RetrogeneDB ID: retro_ogar_3514

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL874122.1:653..1382(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: COPS4
• Ensembl ID: ENSOGAG00000027198
• Aliases: None
• Description: COP9 signalosome subunit 4 [Source:HGNC Symbol;Acc:16702]

Sequence

>retro_ogar_3514
ATGGCTGCAGCCGCGCGACAGGATTTGGCCCAGCTCATGAATTCGAGCGGCTCTCATAAAGATCTGGCTGGAAAGTATCG
TCAGATCCTGGAAAAAGCTATTCAACTATCTGGAGCAGATCGACTAGAAGCTTTGAAAGCTTTTGTGGAAGCAACGGTAA
ATGAGAATGTTAGTCTCGTGATCTCTCGACAGTTGCTCACTGATTTCTGCACACATCACCCTAACCTGCCAGATAGCATA
GCCAAAGAAATTTATCACTTCACCTTGGAAAAGATCCAGCCTAGAGTCATTTCATTTGAGGAACAGGTTGCTTCCATAAG
ACAGCAACTTGCATCCATATATGAAAAAGAAGAAGACTGGAGAAATGCAGCCCAAGTGTTGGTGGGAATTTCTTTGGAAA
CATGACAAAAACAGTACAATGTAGATTATAAGCTGGAGACTTATCTGAAGGTTGCTAGGCTATATTTGGAAGATGATGAT
CCAGTCCAGGCAGAGGCTTATATAAATCGAGCATCATTGCTTCAGAATGAATCAACCAATGAACAATTACAGATACATTA
TAAGGTATGCTATGCACGTGTTCTTGATTATAGAAGAAAATTCATTGAAGCTGCACAAAGGTACAATGAGCTCTCTTACA
AGACAATAGTCCATGAGAGTGAAAGACTAGAGGCCTTAAAACATGCTTTCCACTGTACCATCTTAGCATCAGCAGGACAG
CAGCATTCT

Alignment

ORF - retro_ogar_3514 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.06 %
• Parental protein coverage: 59.85 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAAAVRQDLAQLMNSSGSHKDLAGKYRQILEKAIQLSGADQLEALKAFVEQVVNENVSLVISRQLLTDFC
          MAAA.RQDLAQLMNSSGSHKDLAGKYRQILEKAIQLSGAD.LEALKAFVE..VNENVSLVISRQLLTDFC
Retrocopy MAAAARQDLAQLMNSSGSHKDLAGKYRQILEKAIQLSGADRLEALKAFVEATVNENVSLVISRQLLTDFC

Parental  THLPNLPDSTAKEIYHFTLEKIQPRVISFEEQVASIRQHLASIYEKEEDWRNAAQVLVGIPLETGQKQYN
          TH.PNLPDS.AKEIYHFTLEKIQPRVISFEEQVASIRQ.LASIYEKEEDWRNAAQVLVGI.LET.QKQYN
Retrocopy THHPNLPDSIAKEIYHFTLEKIQPRVISFEEQVASIRQQLASIYEKEEDWRNAAQVLVGISLET*QKQYN

Parental  VDYKLETYLKIARLYLEDDDPVQAEAYINRASLLQNESTNEQLQIHYKVCYARVLDYRRKFIEAAQRYNE
          VDYKLETYLK.ARLYLEDDDPVQAEAYINRASLLQNESTNEQLQIHYKVCYARVLDYRRKFIEAAQRYNE
Retrocopy VDYKLETYLKVARLYLEDDDPVQAEAYINRASLLQNESTNEQLQIHYKVCYARVLDYRRKFIEAAQRYNE

Parental  LSYKTIVHESERLEALKHALHCTILASAGQQRS
          LSYKTIVHESERLEALKHA.HCTILASAGQQ.S
Retrocopy LSYKTIVHESERLEALKHAFHCTILASAGQQHS

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_3514 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 5 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000015209	2 retrocopies	retro_ecab_315, retro_ecab_600,
Monodelphis domestica	ENSMODG00000019311	1 retrocopy	retro_mdom_824,
Mustela putorius furo	ENSMPUG00000014708	1 retrocopy	retro_mputfur_1010,
Otolemur garnettii	ENSOGAG00000027198	1 retrocopy	retro_ogar_3514 ,
Tupaia belangeri	ENSTBEG00000017599	2 retrocopies	retro_tbel_2134, retro_tbel_53,