RetrogeneDB ID: retro_ogar_2927

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873682.1:1381167..1381754(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: APOO
• Ensembl ID: ENSOGAG00000001960
• Aliases: None
• Description: apolipoprotein O [Source:HGNC Symbol;Acc:28727]

Sequence

>retro_ogar_2927
ATGTTTAAGGTAAATCAGAGTTCCATGGGGCCAGCCAGTCTGAACCTGCTCCCCTTCCAAGTCTATATAGCACCAAAAAA
GTACTCTCCTCCCCTAAATGCCACAAAGGTTAACAAGCTTGTACCTACTCAGTTTCTGAGGGTCAATCTCTTGTAGAGGA
ACCATGAACCCAACTTGAAGAAAGCATCTCCCAGCTCGGTGTTACTGGAAGCCACATACAGGTCAATGTTAGGAAACATA
CTCCCGAATTAAGCCCAAGATGCAAAGGTTGGTTCACTGGCGGTTAGACTGCTATGAAGCTCCCAAATGCCCTTCTTGGA
TTTTTTCCAGGACGTGATGTTATTGGTTTTGCTGACCTTGTTGGATCCCTTTTGGCTACAGGTTCTACAGTAATGAAGCT
GGTGTATCCCTGTGTTTTCATGGGATTAGCTGCCTCGCTCTATTATCCACGACAAGCCATCGTATTTGTCCAGGTCAGTG
GGGAGAAATTATGTGATTGGGATTTATGAGGATACATAGTTATAAAAGATTTGTGGAAAGGGAACTTGGAAAAGCCAGAA
AATGAGAAAAATTCACCTAGAAATAAG

Alignment

ORF - retro_ogar_2927 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.18 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  VFQVLQRSVGPASLSLLAFKVYAAPRKDSPPTNPMKVNEL-SLYSVPEGQSKYVEEPRTQLEETISQL-R
          .F.V.Q.S.GPASL.LL.F.VY.AP.K.SPP.N..KVN.L...YSV.EGQS..VEEP.TQLEE.ISQL.R
Retrocopy MFKVNQSSMGPASLNLLPFQVYIAPKKYSPPLNATKVNKL<CTYSVSEGQS-LVEEP*TQLEESISQL<R

Parental  NHCEPYTSWCQETYSQTKPKMQSLVQLGLDSYEYLQHAPPGFFPRL-GVIGFAGLVGLLLARGSKVKKLV
          ....P.T..C.ETYS..KPKMQ.LV...LD.YE.....P...F.R...VIGFA.LVG.LLA.GS.V.KLV
Retrocopy CYWKPHTGQC*ETYSRIKPKMQRLVHWRLDCYE-APKCPSWIFSRT>DVIGFADLVGSLLATGSTVMKLV

Parental  YPPGFMGLAASIYYPQQAIAFVQVGGEKLYDWGLRGYIVVEDLWKRNFQKPGSVKNSPGNK
          YP..FMGLAAS.YYP.QAI.FVQV.GEKL.DW.L.GYIV..DLWK.N..KP...KNSP.NK
Retrocopy YPCVFMGLAASLYYPRQAIVFVQVSGEKLCDWDL*GYIVIKDLWKGNLEKPENEKNSPRNK

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_2927 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 20 parental genes, and 49 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000012749	1 retrocopy	retro_amel_1282,
Choloepus hoffmanni	ENSCHOG00000000226	2 retrocopies	retro_chof_2372, retro_chof_839,
Callithrix jacchus	ENSCJAG00000004909	8 retrocopies	retro_cjac_1360, retro_cjac_1417, retro_cjac_1448, retro_cjac_1767, retro_cjac_1792, retro_cjac_1896, retro_cjac_2038, retro_cjac_2063,
Cavia porcellus	ENSCPOG00000004197	1 retrocopy	retro_cpor_309,
Dasypus novemcinctus	ENSDNOG00000006710	1 retrocopy	retro_dnov_2450,
Equus caballus	ENSECAG00000013441	1 retrocopy	retro_ecab_145,
Echinops telfairi	ENSETEG00000014150	3 retrocopies	retro_etel_1052, retro_etel_516, retro_etel_711,
Felis catus	ENSFCAG00000000029	3 retrocopies	retro_fcat_1203, retro_fcat_1657, retro_fcat_1798,
Loxodonta africana	ENSLAFG00000029070	1 retrocopy	retro_lafr_1114,
Macropus eugenii	ENSMEUG00000014222	1 retrocopy	retro_meug_700,
Macaca mulatta	ENSMMUG00000016361	4 retrocopies	retro_mmul_1584, retro_mmul_1886, retro_mmul_2051, retro_mmul_814,
Monodelphis domestica	ENSMODG00000025554	1 retrocopy	retro_mdom_1510,
Mustela putorius furo	ENSMPUG00000000109	1 retrocopy	retro_mputfur_109,
Mus musculus	ENSMUSG00000079508	1 retrocopy	retro_mmus_282,
Otolemur garnettii	ENSOGAG00000001960	6 retrocopies	retro_ogar_1083, retro_ogar_1104, retro_ogar_2092, retro_ogar_2466, retro_ogar_2927 , retro_ogar_3094,
Pteropus vampyrus	ENSPVAG00000002530	2 retrocopies	retro_pvam_128, retro_pvam_594,
Rattus norvegicus	ENSRNOG00000046918	4 retrocopies	retro_rnor_1022, retro_rnor_1986, retro_rnor_2096, retro_rnor_2308,
Sarcophilus harrisii	ENSSHAG00000008734	1 retrocopy	retro_shar_125,
Sus scrofa	ENSSSCG00000012174	1 retrocopy	retro_sscr_774,
Tupaia belangeri	ENSTBEG00000014888	6 retrocopies	retro_tbel_1153, retro_tbel_4004, retro_tbel_4261, retro_tbel_4698, retro_tbel_715, retro_tbel_96,