RetrogeneDB ID: retro_ogar_2263

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873607.1:8081479..8081895(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MRPL20
• Ensembl ID: ENSOGAG00000005968
• Aliases: None
• Description: mitochondrial ribosomal protein L20 [Source:HGNC Symbol;Acc:14478]

Sequence

>retro_ogar_2263
GTGTTCCTCATGATGCAACTCTAGCTGTGGAAATCACCTGACCTGTACTACTGGTGGGTCTAGAAGGTACTAAAGTAAGT
TTGGTACTTTGCGGGGAGGAAAAATCACTGTTATATGTTGGCTGTAACAGCTGTGCCTACACCCTCTGTGAAATGCACAA
AAGCCCAAAGACTGAAGATGAAGAACAATGAGGACACTCTGGATTAATCAAATTACAGGTGATTCTAGGAATAAGGCTAA
AAGAGTACCCAGTGTCCACTGTCAATCTAACTAAGTGCAAAGTGGAGATAACCAGGAAAGTACTTACAGTTCTAGCCATC
TATGAACCAAAGACTTCTAAATCCTTAGCTGCTCTGGTTAAGAGACAATGGTAAGAAAGATTTCCTGCTACCTTGGGGAA
TGGGAAGAATCCAGAG

Alignment

ORF - retro_ogar_2263 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.43 %
• Parental protein coverage: 92.62 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  VFLTAQLWLRNRLTDRYWRIQDVLKHARHFRGRKNRCYRLAIRAVTRAFVKCTKARSLKK-RTMRTLWIN
          VFL..QL.L.......YW....VLK....F.GRKN.CY.LA..AV....VKCTKA..LK..RTMRTLWIN
Retrocopy VFLMMQL*LWKSPDLYYWWV*KVLK*VWYFAGRKNHCYMLAVTAVPTPSVKCTKAQRLKM>RTMRTLWIN

Parental  RITAASQEHGLK-YPAFIGNLIKCQVELNRKVLADLAIYEPKTFKSLAALAKRRRQEGFAAALGDGKEPE
          .IT..S.......YP....NL.KC.VE..RKVL..LAIYEPKT.KSLAAL.KR...E.F.A.LG.GK.PE
Retrocopy QITGDSRNKAKR>YPVSTVNLTKCKVEITRKVLTVLAIYEPKTSKSLAALVKRQW*ERFPATLGNGKNPE

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_2263 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 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000013932	2 retrocopies	retro_amel_143, retro_amel_545,
Canis familiaris	ENSCAFG00000019259	2 retrocopies	retro_cfam_2112, retro_cfam_826,
Dasypus novemcinctus	ENSDNOG00000010105	1 retrocopy	retro_dnov_1620,
Homo sapiens	ENSG00000242485	1 retrocopy	retro_hsap_2508,
Gorilla gorilla	ENSGGOG00000027251	1 retrocopy	retro_ggor_1565,
Myotis lucifugus	ENSMLUG00000011857	1 retrocopy	retro_mluc_1423,
Monodelphis domestica	ENSMODG00000006562	2 retrocopies	retro_mdom_1424, retro_mdom_719,
Mus musculus	ENSMUSG00000029066	1 retrocopy	retro_mmus_1624,
Otolemur garnettii	ENSOGAG00000005968	1 retrocopy	retro_ogar_2263 ,
Procavia capensis	ENSPCAG00000001425	1 retrocopy	retro_pcap_238,
Tupaia belangeri	ENSTBEG00000008735	2 retrocopies	retro_tbel_2193, retro_tbel_892,