RetrogeneDB ID: retro_ogar_3359

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873801.1:343189..344147(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: C11orf54
• Ensembl ID: ENSOGAG00000002523
• Aliases: None
• Description: chromosome 11 open reading frame 54 [Source:HGNC Symbol;Acc:30204]

Sequence

>retro_ogar_3359
AAGAAGAAAATGGCTTTTCCTGAGTTTTCTTTTCATGTGCCAAGTCTGGAGGAGCTTGATGGAGTTATGTAGAAAGGACT
AAAAGATAACTTTGCAGATGTCCAGGTCTCTGTAGTTGATTGCCCTGACTTGACTAAGGAACCATTTACCTTTCCTATAA
AAGGCATCTGTGGGAAAACTAGAATTGCAGAAGTAGGAGGTGTGCCATACTTATTGCCTCATGTAAACAAACAAACAAAA
AAAAGTTTATGATGTGAATAGTATTGCAAAAGAAATCAAGCTGCCTGGAGCTTTCATTCTTGGAGCGGGGGCAGGTCTGT
TTCAGACTTTTGAGTTTAATTCTAAGTTTATGCCAATTATTCAAACAGAATGTGAACACAAACCTCCTGTGAATGGAAGT
TATTTTGCCCATGTTAACCCTGCAGATGGAGGGTTCCTACTAGAGAAATTCAGTGAGAAATATCATGATTTTGGGTGTGC
ATTACCGGCTAATCTTTTTGCCAGTGAAGTTCAACCTGGCAAGGTCATTGAGGTACAAGCAAAAAGAACTGGACATCTTA
ATTTTGTGACTTGTATGAGATAAACTCTGGAAAAACATTATGGAGATAAACCTGTAGGGATGGGAGGTACTTTTGTAATT
CAGAAAGGAAAAGTGAAGTATCACATTATGCCAGCAGGATTTTCTTCCTGCCCCTTGAACTCAGATGAAGAAGTCAATAA
ATGGCTTAATTTTTATGAGATGAAGACTCCTTTAGTTTGTCTGCCAGTTTTTGTCTCCAGAGTTCCAGGTTTTGACTTGC
AACTGGAGCACACTCATTTTTTTAGTCATCATGGAGAAAGTGTACACTACCATTATGACACTACCCCAGATATAGTGGGA
TATCTTGGATACTTCTTAACTGCAGAATTTCTGTATCATATTGATCAGCCAAAAGAGACCCATACAATTGGACAAGAT

Alignment

ORF - retro_ogar_3359 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.55 %
• Parental protein coverage: 99.69 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KKKMAFAEFSFHVPSLEELAGVMQKGLKDNFADVQVSIVDCPDLTKEPFTFPV-KGICGKTRIA--EVGG
          KKKMAF.EFSFHVPSLEEL.GVM.KGLKDNFADVQVS.VDCPDLTKEPFTFP..K...GK......EV..
Retrocopy KKKMAFPEFSFHVPSLEELDGVM*KGLKDNFADVQVSVVDCPDLTKEPFTFPI>KASVGKLELQK*EVCH

Parental  VPYLLPLVNQKKVYDVNKIAKEIKLPGAFILGAGAGPFQTLGFNSEFMPIIQTESEHKPPVNGSYFARVN
          ...L........VYDVN.IAKEIKLPGAFILGAGAG.FQT..FNS.FMPIIQTE.EHKPPVNGSYFA.VN
Retrocopy TYCLMXXXXXXXVYDVNSIAKEIKLPGAFILGAGAGLFQTFEFNSKFMPIIQTECEHKPPVNGSYFAHVN

Parental  PADGGCLLEKYSEKYHDFGCALLANLFASEGQPGKVIEVKAKRRTGHLNFVTCMRQTLEKHYGDKPVGMG
          PADGG.LLEK.SEKYHDFGCAL.ANLFASE.QPGKVIEV.AKR.TGHLNFVTCMR.TLEKHYGDKPVGMG
Retrocopy PADGGFLLEKFSEKYHDFGCALPANLFASEVQPGKVIEVQAKR-TGHLNFVTCMR*TLEKHYGDKPVGMG

Parental  GTFVIQKGKVKSHIMPAGFSSCPLNSDEDVNKWLHFYEMNAPLVCLPVFVSRDPGFDLRLEHTHFFSHHG
          GTFVIQKGKVK.HIMPAGFSSCPLNSDE.VNKWL.FYEM..PLVCLPVFVSR.PGFDL.LEHTHFFSHHG
Retrocopy GTFVIQKGKVKYHIMPAGFSSCPLNSDEEVNKWLNFYEMKTPLVCLPVFVSRVPGFDLQLEHTHFFSHHG

Parental  EGGHYHYDTTPDTVEYLGYFLPAEFLYRIDQPKETHTIGRD
          E..HYHYDTTPD.V.YLGYFL.AEFLY.IDQPKETHTIG.D
Retrocopy ESVHYHYDTTPDIVGYLGYFLTAEFLYHIDQPKETHTIGQD

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_3359 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 6 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000013446	1 retrocopy	retro_chof_593,
Cavia porcellus	ENSCPOG00000014146	1 retrocopy	retro_cpor_1286,
Monodelphis domestica	ENSMODG00000000412	2 retrocopies	retro_mdom_1467, retro_mdom_852,
Otolemur garnettii	ENSOGAG00000002523	1 retrocopy	retro_ogar_3359 ,
Tupaia belangeri	ENSTBEG00000007819	1 retrocopy	retro_tbel_4251,
Tursiops truncatus	ENSTTRG00000001140	3 retrocopies	retro_ttru_244, retro_ttru_334, retro_ttru_560,