RetrogeneDB ID: retro_ogar_1047

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873534.1:4528589..4528981(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOGAG00000029251
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: YWHAQ
• Ensembl ID: ENSOGAG00000000547
• Aliases: None
• Description: tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, theta polypeptide [Source:HGNC Symbol;Acc:12854]

Sequence

>retro_ogar_1047
ATTGGTGAGTACATATTTAACGGCCAGTGCAACCACAGGGTTAAGGTTGTCTATATGAAAATGAAGGGAGATTACTTCCA
GATGCTTGCTGAAGATGCATGTGGTGATGTTCCAAACCAAATGACACATCATTTCCAAGGAGTTTCCCAAGAGGCATTTG
ATACAAACAAGAAAGAGATGATGCCCACATACTCAGTCTGCCTGGGGCTGGCTCTTAATGTTTCTCTATTTTACTACAAG
ATCCTTGATAGCCCAGAGCTTTCCTGCACATTGACTAAAATGTCTTTTAATGAGGCCATCGCAGAACTGGATACACTAAA
TAAGACTAATACAAAGACAGCAGGCTTCTCATGACGTTACTTAGCGACAACCTAATTCTACGGATATCAGAT

Alignment

ORF - retro_ogar_1047 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.09 %
• Parental protein coverage: 53.47 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LDKYLIANATNPESKVFYLKMKGDYFRYLAEVACGDDRKQTIDNSQGAYQEAFDISKKEMQPTHPIRLGL
          ...Y......N...KV.Y.KMKGDYF..LAE.ACGD...Q.....QG..QEAFD..KKEM.PT....LGL
Retrocopy IGEYIFNGQCNHRVKVVYMKMKGDYFQMLAEDACGDVPNQMTHHFQGVSQEAFDTNKKEMMPTYSVCLGL

Parental  ALNFSVFYYEILNNPELACTLAKTAFDEAIAELDTLNE-DSYKDSTLIMQLLRDNLTLWTSD
          ALN.S.FYY.IL..PEL.CTL.K..F.EAIAELDTLN..D.YKDS.L.M.LL.DNL.L..SD
Retrocopy ALNVSLFYYKILDSPELSCTLTKMSFNEAIAELDTLNK<D*YKDSRLLMTLLSDNLILRISD

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_1047 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 44 retrocopies.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000004925	1 retrocopy	retro_ecab_134,
Echinops telfairi	ENSETEG00000015359	4 retrocopies	retro_etel_1027, retro_etel_1048, retro_etel_235, retro_etel_65,
Felis catus	ENSFCAG00000007854	2 retrocopies	retro_fcat_1702, retro_fcat_771,
Myotis lucifugus	ENSMLUG00000005383	1 retrocopy	retro_mluc_1817,
Monodelphis domestica	ENSMODG00000014740	1 retrocopy	retro_mdom_1339,
Mus musculus	ENSMUSG00000076432	10 retrocopies	retro_mmus_1076, retro_mmus_1378, retro_mmus_1926, retro_mmus_2250, retro_mmus_2299, retro_mmus_2471, retro_mmus_2689, retro_mmus_3250, retro_mmus_3308, retro_mmus_406,
Nomascus leucogenys	ENSNLEG00000013534	3 retrocopies	retro_nleu_2543, retro_nleu_750, retro_nleu_869,
Oryctolagus cuniculus	ENSOCUG00000010482	1 retrocopy	retro_ocun_1463,
Otolemur garnettii	ENSOGAG00000000547	3 retrocopies	retro_ogar_1047 , retro_ogar_1732, retro_ogar_39,
Otolemur garnettii	ENSOGAG00000006155	2 retrocopies	retro_ogar_1003, retro_ogar_2144,
Otolemur garnettii	ENSOGAG00000008909	3 retrocopies	retro_ogar_122, retro_ogar_1243, retro_ogar_2934,
Rattus norvegicus	ENSRNOG00000008104	5 retrocopies	retro_rnor_1569, retro_rnor_2065, retro_rnor_2123, retro_rnor_2180, retro_rnor_2746,
Sorex araneus	ENSSARG00000012476	4 retrocopies	retro_sara_1, retro_sara_162, retro_sara_179, retro_sara_23,
Tursiops truncatus	ENSTTRG00000000871	4 retrocopies	retro_ttru_1006, retro_ttru_1109, retro_ttru_1530, retro_ttru_1536,