RetrogeneDB ID: retro_ogar_2398

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873619.1:5377007..5377737(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOGAG00000027313
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: CMBL
• Ensembl ID: ENSOGAG00000016909
• Aliases: None
• Description: carboxymethylenebutenolidase homolog (Pseudomonas) [Source:HGNC Symbol;Acc:25090]

Sequence

>retro_ogar_2398
ATGGCTAACGAAGCTTGCCCTTGCCCGTGTGACAATAGACTGGAGTATGGAGGGATGGGCCATGAAGTTCAAGTCCAGTA
CACCAAGGATTATGTCACCAAGTCCCCTGTTGCTGCAGGCAAAGCTGTGATTGTCATTCAAGATATATTTGGCTGGCGGT
TACCTAATACCAGGTATATGGCTGACAAGATCCCAGGAAATGGATACACAACCATCATTCCAGACTTCTTCGTAGGGAGG
AGCCGTGGGACCCCTCTGCCGACTGGTCCACCTTCCCTGAGTGGTTGAAAACAAGGAATACCCAGAAAATCAATAAAGAG
GTTGATGCTGTCTTAAGGTATCTGAAAAAAATGGTATCAAGTACAGAAAATTGGTGTTGTGGGATTCTGCTGTGGTGGAA
CTGCTGTCCATCATTTGATGATAAAATACTCTCAAGTTCAGGGCTGGGGTCTCCATTTATGGCATTGTCAAGGATTCTCA
AGACATTTATAGTTTAAAGAACCCCACATTGTTCATTTTCACTGAAAATGATATTATGATTCCACTTGAGCAAGTCTCTT
TGCTGACCCAGAAGTTGAAGGAACACTGCAAAGTTGATTATCAAATTAAAACATTTTCTGGGCAAACTCATGGGTTCATG
CATAAAAAGAGAGAGGATTGTTCACCTGCTGACAAGCCCTACATTGATGAGGCAAGAAGGAATTTAGTCGGGTGACTAAA
CAAGTACATT

Alignment

ORF - retro_ogar_2398 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.48 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MANEAYPCPCDIGHRLEYGGMGHELQVEHIKAYVTKSPVAAGKAVIVIQDIFGWQLPNTRYMADMIAGNG
          MANEA.PCPCD...RLEYGGMGHE.QV...K.YVTKSPVAAGKAVIVIQDIFGW.LPNTRYMAD.I.GNG
Retrocopy MANEACPCPCD--NRLEYGGMGHEVQVQYTKDYVTKSPVAAGKAVIVIQDIFGWRLPNTRYMADKIPGNG

Parental  YTTIVPDFFVG-QEPWDPSADWSTFPEWLKTRNARKIDKEVDAVLRYLKEQC-QAQKIGVVGFCWGGTAV
          YTTI.PDFFVG..EPWDPSADWSTFPEWLKTRN..KI.KEVDAVLRYLK....Q.QKIGVVGFC.GGTAV
Retrocopy YTTIIPDFFVG<EEPWDPSADWSTFPEWLKTRNTQKINKEVDAVLRYLKKMV>QVQKIGVVGFCCGGTAV

Parental  HHLMMKYSE-FRAGVSIYGIVKDSEDIYSLKNPTLFIFAENDVVIPLEQVSLLTQKLKEHCKVDYQIKTF
          HHLM.KYS..FRAGVSIYGIVKDS.DIYSLKNPTLFIF.END..IPLEQVSLLTQKLKEHCKVDYQIKTF
Retrocopy HHLMIKYSQ>FRAGVSIYGIVKDSQDIYSLKNPTLFIFTENDIMIPLEQVSLLTQKLKEHCKVDYQIKTF

Parental  SGQTHGFVHRKREDCSPADKPYIDEARRNLLEWLNKYI
          SGQTHGF.H.KREDCSPADKPYIDEARRNL...LNKYI
Retrocopy SGQTHGFMHKKREDCSPADKPYIDEARRNLVG*LNKYI

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_2398 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 6 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000009759	1 retrocopy	retro_chof_2582,
Callithrix jacchus	ENSCJAG00000009079	1 retrocopy	retro_cjac_613,
Dasypus novemcinctus	ENSDNOG00000024697	2 retrocopies	retro_dnov_1840, retro_dnov_2561,
Microcebus murinus	ENSMICG00000000533	1 retrocopy	retro_mmur_1038,
Otolemur garnettii	ENSOGAG00000016909	1 retrocopy	retro_ogar_2398 ,
Tupaia belangeri	ENSTBEG00000001698	1 retrocopy	retro_tbel_4449,