RetrogeneDB ID: retro_ogar_2123

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873592.1:6445078..6445752(-)
• Located in intron of: ENSOGAG00000000392

Retrocopy information

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

Parental gene information

• Parental gene symbol: CCNC
• Ensembl ID: ENSOGAG00000001116
• Aliases: None
• Description: cyclin C [Source:HGNC Symbol;Acc:1581]

Sequence

>retro_ogar_2123
TCTCACTATTTGTACTGGATTTTGGATGAACAAGATCTGTTCAAGGAGTGCCAAAAAGACTTAAAGTTTTTCTTAGTAGA
AGAGTATTGGAAATTACAACTATTTTTTACAAATGTTATCTAAGCATTAGGTGAACGTCTTAAATTAAGACAAGTTATTG
CCAGTCCCGCAATCTATTTCAACAGATTCTATGCCAGATATTATTTATAAAGTATGGATCCTGTATTAATGGCTCCTACA
TGTATGTTTTTGGCATCCAAAGTAGAGGACTTTGGAGTAGTCTCAAATACAAAATTGATTTCTGCTGCTACTTCTGTATT
AAAAACTAGATTTTCATGTGCCTTTCCAAAGGAATTTCCTTATAAGATGAACCATATATTAGAATGTTAATTCTGTTTTT
TAGAACTGATGGATTATTGCTTGATACTGTATCATCCTTATAGACCTTTGCTCTAGTGTGTGCAGGATATGAGCCAGAAA
GACATGTTGCTTCCCCTTGCGTGGAAGATAGTGAGTGATACCTATTTACAGAACAAATCTCTGCCTATCGTACTGTCCTT
TCATGATAACTTTAGCTTGCCTACATGTAGTCTCTGTTGTACAGCATAAAGATGACAGACAGTGGTTTGCTGAGCTTTCT
GTTGATATGGAAAAAGATTTTGGAAATGATCAGA

Alignment

ORF - retro_ogar_2123 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.53 %
• Parental protein coverage: 79.15 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  SHYLQWILDKQDLLKERQKDLKFLSEEEYWKLQIFFTNVIQALGEHLKLRQQVIATATVYFKRFYARYSL
          SHYL.WILD.QDL.KE.QKDLKF...EEYWKLQ.FFTNVI.ALGE.LKLRQ.VIA....YF.RFYARY.L
Retrocopy SHYLYWILDEQDLFKECQKDLKFFLVEEYWKLQLFFTNVI*ALGERLKLRQ-VIASPAIYFNRFYARYYL

Parental  KSIDPVLMAPTCVFLASKVEEFGVVSNTRLISAATSVLKTRFSYAFPKEFPYRMNHILECEFYLLELMDC
          .S.DPVLMAPTC.FLASKVE.FGVVSNT.LISAATSVLKTRFS.AFPKEFPY.MNHILEC.F..LELMD.
Retrocopy *SMDPVLMAPTCMFLASKVEDFGVVSNTKLISAATSVLKTRFSCAFPKEFPYKMNHILEC*FCFLELMDY

Parental  CLIVYHPYRPLLQYVQDMGQEDMLL-PLAWRI-VNDTYRTDLCLLYPPFMIALACLHVACVVQQKDARQW
          CLI.YHPYRPLL..VQDM.Q.DMLL.PL..R..V...YRT.LCL.Y.PFMI.LACLHV..VVQ.KD.RQW
Retrocopy CLILYHPYRPLL*CVQDMSQKDMLL>PLRGR**VIPIYRTNLCLSYCPFMITLACLHVVSVVQHKDDRQW

Parental  FAELSVDMEK-ILEIIR
          FAELSVDMEK.ILE.IR
Retrocopy FAELSVDMEK>ILEMIR

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_2123 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 8 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000015744	3 retrocopies	retro_btau_1206, retro_btau_1536, retro_btau_1836,
Callithrix jacchus	ENSCJAG00000001388	1 retrocopy	retro_cjac_780,
Dasypus novemcinctus	ENSDNOG00000011999	3 retrocopies	retro_dnov_1153, retro_dnov_216, retro_dnov_2243,
Echinops telfairi	ENSETEG00000002643	1 retrocopy	retro_etel_1441,
Otolemur garnettii	ENSOGAG00000000469	1 retrocopy	retro_ogar_2588,
Otolemur garnettii	ENSOGAG00000001116	1 retrocopy	retro_ogar_2123 ,
Otolemur garnettii	ENSOGAG00000033279	1 retrocopy	retro_ogar_70,
Sorex araneus	ENSSARG00000004726	2 retrocopies	retro_sara_141, retro_sara_583,