RetrogeneDB ID: retro_ogar_1115

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873536.1:12237923..12239143(+)
• Located in intron of: ENSOGAG00000002145

Retrocopy information

• Ensembl ID: ENSOGAG00000024290
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSOGAG00000010065
• Aliases: None
• Description: None

Sequence

>retro_ogar_1115
ATGATCACCAAGACCCAAAAAGTAGACCTGGGCCTTGGGCTGCCAGAGAAGAAAAAGAAGAAGAAGAAGGTGGTCAAAGA
ACCAGAGACTCAATACTCAGTTTTAAATAGTAACAGTTGTTTTGCCAATGCTTCTCCTATAAGAGCCACATCCCCCTCTA
AGAATGTGGTCCAAGGGCAGATACCTGAGATGCCTCTAGTGAAGAAAAAGAAAAAAAAGAAGGGCTACAGCACCCCTTGT
GAGGAGCAACTAGAACCTGAGACCACCTGTCATGCCAGACAGACAGAGAAGTCACCCAGCCCCAGGAAGCAGGTGCTTGG
CCACTGGGAATTTCTCTGTGGGGAGAAGAAAAAGAAGAGGAAGTCCTCATTACCTCCAAACATGTCCCATGGGTTGGGGG
CAAAGACCTCTCCAGACCCCAGACAGAATGAGGCGGTGGTGACCAGAGTTGGCAAGAAGGTCAGAAAACCAAGAAGGATA
AAAAGGCCCAGGACCCCGCAGCCTTTTCATTCTGGTACCCTTGGTTCTGCGATGCTGGGGCCGGGTACACCTGCTCAGTG
CGAGGGAGGGTAAGGAGCAGGCAGCCGCAGGGCAGAAACGGAAGCAGGGGAGTGCCAGGGAACAGAGCGGGAAAGGAAGG
AGAGAAAAAGATCCACCAGGAGGGAGACACCCTCCTAGGGCACTCCAGGCTCTCCGGGTCCACGGAGAGCAGTCCTGGGA
AAGGAAGTCGAATGAGGCCAGTTAAAATTGATGCTCCAGAATACATCCCCTAGGAGATGCCCCGAGGCACCAGCAAAGAA
AAAAATGAAATCCAAGAAGAAGGTAGAGCAGCCAGTCATGGAGGAGGTGGCTCTGAAAGGGAAGAAGAAGAGGAAGAAAG
ACAGCGGGCAGCAGGAGACCCTTGGGAGGAGGATCCAGACCCAGACCTGGACGTGGTGGCGGAAAAGAAAGGAAACGTGG
ACGAGGCGCACACTGACCGGGGAGGCGAAGGCCTTACGAGAAGAGACTGACCATGAGTCGGGCAAAACGGAAACGTCTGA
AACCAGCAAGTGACGGGAACCCAGTTTGACCGGTGGGATACTGCTGGTTTTCAAAATGAGGACCAGAAACTGAAATTTCT
CAAACTTATGGGCGGCTTTAAAAACTTGTCCCCTCCATTCAGCCGGCCCCCTGGCATGGCTGGAAGGTCCAACATGGCCC
TCAACAGGAAGGCAGCTGAC

Alignment

ORF - retro_ogar_1115 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.86 %
• Parental protein coverage: 89.57 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 9

Retrocopy - Parental Gene Alignment:

Parental  MITKTPKVDLGLGLPEKKKKKKKVIKEPETQYSVLNSNNCFANVSPIRATSPPKIMVQGETPEMPLVKKK
          MITKT.KVDLGLGL.........V.KEPETQYSVLNSN.CFAN.SPIRATSP.K..VQG..PEMPLVK..
Retrocopy MITKTQKVDLGLGLXXXXXXXXXVVKEPETQYSVLNSNSCFANASPIRATSPSKNVVQGQIPEMPLVKXX

