RetrogeneDB ID: retro_ogar_2314

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873611.1:4733337..4733857(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOGAG00000028108
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RPS10
• Ensembl ID: ENSOGAG00000001365
• Aliases: None
• Description: ribosomal protein S10 [Source:HGNC Symbol;Acc:10383]

Sequence

>retro_ogar_2314
TTGGCTCCAGACACTGCAGCCGTCGTGATGTTGATGCCCAAGAGGAACCAATTGCCATTTATGAACTCCTTTTTAAGGAG
GGTGTGATGGTGGCCAAGAAGGATGTCCGTATGCCTAAGCACCCAGGGTTGGCAGACAAGAACGTGCCCAACCTTAATGT
CATGAAGGCCATGCAGTCTCTCAAATCACAAGGCTATGTGAAGGAACAGTTTGCCTGGAGACATTTCTACTGGTACCTTA
CCAATGAGGGTATCCAGTATCTCCACGATTACCTCCACTTGCCCCCTGAGATCGTGCCCGCCACTTTGTACTGCAGCTAT
CCAGAGACAGGCAGACTTTGGCCAAAAGGTCTGGAAGGTGAGTGACTTGCAAGACTCACTAGAGGGAAAGCTGACAGAGA
CACCTACAGGCAGAGTGCTGTGCCCCTGGTGCCAACACAAAAGCCGAGGCTGGGGCTGGGTCAGCAACTGATTTCCGGTT
TAGAGGTGGATTTGGTTGTGGATGTGGTCAGCCACCTCAG

Alignment

ORF - retro_ogar_2314 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.82 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  IALKSSSLQMLMPKKNR-IAIYELLFKEGVMVAKKDVHMPKHPELADKNVPNLHVMKAMQSLKSRGYVKE
          .A.......MLMPK.N..IAIYELLFKEGVMVAKKDV.MPKHP.LADKNVPNL.VMKAMQSLKS.GYVKE
Retrocopy LAPDTAAVVMLMPKRNQ<IAIYELLFKEGVMVAKKDVRMPKHPGLADKNVPNLNVMKAMQSLKSQGYVKE

Parental  QFAWRHFYWYLTNEGIQYLRDYLHLPPEIVPATLRRSRPETGRPRPKGLEGERPARLTRGEADRDTYRRS
          QFAWRHFYWYLTNEGIQYL.DYLHLPPEIVPATL..S.PETGR..PKGLEGE..ARLTRG.ADRDTYR.S
Retrocopy QFAWRHFYWYLTNEGIQYLHDYLHLPPEIVPATLYCSYPETGRLWPKGLEGE*LARLTRGKADRDTYRQS

Parental  AVP-PGADKKAEAGAGSATEFQFRGGFGRGRGQPPQ
          AVP.PGA..KAEAGAGSAT.F.FRGGFG.G.GQPPQ
Retrocopy AVP<PGANTKAEAGAGSATDFRFRGGFGCGCGQPPQ

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_2314 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 14 parental genes, and 45 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000001047	4 retrocopies	retro_amel_1408, retro_amel_1706, retro_amel_446, retro_amel_890,
Canis familiaris	ENSCAFG00000001214	2 retrocopies	retro_cfam_1, retro_cfam_92,
Callithrix jacchus	ENSCJAG00000015250	4 retrocopies	retro_cjac_215, retro_cjac_296, retro_cjac_325, retro_cjac_63,
Felis catus	ENSFCAG00000015355	3 retrocopies	retro_fcat_1443, retro_fcat_1681, retro_fcat_1757,
Latimeria chalumnae	ENSLACG00000017219	1 retrocopy	retro_lcha_26,
Loxodonta africana	ENSLAFG00000008539	1 retrocopy	retro_lafr_756,
Macaca mulatta	ENSMMUG00000000267	2 retrocopies	retro_mmul_332, retro_mmul_555,
Monodelphis domestica	ENSMODG00000013929	2 retrocopies	retro_mdom_1889, retro_mdom_437,
Mustela putorius furo	ENSMPUG00000003117	3 retrocopies	retro_mputfur_1347, retro_mputfur_1533, retro_mputfur_1579,
Mus musculus	ENSMUSG00000052146	9 retrocopies	retro_mmus_1376, retro_mmus_1500, retro_mmus_1831, retro_mmus_2431, retro_mmus_2551, retro_mmus_2708, retro_mmus_3651, retro_mmus_5, retro_mmus_858,
Otolemur garnettii	ENSOGAG00000001365	5 retrocopies	retro_ogar_2166, retro_ogar_2314 , retro_ogar_2553, retro_ogar_415, retro_ogar_873,
Pongo abelii	ENSPPYG00000016516	2 retrocopies	retro_pabe_2319, retro_pabe_97,
Rattus norvegicus	ENSRNOG00000000490	4 retrocopies	retro_rnor_169, retro_rnor_224, retro_rnor_359, retro_rnor_74,
Sarcophilus harrisii	ENSSHAG00000000731	3 retrocopies	retro_shar_243, retro_shar_334, retro_shar_724,