RetrogeneDB ID: retro_ogar_2856

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873672.1:1349802..1350237(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOGAG00000030410
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: LAPTM4B
• Ensembl ID: ENSOGAG00000000512
• Aliases: None
• Description: lysosomal protein transmembrane 4 beta [Source:HGNC Symbol;Acc:13646]

Sequence

>retro_ogar_2856
TGGTACCTGATCATCAATGCTGTGGTACTGCGGATTTTATTGAGCGCCCTGGCTGACCCAGATCAGCAACACTTTTCAAG
TTCTGAACTGGAAGGTGACTTTGAGTTCATGGATGATGCCAACATGTGCATCGCTATTGCAATTTCTTTTCTCATGATCC
TGATATGTGCAATGGCTACGTATGGAGCATATAAGCAGCGTGCTGCCTGGATTGTCCCGTTCTTCTGTTACCAGATCTTT
GACTTTGCCCTGAACGCCTTGGTTGCAGTCACTGTGCTCGTCTATCCAAACTCCATCCAGGAGTGCATACGGCAGCTGCG
TCCTAATTTTCCCTACAAAGATGATATCATGTCTGTGAATCCTACCTGTTTGGTCCTTTTTATTCTTCTGTTCATTAGCA
TTATCTTGACTTTTAAGGGTTACTTGATTAACTGT

Alignment

ORF - retro_ogar_2856 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.41 %
• Parental protein coverage: 82.86 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  WFQIINAVVLLILLSALADPDQQHFSSSELGGDFEFMDDANMCIAIAISFLMILICAMATYGAYKQRAAW
          W..IINAVVL.ILLSALADPDQQHFSSSEL.GDFEFMDDANMCIAIAISFLMILICAMATYGAYKQRAAW
Retrocopy WYLIINAVVLRILLSALADPDQQHFSSSELEGDFEFMDDANMCIAIAISFLMILICAMATYGAYKQRAAW

Parental  IVPFFCYQIFDFALNALVAVTVLVYPNSIQEYIRQLPPNFPYKDDIMSVNPTCLVLIILLFISIILTFKW
          IVPFFCYQIFDFALNALVAVTVLVYPNSIQE.IRQL.PNFPYKDDIMSVNPTCLVL.ILLFISIILTFK.
Retrocopy IVPFFCYQIFDFALNALVAVTVLVYPNSIQECIRQLRPNFPYKDDIMSVNPTCLVLFILLFISIILTFKG

Parental  KAISC
          ..I.C
Retrocopy YLINC

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_2856 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 11 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000016959	3 retrocopies	retro_btau_1493, retro_btau_1759, retro_btau_786,
Callithrix jacchus	ENSCJAG00000031235	3 retrocopies	retro_cjac_1368, retro_cjac_1664, retro_cjac_3027,
Myotis lucifugus	ENSMLUG00000003618	1 retrocopy	retro_mluc_1182,
Macaca mulatta	ENSMMUG00000008926	1 retrocopy	retro_mmul_532,
Mus musculus	ENSMUSG00000022257	1 retrocopy	retro_mmus_1549,
Nomascus leucogenys	ENSNLEG00000003756	1 retrocopy	retro_nleu_1531,
Oryctolagus cuniculus	ENSOCUG00000013689	1 retrocopy	retro_ocun_627,
Otolemur garnettii	ENSOGAG00000000512	3 retrocopies	retro_ogar_1977, retro_ogar_2856 , retro_ogar_2902,
Pongo abelii	ENSPPYG00000018771	2 retrocopies	retro_pabe_2311, retro_pabe_279,
Pan troglodytes	ENSPTRG00000020448	1 retrocopy	retro_ptro_546,
Tursiops truncatus	ENSTTRG00000003124	1 retrocopy	retro_ttru_76,