Parental  KKKKGYSTPCEEQLEPETTCHARQTEKSPSPRKQVLSHTEFLRGEKKKKRKSSLPPTMSHGLGAKTSPDP
          ...KGYSTPCEEQLEPETTCHARQTEKSPSPRKQVL.H.EFL.GEKKKKRKSSLPP.MSHGLGAKTSPDP
Retrocopy XXXKGYSTPCEEQLEPETTCHARQTEKSPSPRKQVLGHWEFLCGEKKKKRKSSLPPNMSHGLGAKTSPDP

Parental  RQNEEVATRVGKKVKKH-KKDKKAQDPAAFSVQDPWFCNAGDGYTCSV-GREGKEQAAPGQKRKQGSARE
          RQNE.V.TRVGKKV.K..KKDKKAQDPAAFS...PWFC.AG.GYTCSV..REGKEQAA.GQKRKQGSARE
Retrocopy RQNEAVVTRVGKKVRKP<KKDKKAQDPAAFSFWYPWFCDAGAGYTCSV<AREGKEQAAAGQKRKQGSARE

Parental  PS-GKGKKKKKIYQEGDTLLGHSKLSRSTESSPRKGSRMKPVKIDAPEYIP-LGDGPK-APAKKKMKSKK
          .S.GK....KKI.QEGDTLLGHS.LS.STESSP.KGSRM.PVKIDAPEYIP.LGD.P..APAKKKMKSKK
Retrocopy QS>GK-EGEKKIHQEGDTLLGHSRLSGSTESSPGKGSRMRPVKIDAPEYIP<LGDAPR<APAKKKMKSKK

Parental  KVEQPVMEEVALKRKKKKKRKKDSG-VVGDPWKEDPDPDLEVVLEKKGNMDEAHIDQ-VRRKALQE-EID
          KVEQPVMEEVAL..K.KKKRKKDSG...GDPW.EDPDPDL.VV.EKKGN.DEAH.D...RR......E.D
Retrocopy KVEQPVMEEVAL--KGKKKRKKDSG<AAGDPWEEDPDPDLDVVAEKKGNVDEAHTDR<GRRRPYEK<ETD

Parental  RESGKTETSETRK-WTGTQFGQWDTAGFENEEQKVKFLKLMGGFKNLSPSFSRPPSMAGRPNMALNKKAA
          .ESGKTETSET.K..TGTQF..WDTAGF.NE.QK.KFLKLMGGFKNLSP.FSRPP.MAGR.NMALN.KAA
Retrocopy HESGKTETSETSK<VTGTQFDRWDTAGFQNEDQKLKFLKLMGGFKNLSPPFSRPPGMAGRSNMALNRKAA

Parental  D
          D
Retrocopy D

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_1115 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 9 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000018032	2 retrocopies	retro_cfam_1557, retro_cfam_1763,
Callithrix jacchus	ENSCJAG00000009625	1 retrocopy	retro_cjac_3199,
Homo sapiens	ENSG00000103550	3 retrocopies	retro_hsap_3487, retro_hsap_4007, retro_hsap_979,
Gorilla gorilla	ENSGGOG00000005673	1 retrocopy	retro_ggor_2691,
Macaca mulatta	ENSMMUG00000002707	2 retrocopies	retro_mmul_1771, retro_mmul_798,
Nomascus leucogenys	ENSNLEG00000012496	2 retrocopies	retro_nleu_1618, retro_nleu_551,
Otolemur garnettii	ENSOGAG00000010065	4 retrocopies	retro_ogar_1115 , retro_ogar_1480, retro_ogar_1481, retro_ogar_2259,
Pongo abelii	ENSPPYG00000007151	3 retrocopies	retro_pabe_3293, retro_pabe_828, retro_pabe_920,
Pan troglodytes	ENSPTRG00000007836	3 retrocopies	retro_ptro_2360, retro_ptro_767, retro_ptro_924,