RetrogeneDB ID: retro_ogar_2375

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873617.1:5379985..5380285(+)
• Located in intron of: ENSOGAG00000016443

Retrocopy information

• Ensembl ID: ENSOGAG00000028263
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: DDA1
• Ensembl ID: ENSOGAG00000003701
• Aliases: None
• Description: DET1 and DDB1 associated 1 [Source:HGNC Symbol;Acc:28360]

Sequence

>retro_ogar_2375
GATTTTTTGGAAGGATTGCCTGTCTACAACAAAAGCAATTTTAGTCAACTTCATGCCGATTCCATGTGCAAAGCCTCCAA
CCGAAGTCTCTCAGTCTACCTGCCCACTCGAGAGTACCCGTCTGAACAGATCATCGTCGCAGATAAGACAAACATTCTCC
TGCGCTACCTATATCAGCAGTGGGACAAAAAGAAGGCCGCCAAGAAGAGAGACCAGCAGCAAGCAGAACTTGAAGGCGAG
GGCTGGGCACCTCCTCGCAAGGTGGCACGGACTGACAGCCTGGACATGCACGAGGACACT

Alignment

ORF - retro_ogar_2375 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.0 %
• Parental protein coverage: 99.01 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  DFLKGLPVYNKSNFSRFHADSVCKASNRRPSVYLPTREYPSEQIIVTEKTNILLRYLHQQWDKKNAAKKR
          DFL.GLPVYNKSNFS..HADS.CKASNR..SVYLPTREYPSEQIIV..KTNILLRYL.QQWDKK.AAKKR
Retrocopy DFLEGLPVYNKSNFSQLHADSMCKASNRSLSVYLPTREYPSEQIIVADKTNILLRYLYQQWDKKKAAKKR

Parental  DQEQVELEGESSAPPRKVARTDSPDMHEDT
          DQ.Q.ELEGE..APPRKVARTDS.DMHEDT
Retrocopy DQQQAELEGEGWAPPRKVARTDSLDMHEDT

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_2375 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 14 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000017068	3 retrocopies	retro_btau_1152, retro_btau_536, retro_btau_74,
Canis familiaris	ENSCAFG00000031251	3 retrocopies	retro_cfam_1089, retro_cfam_2033, retro_cfam_475,
Cavia porcellus	ENSCPOG00000006944	1 retrocopy	retro_cpor_435,
Felis catus	ENSFCAG00000001001	1 retrocopy	retro_fcat_487,
Homo sapiens	ENSG00000130311	1 retrocopy	retro_hsap_1409,
Gorilla gorilla	ENSGGOG00000005802	1 retrocopy	retro_ggor_1093,
Microcebus murinus	ENSMICG00000001763	1 retrocopy	retro_mmur_1162,
Myotis lucifugus	ENSMLUG00000003990	1 retrocopy	retro_mluc_1014,
Macaca mulatta	ENSMMUG00000016231	1 retrocopy	retro_mmul_2248,
Nomascus leucogenys	ENSNLEG00000005738	2 retrocopies	retro_nleu_1427, retro_nleu_1428,
Otolemur garnettii	ENSOGAG00000003701	1 retrocopy	retro_ogar_2375 ,
Pongo abelii	ENSPPYG00000009710	2 retrocopies	retro_pabe_1167, retro_pabe_1214,
Pan troglodytes	ENSPTRG00000010668	1 retrocopy	retro_ptro_966,
Rattus norvegicus	ENSRNOG00000039417	1 retrocopy	retro_rnor_1511,