RetrogeneDB ID: retro_mmur_1377

Retrocopy location

• Organism: Mouse Lemur (Microcebus murinus)
• Coordinates: scaffold_5129:74642..75105(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMICG00000013694
• Aliases: None
• Status: KNOWN_PSEUDOGENE

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_1377
GGCGGCGGAGGCGCAGGAGGACGCGCCCGGGCTGCGGACGAGTGGCAGTTGCTCCATGGTGCCGGCATCTGTAAGTGGTT
CAACGTGCGCATGGGGTTCGGCTTCCCGTCCATGGCCGCCCGCGGCCGGGTCGCCCTCGACCCCCTGCGGACGTCTTTGT
GCACCAGAGTAAGCTGCACATGGAAGGCTTCCGGAGCCTGAAGGAGGGTGAGGCAGTTGAGTTCAACTGGAATCTGTCCG
AGCCACTGGACCTGGTGGGGTGTTCTGTATCGGGAGTGAGAGGCGGCCAAAGGGGAAGAACATGCAGAAGCACAGATCAA
AAGGAGACAGGTGCTACGACTGTGGAGGTCTAGACCATCATGCTAAGGAATGCAAGCTGCCACCCCAGCCCAAGAAGTGC
CACTTCTGCCAGAGCATCAGCCACATGGTAGCCTCGTGTCCACTGAAGGCCCAGCAGGCCCCT

Alignment

ORF - retro_mmur_1377 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.04 %
• Parental protein coverage: 66.67 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  GGGEEPGKLPEPAEEESQVLHGTGHCKWFNVRMGFGFISMINREGSPLDI-PVDVFVHQSKLFMEGFRSL
          GGG...G.....A..E.Q.LHG.G.CKWFNVRMGFGF.SM..R....LD..P.DVFVHQSKL.MEGFRSL
Retrocopy GGGGAGGRAR--AADEWQLLHGAGICKWFNVRMGFGFPSMAARGRVALDP<PADVFVHQSKLHMEGFRSL

Parental  KEGEPVEFTFKKSSKGLESIRVTGPGGSPCLGSERRPKGKTLQKRKPK-GDRCYNCGGLDHHAKECSLPP
          KEGE.VEF....S....E.....G...S...G..R...G.T......K.GDRCY.CGGLDHHAKEC.LPP
Retrocopy KEGEAVEFNWNLS----EPLDLVGCSVSGVRGGQR---GRTCRSTDQK<GDRCYDCGGLDHHAKECKLPP

Parental  QPKKCHYCQSITHMVANCPHKTVAQP
          QPKKCH.CQSI.HMVA.CP.K....P
Retrocopy QPKKCHFCQSISHMVASCPLKAQQAP

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_1377 retrocopy.

TSS

Microcebus murinus was not studied using FANTOM5 data.

Lab

retro_mmur_1377 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,