RetrogeneDB ID: retro_ogar_3000

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873694.1:2141518..2142574(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SURF6
• Ensembl ID: ENSOGAG00000027199
• Aliases: None
• Description: surfeit 6 [Source:HGNC Symbol;Acc:11478]

Sequence

>retro_ogar_3000
ATGGCCTCCCTGCTTGCCAAGGACGCCTACCTGCAGAGCCTGGCCAGGAAAATCTGCTCCCAGCCCGGCCCAGAATCGCA
GAAGCGCCAATGTGCAGGCAAAACTAAAGGCTCAGAAGCTGCTGGACACCCAAAAAAGAAGAGGAAGAAAACACCAAAGA
AACTGCAGAAGCAGGAAGAGAAGGCTGCTGATACCAAGGCCAAGTCCCTGGGGAAGAAGTCTCTAGTGGGTTCTGGTGAT
GGAAGGCCAGAGGAAGCCAAAGAGAAGGAGTCTTCCAGCTCCACAGCGGCCCCTGCAGATGGCGTGGCCACAGGGCCTGA
TTCTCTTTTTGCCCTGGATGTTCTTCGCCAGCGACTGCATGAGAGGATCCAGGAGGCCCAGGGCCAGATCAGTGCCAAAG
AGCTGTCCCCTGCCACTTTGGAGAAAAGACGCAGGAGAAATCTGGAGCGGGACCAGAAGAAGAGGAAGCGAAAGGAGCTG
CGGGCCAAGGAGAAGCCAACCAAGGCCGAGGAGGCTGCTGAGCCTGCCCCAGAGGCAGCCTGCGATGAGCCCGTGGAGCC
AGCGGGCCTGATCTTCAACAAGGTGGAGGTAGGTGAGGACAAACCGGCCAGCAAGGTGCAGCGGAGGAAGAAGAGGCAGA
AGGTGAAGGGGAACCTCACTCCGTCGACAGGCAGGAACTACTGGCAGCTGCAAGAGTGTTTGCAGGCATGGCAGAGCTGG
CTGGAGGAGCTGCAGGACTAGGATGAGGGGAAGGCGCGCGAGCTGGAGGTCAAGATGGGCTGGACCAATCTGCTGTACAA
GGACGAGGGCGTGCACATCCAAGATGATGAGCACCCGCTACAGGAGGCCCTGCGGCGCAAAGAGAAGCGCAAGGCACAGC
GGCAGCGCCCGTGGGAGAAGCGCATGGTGCACGTGGTGGAGAAGATGCAGCAGTGCCAGGACCAGCGGCGCCAGAACCCG
CACAAGAAGAAGGCCGCCTGGACAGAGCGCCACCTGCACAAGGCCCACAAGAAGGGCGGGATCCTGCCGCAGGATCTGGA
GCAGGCTGGCCTGGCC

Alignment

ORF - retro_ogar_3000 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.69 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MASLLAKDAYLQSLARKICSQPGPESQKRQWAGKTKGSEAAGHPKKKRKKTPKKFQKQEEKAADTKAKSL
          MASLLAKDAYLQSLARKICSQPGPESQKRQ.AGKTKGSEAAGHPKKKRKKTPKK.QKQEEKAADTKAKSL
Retrocopy MASLLAKDAYLQSLARKICSQPGPESQKRQCAGKTKGSEAAGHPKKKRKKTPKKLQKQEEKAADTKAKSL

Parental  GKKSLGSSGDRRPEEAKEKELSSSTVAPADGLATGPDSLFALDVLRQRLHERIQEARGQ--SKELSPATL
          GKKSL..SGD.RPEEAKEKE.SSST.APADG.ATGPDSLFALDVLRQRLHERIQEA.GQ...KELSPATL
Retrocopy GKKSLVGSGDGRPEEAKEKESSSSTAAPADGVATGPDSLFALDVLRQRLHERIQEAQGQISAKELSPATL

Parental  EKRRRRKLERDRKKRKRKELRAKEKATKAEEAAEPAPEAACDKPVEPVGLIFNKVEVGEDEPASKAQRRK
          EKRRRR.LERD.KKRKRKELRAKEK.TKAEEAAEPAPEAACD.PVEP.GLIFNKVEVGED.PASK.QRRK
Retrocopy EKRRRRNLERDQKKRKRKELRAKEKPTKAEEAAEPAPEAACDEPVEPAGLIFNKVEVGEDKPASKVQRRK

Parental  EKRQKVKGNLTPLTGRNYRQLLERLQTRQSRLEELRDQDEGKARELEAKMGWTNLLYKAEGVRIRDDERL
          .KRQKVKGNLTP.TGRNY.QL.E.LQ..QS.LEEL.D.DEGKARELE.KMGWTNLLYK.EGV.I.DDE..
Retrocopy -KRQKVKGNLTPSTGRNYWQLQECLQAWQSWLEELQD*DEGKARELEVKMGWTNLLYKDEGVHIQDDEHP

Parental  LQEALRRKEKRKAQRQRRWEKRTAHVVEKMQQRQDQRRQNLRKKKAARAERRLHKARKKGRILPQDLERA
          LQEALRRKEKRKAQRQR.WEKR..HVVEKMQQ.QDQRRQN..KKKAA..ER.LHKA.KKG.ILPQDLE.A
Retrocopy LQEALRRKEKRKAQRQRPWEKRMVHVVEKMQQCQDQRRQNPHKKKAAWTERHLHKAHKKGGILPQDLEQA

Parental  GLA
          GLA
Retrocopy GLA

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_3000 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000019758	1 retrocopy	retro_cfam_162,
Otolemur garnettii	ENSOGAG00000027199	1 retrocopy	retro_ogar_3000 ,
Rattus norvegicus	ENSRNOG00000005031	1 retrocopy	retro_rnor_1538,