RetrogeneDB ID: retro_ogar_3070

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873709.1:2032209..2032590(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMD
• Ensembl ID: ENSOGAG00000005902
• Aliases: None
• Description: monocyte to macrophage differentiation-associated [Source:HGNC Symbol;Acc:7153]

Sequence

>retro_ogar_3070
TTGTGCCCTCTTCATTATCTCTACAGTAAACGTGAAAATATTATATCATGGACAAAGAGCCACTTAAGGACAGTGGAGCT
TTGTTTCCACATGTGTGATATAATGGTTATCTATTTCTTCATTGCTGCTTCTTATGCTCCATGGTTAAATCTCCATGAAC
TTGGACCCCTGGCATCTCATATGCATTGGTTTACCTGGCTCCTGGCAACTGGAGTAACCATTCATGTATTTCTCTACCAT
TAAAAGTATAAAGTGGTTGAATTCTTTTTCCATCTCATGATGGGATTTTCTCCAGCCTTGGTGGTAACATCAATGAATAA
CACTGACGAACTTCATGAACTTGCCTGTGGAGGCTTCACAGGCTTAATTTATTGCCTAGGT

Alignment

ORF - retro_ogar_3070 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.95 %
• Parental protein coverage: 51.46 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LCAL-FIVSTVFHIVSWKKSHLRTVEHCFHMCDRMVIYFFIAASYAPWLNLRELGPLASHMRWFIWLMAA
          LC.L....S....I.SW.KSHLRTVE.CFHMCD.MVIYFFIAASYAPWLNL.ELGPLASHM.WF.WL.A.
Retrocopy LCPLHYLYSKRENIISWTKSHLRTVELCFHMCDIMVIYFFIAASYAPWLNLHELGPLASHMHWFTWLLAT

Parental  GGTIYVFLYHEKYKVVELFFYLTMGFSPALVVTSMNNTDGLHELACGG---LIYCLG
          G.TI.VFLYH.KYKVVE.FF.L.MGFSPALVVTSMNNTD.LHELACGG...LIYCLG
Retrocopy GVTIHVFLYH*KYKVVEFFFHLMMGFSPALVVTSMNNTDELHELACGGFTGLIYCLG

Legend:

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

Expression

RNA-Seq

Otolemur garnettii was not studied using RNA-Seq expression data.

ChIP-Seq

Otolemur garnettii was not studied using ChIP-Seq data.

EST

Otolemur garnettii was not studied using EST data.

TSS

Otolemur garnettii was not studied using FANTOM5 data.

Lab

retro_ogar_3070 was not experimentally validated.

Homology

Retrocopy orthology:

Otolemur garnettii 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 11 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000000205	1 retrocopy	retro_btau_777,
Choloepus hoffmanni	ENSCHOG00000013437	1 retrocopy	retro_chof_1814,
Dasypus novemcinctus	ENSDNOG00000017248	1 retrocopy	retro_dnov_2313,
Macropus eugenii	ENSMEUG00000007054	1 retrocopy	retro_meug_714,
Myotis lucifugus	ENSMLUG00000012876	1 retrocopy	retro_mluc_289,
Monodelphis domestica	ENSMODG00000014847	5 retrocopies	retro_mdom_1029, retro_mdom_1569, retro_mdom_1591, retro_mdom_670, retro_mdom_951,
Oryctolagus cuniculus	ENSOCUG00000010549	1 retrocopy	retro_ocun_222,
Otolemur garnettii	ENSOGAG00000005902	2 retrocopies	retro_ogar_3070 , retro_ogar_3071,
Procavia capensis	ENSPCAG00000004969	1 retrocopy	retro_pcap_231,
Ictidomys tridecemlineatus	ENSSTOG00000016227	1 retrocopy	retro_itri_913,
Tursiops truncatus	ENSTTRG00000007915	1 retrocopy	retro_ttru_469,