RetrogeneDB ID: retro_ogar_1655

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873559.1:630192..631063(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOGAG00000029129
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: SEC13
• Ensembl ID: ENSOGAG00000017050
• Aliases: None
• Description: SEC13 homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:10697]

Sequence

>retro_ogar_1655
ATGGTATCAATAATTAACATTGTGGACTCCTTCCATGATCATCGTGATATGATTCACAATGCCCAGATGGACTACGATGG
CACCTGCCTGGCAACCTGTTCATCAGACAGGTCCATCAAAATCTTCGATGTGCTCCATGAGGGGCAGATCCTCATCGCTG
ACTCAGAGGTCATGAGGGTCCTGTGTGGCAAGTGGCCTTGGCCACCCCACGTATGGCAATATCCTGACATCCTGCTTTTA
TGACCACAAAGTCATTATCTGGAAAGAGGAAAATGGCACCTGGGAGAAGACCCATGAGCACTCAGGACATAACTCCTCAG
TAAACGCTGTGTGCTGGGTCCCCCAGGACTATGGCCTGATCCTAGCCTGTGGAAGCTCCGATAGGGCTAACTCCTTGGTG
ACCTACACTGGGGAAGGCCAATGGGAAGTGAAGACGACCAGTAGTAATGCTCACACTATTGGCTGCAATGCTGGTAATTG
GGCCCCGCTGTTGTACCTAGAGCAGCCATCAGGACAGAAACCCAATTACATCCAGAAGTTTGCCTCAGGTGGCTGTGACA
ACCTCATCAAGCTGTGGAAAGAGGATGAGGATGACCAGTGGAAGGGGGAACAGAAGCTGGAAGCACACAGTGACTCAGTC
CGAGATGTGGCCTGGGCCCCCTCCATTGGCCTGCCCACCAGCACCATCGCCAGCTGCTCCCAGGATGGTCATGTGTTTAT
CTGGACCTGTGACCATTCATCAGGCAACACGTGGTCCCCCAAATTGCTGCACAAGTTCAATGATGTGTGGCATGTGAGCT
GGTCCATCACAGCTAACATTCTGGCCATCTCTGGCAGGGACAATAAGGTGACCTTGTGGAAAGAGTCTGTG

Alignment

ORF - retro_ogar_1655 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.55 %
• Parental protein coverage: 82.3 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MVSVINTVDTSHE--DMIHDAQMDYYGTRLATCSSDRSVKIFDVRNGGQILIAD-LRGHEGPVWQVAWA-
          MVS.IN.VD..H...DMIH.AQMDY.GT.LATCSSDRS.KIFDV...GQILIAD.LRGHEGPVWQVA.A.
Retrocopy MVSIINIVDSFHDHRDMIHNAQMDYDGTCLATCSSDRSIKIFDVLHEGQILIAD<LRGHEGPVWQVALA<

Parental  HPMYGNILASCSYDRKVIIWKEENGTWEKTHEHSGHDSSVNSVCWAPHDYGLILACGSSDGAISLLTYTG
          HP.YGNIL.SC.YD.KVIIWKEENGTWEKTHEHSGH.SSVN.VCW.P.DYGLILACGSSD.A.SL.TYTG
Retrocopy HPTYGNILTSCFYDHKVIIWKEENGTWEKTHEHSGHNSSVNAVCWVPQDYGLILACGSSDRANSLVTYTG

Parental  EGQWEVKKIN-NAHTIGCNAVSWAPAVVPGSLLDQPSGQKPNYIKKFASGGCDNLIKLWKEDEDGQWKEE
          EGQWEVK....NAHTIGCNA..WAP.......L.QPSGQKPNYI.KFASGGCDNLIKLWKEDED.QWK.E
Retrocopy EGQWEVKTTSSNAHTIGCNAGNWAPLLY----LEQPSGQKPNYIQKFASGGCDNLIKLWKEDEDDQWKGE

Parental  QKLEAHSDWVRDVAWAPSIGLPTSTIASCSQDGRVFIWTCDDASGNTWSPKLLHKFNDVVWHVSWSITAN
          QKLEAHSD.VRDVAWAPSIGLPTSTIASCSQDG.VFIWTCD..SGNTWSPKLLHKFND.VWHVSWSITAN
Retrocopy QKLEAHSDSVRDVAWAPSIGLPTSTIASCSQDGHVFIWTCDHSSGNTWSPKLLHKFND-VWHVSWSITAN

Parental  ILAVSGGDNKVTLWKESV
          ILA.SG.DNKVTLWKESV
Retrocopy ILAISGRDNKVTLWKESV

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_1655 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 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000005118	1 retrocopy	retro_cfam_278,
Callithrix jacchus	ENSCJAG00000016439	2 retrocopies	retro_cjac_1574, retro_cjac_908,
Felis catus	ENSFCAG00000011245	1 retrocopy	retro_fcat_541,
Homo sapiens	ENSG00000157020	1 retrocopy	retro_hsap_2630,
Microcebus murinus	ENSMICG00000002401	1 retrocopy	retro_mmur_1509,
Mus musculus	ENSMUSG00000030298	2 retrocopies	retro_mmus_2159, retro_mmus_3443,
Nomascus leucogenys	ENSNLEG00000004482	1 retrocopy	retro_nleu_642,
Otolemur garnettii	ENSOGAG00000017050	1 retrocopy	retro_ogar_1655 ,
Pongo abelii	ENSPPYG00000013658	1 retrocopy	retro_pabe_2333,
Pan troglodytes	ENSPTRG00000014619	1 retrocopy	retro_ptro_1774,
Rattus norvegicus	ENSRNOG00000010628	2 retrocopies	retro_rnor_1375, retro_rnor_1454,
Tursiops truncatus	ENSTTRG00000004395	1 retrocopy	retro_ttru_917,