RetrogeneDB ID: retro_mmus_2035

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 2:59398997..59399679(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000080982
• Aliases: None
• Status: KNOWN_PSEUDOGENE

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_2035
GGGGGCCGTCAGCAAGAGGGAGAGAGCCGACTCAATATGGTCCAGCGAAATGTGAACATCTTCAAGTTCACCATTCCAAA
CTCTGTGAAGTACAGTCCACACTGCAAGCTGCTGATTGTCTCAAATTCAGTGGATATCTTGACCTATGTGGCTTGGAAAA
CCAGTGGCTTTCCCAAAAGCCAAGTTATCGGAAGTGGTTGCCATCTGGATTCAGCTCAGTTCCATTACCTGATGGGAGAA
AGGCTGGGGGTTCACCCTGAGCTGTCACGGCTGGGTCCTGGGAGAACATGGCGACTCCAGTGTGCCTGTGTGGAGTGGTG
TGAATGTTGTCTGCATCTCCCTGAAGTCTCTGAACCCAGAACTGGGCACTGATGCAGACAAGGAGCAGTGGAAGGAGGTT
CACAAGCAGGTGGTGGGCAGTGCATAGGAGGTGATCAAGCTGAGAGGTTACACATCCTGGGCCATTGGCCTCTCTGTGGC
AGACTTGGCCAAGAGCATAATGAAGAACCTTAGGTGGGTGCATCCCATTTCCACCATGATTAAGGGTCTCTATGGAATCA
ATGATGATGTCTTCCTCAGTGTCCCGTGTATCCTGGGACAAAATGGAATCTCAGATATTGTGAAGGTGACACTGACTCCT
GAGAAAGAGGCCCGCCTGAAGAAGAGTGCAGATACCCTTTTT

Alignment

ORF - retro_mmus_2035 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.96 %
• Parental protein coverage: 68.26 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  GVRQQEGESRLNLVQRNVNVFKFIIPQIVKYSPDCTIIVVSNPVDILTYVTWKLSGLPKHRVIGSGCNLD
          G.RQQEGESRLN.VQRNVN.FKF.IP..VKYSP.C....VSN.VDILTYV.WK.SG.PK..VIGSGC.LD
Retrocopy GGRQQEGESRLNMVQRNVNIFKFTIPNSVKYSPHCKLLIVSNSVDILTYVAWKTSGFPKSQVIGSGCHLD

Parental  SARFRYLMAE-KLGIHP-SSCHGWILGEHGDSSVAVWSGVNVAGVSLQELNPEMGTDNDSENWKEVHKMV
          SA.F.YLM.E.K.G..P..SCHGW.LGEHGDSSV.VWSGVNV...SL..LNPE.GTD.D.E.WKEVHK.V
Retrocopy SAQFHYLMGE<KAGGSP<LSCHGWVLGEHGDSSVPVWSGVNVVCISLKSLNPELGTDADKEQWKEVHKQV

Parental  VDSAYEVIKLKGYTNWAIGLSVADLIESMLKNLSRIHPVSTMVKGMYGIENEVFLSLPCILNARGLTSVI
          V.SA.EVIKL.GYT.WAIGLSVADL..S..KNL...HP.STM.KG.YGI...VFLS.PCIL...G.....
Retrocopy VGSA*EVIKLRGYTSWAIGLSVADLAKSIMKNLRWVHPISTMIKGLYGINDDVFLSVPCILGQNGISDIV

Parental  NQKLKDDEVAQLRKSADTLW
          ...L.....A.L.KSADTL.
Retrocopy KVTLTPEKEARLKKSADTLF

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	0.00 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 activity near the 5' end of retro_mmus_2035 was not detected

EST

No EST(s) were mapped for retro_mmus_2035 retrocopy.

TSS

No TSS is located nearby retro_mmus_2035 retrocopy 5' end.

Lab

retro_mmus_2035 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2035 has 0 orthologous retrocopies within eutheria group .

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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,