RetrogeneDB ID: retro_ogar_3334

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873781.1:544939..546072(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSOGAG00000003532
• Aliases: None
• Description: None

Sequence

>retro_ogar_3334
ATGGCAAAAGATGCTGGTTTAATTGAAGCCAATGGAAATCTAAAGGTCTTCATAGACCAGAACCTTAGCCCTGGAAAAGG
TGTCCTACACTTGGTGGCCATTCACCCTTCTGGGGTAAACCCACTGGGGAAGCAGCTCTTGCCAAAAATCTTTGAACAGT
ACAATGTTAACATTGCCCAGCAAGTGGTAATCGGTACACCTCAGAGACCTGCAGAGTCAAACACTCTTGGTGGTAGGAAG
CCCACAACCCCCCACCCAACACACACTTTGTCTCTCAGAACCAGCCTTCTGACTCCACCTTGGTCTGCTGGGAAATGCAA
CAGGAAAGGAGAGAAGAATGGCAAGGGCTTGTGGCACTTCTCCATGAAAGTCTGTGAGAAGGTGCAGAGGAAGAGGACCA
CCTCCTACAACGAGGTGATGGAGGAGCTGGTGGCCTAGTTCAGTGCCATAGATAACCACATTCTGCCCAATGAGTCAGCT
TATGACCCGAGCATAAGACAGCAAGTCTATGATGCCTTAAATATGTTGGTGGCCATGAACATCATCTCCAGGGAGAAGAA
GGAGATCAGGTGGATTGGTCTGCCCACCAACTTGGCTCAGGAGTGCCAAAATTTGGAGGTGGAAAGACAGAGAAGACTCA
AAAGAATAAAACAGAAGCAGTCTCAGGTTTAAGAACTTATTCTACAGCAAATTGCCTTCAAGAACCTGATGCAGAGGAAC
TGCCATGAGGAGCAGCAGGCCTGCTGGCTGCCCCCACCCAACTCGGTCATCCACCTGCCCTCCATCATCGTTAACACCAG
AAAGAAGATCGTCATTGATTGCAGCATCTCCAATGACAAATTTGAGTATCTGTTTAACTTTGACAACAGTTTGAGATTCC
ATGATGACATCGAGGTGCAAAAGCGGATGGGCGTGAACTGCAGGCTGGAGTCTGGCAGCTGCTCTGCTGAAGACCTAAAA
ATGGCCAGAAGTTTGTTACCAAAAGCTCTGGAACCATATGTGACTGAAATGGCTCAGGGATCCTTTATAGGTGTATTCAT
CATGATAGCAGGCTCCACGTCCAACTGCACAAGACTCTCTGCCAGTGACCTGACTAATGGTGCTCCAAGTGTCTAAGTAC
AGCTGCTCGCGGG

Alignment

ORF - retro_ogar_3334 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.74 %
• Parental protein coverage: 92.2 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAKDAGLIEANGELKVFIDQNLSPGKGVVSLVAVHPSTVNPLGKQLLPKTFGQSNVNIAQQVVIGTPQRP
          MAKDAGLIEANG.LKVFIDQNLSPGKGV..LVA.HPS.VNPLGKQLLPK.F.Q.NVNIAQQVVIGTPQRP
Retrocopy MAKDAGLIEANGNLKVFIDQNLSPGKGVLHLVAIHPSGVNPLGKQLLPKIFEQYNVNIAQQVVIGTPQRP

Parental  AASNTLVVGSPHTPN-THFVSQNQPSDSSPWSAGKRNRKGEKNGKGLRHFSMKVCEKVQRKGTTSYNEVA
          A.SNTL....P.TP..TH..S........PWSAGK.NRKGEKNGKGL.HFSMKVCEKVQRK.TTSYNEV.
Retrocopy AESNTLGGRKPTTPHPTHTLSLRTSLLTPPWSAGKCNRKGEKNGKGLWHFSMKVCEKVQRKRTTSYNEVM

Parental  DELVAEFSAADNHILPNESAYDQKNIRRRVYDALNVLMAMNIISKEKKEIKWIGLPTNSAQECQNLEVER
          .ELVA.FSA.DNHILPNESAYD...IR..VYDALN.L.AMNIIS.EKKEI.WIGLPTN.AQECQNLEVER
Retrocopy EELVA*FSAIDNHILPNESAYDP-SIRQQVYDALNMLVAMNIISREKKEIRWIGLPTNLAQECQNLEVER

Parental  QRRLERIKQKQSQLQELILQQIAFKNLVQRNRHAEQQASRPPPPNSVIHLPFIIVNTSKKTVIDCSISND
          QRRL.RIKQKQSQ..ELILQQIAFKNL.QRN.H.EQQA...PPPNSVIHLP.IIVNT.KK.VIDCSISND
Retrocopy QRRLKRIKQKQSQV*ELILQQIAFKNLMQRNCHEEQQACWLPPPNSVIHLPSIIVNTRKKIVIDCSISND

Parental  KFEYLFNFDNTFEIHDDIEVLKRMGMACGLESGSCSAEDLKMARSLVPKALEPYVTEMAQGSIGGVFITT
          KFEYLFNFDN....HDDIEV.KRMG..C.LESGSCSAEDLKMARSL.PKALEPYVTEMAQGS..GVFI..
Retrocopy KFEYLFNFDNSLRFHDDIEVQKRMGVNCRLESGSCSAEDLKMARSLLPKALEPYVTEMAQGSFIGVFIMI

Parental  AGSTSNGTRLSASDLTNGADGM-LATSSNG
          AGSTSN.TRLSASDLTNGA....L.T...G
Retrocopy AGSTSNCTRLSASDLTNGAPSV<LSTAARG

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_3334 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 12 parental genes, and 29 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000004467	8 retrocopies	retro_chof_2187, retro_chof_2229, retro_chof_2621, retro_chof_506, retro_chof_529, retro_chof_837, retro_chof_854, retro_chof_895,
Callithrix jacchus	ENSCJAG00000006950	2 retrocopies	retro_cjac_179, retro_cjac_4094,
Homo sapiens	ENSG00000198176	4 retrocopies	retro_hsap_1601, retro_hsap_299, retro_hsap_4803, retro_hsap_61,
Gorilla gorilla	ENSGGOG00000004908	2 retrocopies	retro_ggor_17, retro_ggor_335,
Loxodonta africana	ENSLAFG00000007927	1 retrocopy	retro_lafr_914,
Myotis lucifugus	ENSMLUG00000012165	1 retrocopy	retro_mluc_896,
Macaca mulatta	ENSMMUG00000007423	1 retrocopy	retro_mmul_177,
Mus musculus	ENSMUSG00000038482	2 retrocopies	retro_mmus_3243, retro_mmus_338,
Nomascus leucogenys	ENSNLEG00000000849	3 retrocopies	retro_nleu_2177, retro_nleu_2598, retro_nleu_49,
Otolemur garnettii	ENSOGAG00000000168	1 retrocopy	retro_ogar_2100,
Otolemur garnettii	ENSOGAG00000003532	1 retrocopy	retro_ogar_3334 ,
Pongo abelii	ENSPPYG00000025889	3 retrocopies	retro_pabe_1314, retro_pabe_132, retro_pabe_378,