RetrogeneDB ID: retro_ogar_3039

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873700.1:1809136..1809541(-)
• Located in intron of: ENSOGAG00000004278

Retrocopy information

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

Parental gene information

• Parental gene symbol: NSMCE2
• Ensembl ID: ENSOGAG00000015798
• Aliases: None
• Description: non-SMC element 2, MMS21 homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:26513]

Sequence

>retro_ogar_3039
TCCGATTCTAATTCAGATTCAACTGGTTTCATATCCTTCAGTGGTATAAAGTCTGCTGTCTCCTCCTTAAAAAACTTGTA
AGTATGTATCAACTCTGGGACAGACACCGAGTCTTGTGTTGCCTTGGATCTTGTGGAAATTCAAATAGAAGTGAATATGG
AATATACTATGGACAAGGCGATCACTGAGTTTGTCGTAATTCATCAGCAACTAAACCACTATGTAAACACTGTTCAATCA
GTGATAAATCATGTAAAAGAAGAACATCCAGAAAAAATACCAGATTTAAAAGTGTTGGTGGAGAAGATAATTTTGGCTCT
ACAGAACAAGAATTCTGATGCAGACTTTCCAAATAATGAACAACTTGTACAGTTTAAACAATAGCTGAAATAACTAAAGA
AGCAA

Alignment

ORF - retro_ogar_3039 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.81 %
• Parental protein coverage: 54.22 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SNSNSGSTGFISFSGVESALSSLKNFQACINSGMDTASSVALDLVETQTEVSSEYSMDKAMIEFAIMDRQ
          S.SNS.STGFISFSG..SA.SSLKN...CINSG.DT.S.VALDLVE.Q.EV..EY.MDKA..EF.....Q
Retrocopy SDSNSDSTGFISFSGIKSAVSSLKNL*VCINSGTDTESCVALDLVEIQIEVNMEYTMDKAITEFVVIHQQ

Parental  LNHYVKAVQSAINHVKEERPEKIPDLKVLVEKKFLALQNKNSDADFQNNEKFVQFKQQLKELKKQ
          LNHYV..VQS.INHVKEE.PEKIPDLKVLVEK..LALQNKNSDADF.NNE..VQFKQ.LK.LKKQ
Retrocopy LNHYVNTVQSVINHVKEEHPEKIPDLKVLVEKIILALQNKNSDADFPNNEQLVQFKQ*LK*LKKQ

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_3039 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 7 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000009394	1 retrocopy	retro_btau_669,
Echinops telfairi	ENSETEG00000019897	1 retrocopy	retro_etel_1348,
Macaca mulatta	ENSMMUG00000003542	1 retrocopy	retro_mmul_1641,
Mus musculus	ENSMUSG00000059586	3 retrocopies	retro_mmus_1189, retro_mmus_1190, retro_mmus_3227,
Otolemur garnettii	ENSOGAG00000015798	1 retrocopy	retro_ogar_3039 ,
Rattus norvegicus	ENSRNOG00000003964	2 retrocopies	retro_rnor_2118, retro_rnor_701,
Tupaia belangeri	ENSTBEG00000005371	1 retrocopy	retro_tbel_3224,