKGMYGIENEVFLSLP-CILNARGLTSVI-NQKLKDDEVAQ
          .T.VK.....EN.VFLSLP..IL....LTS.I.NQ.LK...VA.
Retrocopy STAVKETHSTENKVFLSLP<RILGFQRLTSTI>NQTLKVVKVAE

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
SRP007412_brain	0.00 RPM	323.16 RPM
SRP007412_cerebellum	0.00 RPM	420.62 RPM
SRP007412_heart	0.00 RPM	1199.98 RPM
SRP007412_kidney	0.02 RPM	997.84 RPM
SRP007412_liver	0.00 RPM	2.65 RPM
SRP007412_testis	0.00 RPM	63.67 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_335 was not detected

EST

No EST(s) were mapped for retro_mmus_335 retrocopy.

TSS

No TSS is located nearby retro_mmus_335 retrocopy 5' end.

Lab

retro_mmus_335 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_335 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Rattus norvegicus	retro_rnor_2697

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Parental genes homology:

Parental genes homology involve 19 parental genes, and 66 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 ,
Mus musculus	ENSMUSG00000043262	1 retrocopy	retro_mmus_907,
Mus musculus	ENSMUSG00000063229	14 retrocopies	retro_mmus_1044, retro_mmus_1300, retro_mmus_1514, retro_mmus_1608, retro_mmus_1753, retro_mmus_1887, retro_mmus_1889, retro_mmus_1925, retro_mmus_2078, retro_mmus_2592, retro_mmus_2885, retro_mmus_3150, retro_mmus_3694, retro_mmus_497,
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,
Sus scrofa	ENSSSCG00000000576	1 retrocopy	retro_sscr_37,