RetrogeneDB ID: retro_ogar_2580

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873635.1:5464178..5464526(-)
• Located in intron of: ENSOGAG00000007556

Retrocopy information

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

Parental gene information

• Parental gene symbol: LIN52
• Ensembl ID: ENSOGAG00000003009
• Aliases: None
• Description: lin-52 homolog (C. elegans) [Source:HGNC Symbol;Acc:19856]

Sequence

>retro_ogar_2580
ATGGGTTGGAAGATGGCATCTCCCATGGATGGGACAGATCTGGAAGCTTCTCTGCTAAGTTTTGAAAAACTTGACCATGC
CTCACCAGATCTTTGGCCAGAACAATTACCAGGTGTTGATGAATTTGCAGCTTCCTTCAAAAGTCCTATTACTAGCTCTC
CACCCAAATGGATGCCTGAGATAGACCGTGATGATAGCAACATGTTAAAAGAACTGGGGAGCCTAACCACAGCTAATTTG
ATGGAGATGATATGAGGCCTACAGAACTTGGCCTATCAGCTGGGGCTGGATGAGTCCAGAGAAACGACATGGGGGAAATT
CCTCAACATTCTAGAAAAGTCCAAGAAG

Alignment

ORF - retro_ogar_2580 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.93 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VGWKMASPTDGTDLEASLLSFEKLDRASPDLWPEQLPGVAEFAASFKSPITSSPPKWMAEIERDDIDMLK
          .GWKMASP.DGTDLEASLLSFEKLD.ASPDLWPEQLPGV.EFAASFKSPITSSPPKWM.EI.RDD..MLK
Retrocopy MGWKMASPMDGTDLEASLLSFEKLDHASPDLWPEQLPGVDEFAASFKSPITSSPPKWMPEIDRDDSNMLK

Parental  ELGSLTTANLMEKVRGLQNLAYQLGLDESREMTRGKFLNILEKPKK
          ELGSLTTANLME...GLQNLAYQLGLDESRE.T.GKFLNILEK.KK
Retrocopy ELGSLTTANLMEMI*GLQNLAYQLGLDESRETTWGKFLNILEKSKK

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_2580 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 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Loxodonta africana	ENSLAFG00000002534	1 retrocopy	retro_lafr_1097,
Macropus eugenii	ENSMEUG00000007891	1 retrocopy	retro_meug_286,
Mus musculus	ENSMUSG00000085793	1 retrocopy	retro_mmus_750,
Oryctolagus cuniculus	ENSOCUG00000017491	1 retrocopy	retro_ocun_294,
Otolemur garnettii	ENSOGAG00000003009	1 retrocopy	retro_ogar_2580 ,
Ictidomys tridecemlineatus	ENSSTOG00000008100	1 retrocopy	retro_itri_686,
Tupaia belangeri	ENSTBEG00000005405	1 retrocopy	retro_tbel_388,