RetrogeneDB ID: retro_mmur_140

Retrocopy location

• Organism: Mouse Lemur (Microcebus murinus)
• Coordinates: GeneScaffold_1437:67136..67793(+)
• Located in intron of: ENSMICG00000004240

Retrocopy information

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

Parental gene information

• Parental gene symbol: PSMB6
• Ensembl ID: ENSMICG00000014854
• Aliases: None
• Description: proteasome (prosome, macropain) subunit, beta type, 6 [Source:HGNC Symbol;Acc:9543]

Sequence

>retro_mmur_140
ATGCCGTCCACCTTGGTAGCTGCTCAGGGAGTGGGGTCGGCATCAGGCCAGAGACCATCACTCCAGACTGGGAAAACTAC
TAAGTCTCCACGGGGACCACTATCATGGCCATCCAATTTGACGGGAGCGTGGTACTGGGGATGGATTCCAGAACCACCAC
TGAGTCTTACATTGCCAATCAAGTGACTGACAAGCTGACTCTTATTCATGACTGAATTTTCTGCTGCCGCTCAGGCTCAG
TAGCTGATACCCAAGCAGGAGCTGATTCTGTCACTTATCAGCTTGGCTTCCACAGCATTCAGCTGAATGAGCCTCTACTG
GTGCACACAGCAGCCAGCCTCTTTAAAGAAATGTGTTACCGATATCAGGAAAACCTTATGGTGGGAATTATTGTTGCTGG
CTGGGACCCTAAAGAAGGAGGGCAGGTGTATTCAGTGCCCATGGGGGGTATGATGGTAAGACAGTCCTTTGCCATGGGAG
GCTCCAGGAGCTCCTATATCTATGGCTATGTCAATGCTACCTACTGGGAAGGCATGACCAACAAAGAGTGTATACAATTC
ACTGCCAATGCTCTCGCTTTGGCCATGAGCGGATGGCCCCAGTGGAGGGGTGTTCCGCCTGGCAGCCACTGCAGAGTCAG
GGGTAGAGCAGCAGGTA

Alignment

ORF - retro_mmur_140 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.89 %
• Parental protein coverage: 92.89 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MAAALVAARGVGPAPAWG-PEAITPDWENREVSTGTTIMAVQFDGGVVLGADSRTTTGSYIANRVTDKLT
          M...LVAA...G...A.G.PE.ITPDWEN..VSTGTTIMA.QFDG.VVLG.DSRTTT.SYIAN.VTDKLT
Retrocopy MPSTLVAAQ--GVGSASG<PETITPDWENY*VSTGTTIMAIQFDGSVVLGMDSRTTTESYIANQVTDKLT

Parental  PIHDRIFCCRSGSAADTQAVADAVTYQLGFHSIELNEPPLVHTAASLFKEMCYRYREDLMAGIIVAGWDP
          .IHD.IFCCRSGS.ADTQA.AD.VTYQLGFHSI.LNEP.LVHTAASLFKEMCYRY.E.LM.GIIVAGWDP
Retrocopy LIHD*IFCCRSGSVADTQAGADSVTYQLGFHSIQLNEPLLVHTAASLFKEMCYRYQENLMVGIIVAGWDP

Parental  QEGGQVYSVPMGGMMVRQSFAIGGSGSSYIYGYVDATYREGMTKEECLQFTANALALAM-ER-DGSSGGV
          .EGGQVYSVPMGGMMVRQSFA.GGS.SSYIYGYV.ATY.EGMT..EC.QFTANALALAM.ER.DG.SGGV
Retrocopy KEGGQVYSVPMGGMMVRQSFAMGGSRSSYIYGYVNATYWEGMTNKECIQFTANALALAM<ER<DGPSGGV

Parental  IRLAAIAESGVERQV
          .RLAA.AESGVE.QV
Retrocopy FRLAATAESGVEQQV

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_140 retrocopy.

TSS

Microcebus murinus was not studied using FANTOM5 data.

Lab

retro_mmur_140 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 11 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016075	1 retrocopy	retro_amel_1834,
Canis familiaris	ENSCAFG00000015855	1 retrocopy	retro_cfam_2173,
Callithrix jacchus	ENSCJAG00000012010	1 retrocopy	retro_cjac_775,
Loxodonta africana	ENSLAFG00000012859	1 retrocopy	retro_lafr_874,
Macropus eugenii	ENSMEUG00000010676	1 retrocopy	retro_meug_621,
Microcebus murinus	ENSMICG00000014854	2 retrocopies	retro_mmur_140 , retro_mmur_718,
Monodelphis domestica	ENSMODG00000005554	1 retrocopy	retro_mdom_799,
Mus musculus	ENSMUSG00000018286	2 retrocopies	retro_mmus_348, retro_mmus_3569,
Rattus norvegicus	ENSRNOG00000019551	1 retrocopy	retro_rnor_56,
Sorex araneus	ENSSARG00000006615	1 retrocopy	retro_sara_689,
Tursiops truncatus	ENSTTRG00000000566	1 retrocopy	retro_ttru_405,