RetrogeneDB ID: retro_ogar_2912

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873679.1:771787..772885(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: C1orf172
• Ensembl ID: ENSOGAG00000002084
• Aliases: None
• Description: chromosome 1 open reading frame 172 [Source:HGNC Symbol;Acc:26624]

Sequence

>retro_ogar_2912
CTGGAAACAAATGATGGGCCACCTCAACCCTCACTGAGCCATGGCACTCGTAGGCCAGACCCCAGGGACCCTGGTCACCA
TGGGCCAGAAAGCATTACCTTCATCTCGAGCTCTGCGGAGCCAGCCGCTGAGCCCCCCACCTGCTTCCTGCTCTGGAGAC
CCTGGGTATGGAACTGGTGCCGAGCTGCCTTCTGCTTCCGCCACTGCTGGGATTGTCTCTAGCGCTGTGGAGTCTGTGTG
CCGGGCTACAGCCCCTGCTTGTCTGCTGGGGACTCCACTGAAAGGTCTGCTCAAGCCAATTGAGCCAAGGAGCACAATGG
AGTTCCCCCAAGTCCTGACCGTGCACCCCCAGCCAGTGGGATGGCCAGTGGTTCAAGTCAACCATGGGCAGCAGCTTTAG
TTACTCTGATGTCAAGCTCAAAGGCATCACTGTATATCCCTACTGCAAGGCCACCTCCCCAGTCCTGGACACAGACTCCT
GCTGCAAGGAGCCACTGGCCGAGCCCTCGCCCACAAAGCACAGCCTGTCGAGCACCCTTGCCAGCAGCCCTCGTAGCGCT
GAGGAGTACTACTTCCATGAGTCAGACCTGGACCTGCCTGAGATGGGCAGTGGCTCCACATGGAGCAGAGAGACCAATGT
GCTCATCTTCAAGAAGCTGACGGAGCTGTTCAGTATACAGCATATCGATGAGCTAGCCAAGTGCACATTAGACACTGTGT
TCCTGGAGAAAACCAGTAAGATCCCGGACCTAAACAGCAGTGTCACACAGGACTCCCACCTGGACGAGCAGGATGCTGAG
GGCTGCCTGGTACGTGGCATCACTCGCATCAGCACTCCAAAGAGCTGTGCCCGCCCACAGACCACAGAGGGACGTTGGAC
TAGGGCTGCTGCTGCCCTGACAGTGGCCATGAGACCATGGTGGGCTCAGGTCTCAGCCAGGATGAACTGACAGCACAAAT
CTTCCAGGAGATGACAGCAGATGCCATCACCCAGAAGCTAAGGCTTTATGGAGCCTCAGGGTACCCAGCCAGCCACGACT
CATCCTTCCAGGGCACCTACACAGACTCACAGGGCCATTCCTGCTCCAGGTGTACTGC

Alignment

ORF - retro_ogar_2912 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.94 %
• Parental protein coverage: 93.4 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  LETYDEPPQPPPSRRTRRPDPKDPGHHGPESITFISGSAEPAAEPPTCCLLWRPWVWDWCRAAFCFRRCW
          LET.D.PPQP..S..TRRPDP.DPGHHGPESITFIS.SAEPAAEPPTC.LLWRPWVW.WCRAAFCFR.CW
Retrocopy LETNDGPPQPSLSHGTRRPDPRDPGHHGPESITFISSSAEPAAEPPTCFLLWRPWVWNWCRAAFCFRHCW

Parental  DCLQRCGVCVLGCSPCLSAGDSTEGTPDANWAKEHNGVPPSPDRAPP-SRRDGPRFKSTMGSSFSYPDVK
          DCL.RCGVCV.G.SPCLSAGDSTE....AN.AKEHNGVPPSPDRAPP.S..DG..FKSTMGSSFSY.DVK
Retrocopy DCL*RCGVCVPGYSPCLSAGDSTERSAQAN*AKEHNGVPPSPDRAPP<SQWDGQWFKSTMGSSFSYSDVK

Parental  LKGIPVYPYRNATSPVPDTDSCCKEPLAEPPPTRHSLPSTLASSPRGSEEYYSFHESDLDLPEMGSGSMS
          LKGI.VYPY..ATSPV.DTDSCCKEPLAEP.PT.HSL.STLASSPR..EEYY.FHESDLDLPEMGSGS..
Retrocopy LKGITVYPYCKATSPVLDTDSCCKEPLAEPSPTKHSLSSTLASSPRSAEEYY-FHESDLDLPEMGSGSTW

Parental  SREIDVLIFKKLTELFSVHQIDELAKCTSDTVFLEKTSKISDLISSITQDYHLDEQDAEGRLVRGIIRIS
          SRE..VLIFKKLTELFS...IDELAKCT.DTVFLEKTSKI.DL.SS.TQD.HLDEQDAEG.LVRGI.RIS
Retrocopy SRETNVLIFKKLTELFSIQHIDELAKCTLDTVFLEKTSKIPDLNSSVTQDSHLDEQDAEGCLVRGITRIS

Parental  TRKSRARPQTSEGRSTRAAAA-PDSGHETMVGSGLSQDELTVQISQETTADAIARKLRPYGAPGYPASQD
          T.KS.ARPQT.EGR.TRAAAA.PDSGHETMVGSGLSQDELT.QI.QE.TADAI..KLR.YGA.GYPAS.D
Retrocopy TPKSCARPQTTEGRWTRAAAA<PDSGHETMVGSGLSQDELTAQIFQEMTADAITQKLRLYGASGYPASHD

Parental  SSFQGTDTDSSGAP-LLQVYC
          SSFQGT.TDS.G...LLQVYC
Retrocopy SSFQGTYTDSQGHS<LLQVYC

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_2912 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Otolemur garnettii	ENSOGAG00000002084	1 retrocopy	retro_ogar_2912 ,