RetrogeneDB ID: retro_mmur_800

Retrocopy location

• Organism: Mouse Lemur (Microcebus murinus)
• Coordinates: GeneScaffold_976:108817..109272(-)
• Located in intron of: ENSMICG00000004206

Retrocopy information

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

Parental gene information

• Parental gene symbol: LIN28B
• Ensembl ID: ENSMICG00000002297
• Aliases: None
• Description: lin-28 homolog B (C. elegans) [Source:HGNC Symbol;Acc:32207]

Sequence

>retro_mmur_800
GCTGCTGACGAGCCGCAGTTGCTCCATGGTGCCGGCATCTGTAAGTGGTTCAACGTGCGCATGGGGTTCGGCTTCCTGTC
CATGACTGCGGCGCCGGGGTCGCCCTCGACCCCCTTGTGGACGTCTTTGTGCACCAGAGTAAGCTGCACATGGAAGGCTT
CCGGAGCCTGAAGGAGGGTGAGGCAGTTGAGTTCACCTTTAAGAAGTCTGCCAAGGGCCTGGAATCTATCCGAGTCACTG
GACCTGGTGGGGTGTTCTGTATCGGGAGTGAGAGGCTGCCAAAGGGGAAGAACATGCAGAATCGCAGATCAAAAGGAGAC
AGGTGCTACAACTGTGGAGGTCTAGACCATCATGCTAAGGAATGCAAGCTGCCACCCCAGCCCAAGAAGTGCCACTTCTG
CCAGAGCATCAGCCACATGGTAGCCTCGTGTCCACTGAAGGCCCAGCAGGCCCCT

Alignment

ORF - retro_mmur_800 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.12 %
• Parental protein coverage: 61.79 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  AEEESQVLHGTGHCKWFNVRMGFGFISMINREGSP-LDIPVDVFVHQSKLFMEGFRSLKEGEPVEFTFKK
          A..E.Q.LHG.G.CKWFNVRMGFGF.SM....GSP.LD..VDVFVHQSKL.MEGFRSLKEGE.VEFTFKK
Retrocopy AADEPQLLHGAGICKWFNVRMGFGFLSMTAAPGSP<LDPLVDVFVHQSKLHMEGFRSLKEGEAVEFTFKK

Parental  SSKGLESIRVTGPGGSPCLGSERRPKGKTLQKRKPKGDRCYNCGGLDHHAKECSLPPQPKKCHYCQSITH
          S.KGLESIRVTGPGG..C.GSER.PKGK..Q.R..KGDRCYNCGGLDHHAKEC.LPPQPKKCH.CQSI.H
Retrocopy SAKGLESIRVTGPGGVFCIGSERLPKGKNMQNRRSKGDRCYNCGGLDHHAKECKLPPQPKKCHFCQSISH

Parental  MVANCPHKTVAQP
          MVA.CP.K....P
Retrocopy MVASCPLKAQQAP

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_800 retrocopy.

TSS

Microcebus murinus was not studied using FANTOM5 data.

Lab

retro_mmur_800 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.

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Echinops telfairi	ENSETEG00000015340	1 retrocopy	retro_etel_1927,
Microcebus murinus	ENSMICG00000002297	4 retrocopies	retro_mmur_1377, retro_mmur_1390, retro_mmur_660, retro_mmur_800 ,
Oryctolagus cuniculus	ENSOCUG00000017850	1 retrocopy	retro_ocun_532,
Otolemur garnettii	ENSOGAG00000011042	1 retrocopy	retro_ogar_645,
Sorex araneus	ENSSARG00000008374	2 retrocopies	retro_sara_121, retro_sara_746,
Tarsius syrichta	ENSTSYG00000006480	1 retrocopy	retro_tsyr_1815,