RetrogeneDB ID: retro_mmur_275

Retrocopy location

• Organism: Mouse Lemur (Microcebus murinus)
• Coordinates: GeneScaffold_214:759457..760416(-)
• Located in intron of: ENSMICG00000008644

Retrocopy information

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

Parental gene information

• Parental gene symbol: LDHB
• Ensembl ID: ENSMICG00000017183
• Aliases: None
• Description: lactate dehydrogenase B [Source:HGNC Symbol;Acc:6541]

Sequence

>retro_mmur_275
AGCTCGCGCGAGGACCCGGTTCGCAACAACAAGGTCTCATTATAGGCACTGGGTCGGTTGGCATGGCCTGTGCTATCAGC
ATCCTACTAAAAGGCTTGAGTGATGAACTTGCCCTTGTAGATCTTGATGAAGGCAGAATGAAGGGTGAGACGATGGATCT
TCAACATGGCAGCCCTTTCGTGAAAATGCCAACTATTGCTTGCAGCAAAGATTACAGTGTCACGGCATGCTCCAACCTAG
TGATTATCACAGCAGGTGCACGCCAAGAAAAGGGAGAAACACGCCTCAATTTAGTCCAGAGAAACGTGGCCATCTTCAAA
TCAATGATTTCCAGTATTATCCAGTACAGCCCCCACTGCAAGATGATTATTGTTTCAAATCCAGTGGATATCTTAACTTA
CGTAGCCTGGAAGTTGAGTACTTTTCCCAAAAACCGTGTTATTGGAAGTGGCTGTAATCTGGATACTGCTCGTTTTCGTT
TTTTGATTGGGCAAAAGCTTGGTATCCACTCTGAAAGCTGTCATGGATGGGTCCTTGGAGAGCATGGAGACTCAAGTGTT
CCTGTGTGGAGTGGAGTGAATATTGCTGGTGTCCCTTTGAAGAATCTGAATGCAGCCATAGGAACTGATAAAGACCCTGA
GCAATGGGGAAATGTCCACAAAGATGTGATTGCCAGTGCCTATGAGATTATTAAAATGAAAGGTTATACTAATTGGGCCA
TTGGCCTATCTGTAGCTGATTTAACAGAAAGTATTTTGAAGAATCTGAGGAGAACACATCCAGTTTCCACCATAATTAAG
GGCCTCTATGGAGTAAATGAAGAAGTATTCCTTAGTGTTCCTTGTATCCTGGGAGAGAATGGTATTACACACATTATAAA
AATAAAACTGACCCATGAAGAGGAAGCCCGTCTAACGAAGAGCGCAAAAACACTTTGGGAAATTCAGAAGGAGCTCAAA

Alignment

ORF - retro_mmur_275 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.42 %
• Parental protein coverage: 95.81 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  AEEEAAAPNNKIT-VGGVGQVGMACAISILGKSLADELALVDVLEDKLKGEMMDLQHGSLFLQTSKIVAD
          ...E....NNK.....G.G.VGMACAISIL.K.L.DELALVD..E...KGE.MDLQHGS.F.....I...
Retrocopy SSREDPVRNNKVS<IIGTGSVGMACAISILLKGLSDELALVDLDEGRMKGETMDLQHGSPFVKMPTIACS

Parental  KDYSVTANSKIVVVTAGVRQQEGESRLNLVQRNVNVFKFIIPQIVKYSPDCIIIVVSNPVDILTYVTWKL
          KDYSVTA.S..V..TAG.RQ..GE.RLNLVQRNV..FK..I..I..YSP.C..I.VSNPVDILTYV.WKL
Retrocopy KDYSVTACSNLVIITAGARQEKGETRLNLVQRNVAIFKSMISSIIQYSPHCKMIIVSNPVDILTYVAWKL

Parental  SGLPKHRVIGSGCNLDSARFRYLMAEKLGIHPSSCHGWILGEHGDSSVAVWSGVNVAGVSLQELNPEMGT
          S..PK.RVIGSGCNLD.ARFR.L...KLGIH..SCHGW.LGEHGDSSV.VWSGVN.AGV.L..LN...GT
Retrocopy STFPKNRVIGSGCNLDTARFRFLIGQKLGIHSESCHGWVLGEHGDSSVPVWSGVNIAGVPLKNLNAAIGT

Parental  DNDSENWKEVHKMVVESAYEVIKLKGYTNWAIGLSVADLIESMLKNLSRIHPVSTMVKGMYGIENEVFLS
          D.D.E.W..VHK.V..SAYE.IK.KGYTNWAIGLSVADL.ES.LKNL.R.HPVST..KG.YG...EVFLS
Retrocopy DKDPEQWGNVHKDVIASAYEIIKMKGYTNWAIGLSVADLTESILKNLRRTHPVSTIIKGLYGVNEEVFLS

Parental  LPCILNARGLTSVINQKLKDDEVAQLKKSADTLWDIQKDLK
          .PCIL...G.T..I..KL...E.A.L.KSA.TLW.IQK.LK
Retrocopy VPCILGENGITHIIKIKLTHEEEARLTKSAKTLWEIQKELK

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Microcebus murinus was not studied using RNA-Seq expression data.

ChIP-Seq

Microcebus murinus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmur_275 retrocopy.

TSS

Microcebus murinus was not studied using FANTOM5 data.

Lab

retro_mmur_275 was not experimentally validated.

Homology

Retrocopy orthology:

Microcebus murinus does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

---

Parental genes homology:

Parental genes homology involve 18 parental genes, and 52 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	ENSMICG00000003117	1 retrocopy	retro_mmur_1485,
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,
Sus scrofa	ENSSSCG00000000576	1 retrocopy	retro_sscr_37,