RetrogeneDB ID: retro_ogar_2245

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873605.1:3905128..3905615(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CD164
• Ensembl ID: ENSOGAG00000015500
• Aliases: None
• Description: CD164 molecule, sialomucin [Source:HGNC Symbol;Acc:1632]

Sequence

>retro_ogar_2245
AGTGTGGATTTTAACACCAAGATAACTCCAACATTGCCAACATCCCTGCTGCCACCACTCTTACCCCAGAAACCTGTGCA
GGCCACAACAGTTACGTTTCCTGCTTTAATGCTAACACTGTCAATGCTGCTGCTTTGGGATAGAATGTCGAGATGAGAGC
TACTGTTCCCCTAACTCGACAGTTAGTGAACTGCTGTGAGCACGTGGTGAACACAACAAACTGCTCTTCTGTGCTCACTG
CCACCCCAGTGCCAACCAGTCCTCCAGCTGAAACCACAAGCCTCCCTTCCTCCTGCACAATTTCCACCACAGTTTCCGCC
CCAGGTGAACCCATGCTGCTGTGACTCCCACCTCACACCCTAAGCAGAAGTCTACGTTGGATGCCGCCAGTTTCCTGGGA
GGAAACGTCCCTGTCTTGGGGGTGCAGGCTGCAATTTTCTTTCTCTACAGATTCCGTAAATCTAAAGGAAGAACTTACCA
CACTCTG

Alignment

ORF - retro_ogar_2245 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.97 %
• Parental protein coverage: 82.91 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  TVETTTKI-NTSLVTTPAPVTTPVPETCEGRNSCASCTNTSNVNTT-CFWMECKVIDKSYCSHNSTVS-D
          .V...TKI.N......PA..TT..PETC.G.NS..SC.N...VN...CF..EC...D.SYCS.NSTVS..
Retrocopy SVDFNTKI<NSNIANIPA-ATTLTPETCAGHNSYVSCFNANTVNAA<CFGIECR--DESYCSPNSTVS>N

Parental  C--QVVNATHFCSVAPTTIPAPTNSTAENTTLPSSSTTSTVPTSAGP-TNTTLTPTSQPIRKSTFDAASF
          C...VVN.T..CS...T..P.PT...AE.T.LPSS.T.ST.....G..T....TPTS.P..KST.DAASF
Retrocopy CCEHVVNTTN-CSSVLTATPVPTSPPAETTSLPSSCTISTTVSAPGE<THAAVTPTSHPKQKSTLDAASF

Parental  IGGIVLVLGVQAVIFFLYKFCKSKERNYHTL
          .GG.V.VLGVQA.IFFLY.F.KSK.R.YHTL
Retrocopy LGGNVPVLGVQAAIFFLYRFRKSKGRTYHTL

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_2245 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 4 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000017992	3 retrocopies	retro_btau_477, retro_btau_479, retro_btau_503,
Macaca mulatta	ENSMMUG00000007011	1 retrocopy	retro_mmul_2418,
Otolemur garnettii	ENSOGAG00000015500	2 retrocopies	retro_ogar_2245 , retro_ogar_3252,
Tursiops truncatus	ENSTTRG00000004181	2 retrocopies	retro_ttru_436, retro_ttru_532,