RetrogeneDB ID: retro_mmur_162

Retrocopy location

• Organism: Mouse Lemur (Microcebus murinus)
• Coordinates: GeneScaffold_1525:69769..70292(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SLC39A1
• Ensembl ID: ENSMICG00000010310
• Aliases: None
• Description: solute carrier family 39 (zinc transporter), member 1 [Source:HGNC Symbol;Acc:12876]

Sequence

>retro_mmur_162
ATGGGGCCCTGGGGAGGACCAGAGCTCCTGGGGGGATGCCCAGAGGTGGTAGCTTCAGAGCCCTAGTTTCTGTGGGGCTG
GAGGTGACCTTGGGGGCCCTCGTGCTGCTGCTGGTGCTCACCCTCCTCTGCAGTCTGGCGCCTGCGTGCTGCATCAGCTC
AGAGCCAACCACGAAGCATCTGCTTCCCTCCAGAAAGCCCTCAACCTAGTCAGCTGCTTTGCAGGGGGTGTCTTTTTGGC
CATGTATCTCCTGGACCTGTTGCCTGACTATCTGGTTGCCATGGATGAGGCTCTGGCAGCCCTGCATGTGATGCTCCAGT
TCCCCCTGCAAGAGTTCATCCTGGCCATGGGCTTTTTCCTGGTCCTGGTGATGGAGCAGAGCACACTGGCTTACAAGGAG
CAGTCAGGGTCACCACCTCTGGAGGAATAATGGCTCCACTGAGAACAGTGAACAGTGGGCCACAGCACTGGCAAGATGGG
CCAGGGGTCCCACAGGCAGAGGAGCCCCTCATCCCCTTCAGCG

Alignment

ORF - retro_mmur_162 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.18 %
• Parental protein coverage: 54.63 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  MGPWGEPELLVWRPEVVASEP-LVPVGLEVKLGALVLLLVLTLLCSLVP-ICVLRRPGANHEASAFRQKT
          MGPWG.PELL...PEVVASEP.LV.VGLEV.LGAL..LL....L.......CVL....ANHEASA..QK.
Retrocopy MGPWGGPELLGGCPEVVASEP<LVSVGLEVTLGAL-VLLLVLTLLCSLA<ACVLHQLRANHEASASLQKA

Parental  LNLVNCFAGGVFLATCLLDLLPDYLAAIDAALAALHVTLQFPLQEFILAMGFFLVLVMEQITLAYKEQSG
          LNLV.CFAGGVFLA..LLDLLPDYL.A.D.ALAALHV.LQFPLQEFILAMGFFLVLVMEQ.TLAYKEQSG
Retrocopy LNLVSCFAGGVFLAMYLLDLLPDYLVAMDEALAALHVMLQFPLQEFILAMGFFLVLVMEQSTLAYKEQSG

Parental  PPPLEE-TRALLGTVNGGPQHWHDGPGVPQA-GGAP-ASPSA
          .PPLEE...A.L.TVN.GPQHW.DGPGVPQA..GAP..SPSA
Retrocopy SPPLEE<IMAPLRTVNSGPQHWQDGPGVPQA<RGAP<SSPSA

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_162 retrocopy.

TSS

Microcebus murinus was not studied using FANTOM5 data.

Lab

retro_mmur_162 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 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000010006	1 retrocopy	retro_cjac_1476,
Macropus eugenii	ENSMEUG00000006754	1 retrocopy	retro_meug_1551,
Microcebus murinus	ENSMICG00000010310	1 retrocopy	retro_mmur_162 ,
Myotis lucifugus	ENSMLUG00000013282	1 retrocopy	retro_mluc_2366,
Macaca mulatta	ENSMMUG00000005007	1 retrocopy	retro_mmul_28,
Mus musculus	ENSMUSG00000052310	1 retrocopy	retro_mmus_1899,
Oryctolagus cuniculus	ENSOCUG00000003045	1 retrocopy	retro_ocun_1792,