RetrogeneDB ID: retro_ogar_1819

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873568.1:3819918..3820574(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOGAG00000027591
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: MCUR1
• Ensembl ID: ENSOGAG00000013458
• Aliases: None
• Description: mitochondrial calcium uniporter regulator 1 [Source:HGNC Symbol;Acc:21097]

Sequence

>retro_ogar_1819
CTAAGCTTGTCTGTTGGGTACCTGCAACTGTAGCTCAAAAGGAGAGATTTCACTTCTTCGGGAGTAGGAAGCTCTACTTT
GACACCCATGCCTTAGTGTGCCTACTTGAAGAAAACGGGTTTACTGCTGAGCAAGAAGAAATCATTGTATCTGCATTGGT
CAAGATCATGGAGGCCAACATGGATATCATCTACAAAGACATGGTCACCACGATGCAGCAGGAGATCACTCTTCAGCAAA
TAATGTCTCAGCTTGCTAATGTGAAAAAAGATATGATTATTTTGGAGAAGAGTGAATTTTCAGCCCTCAGAGCAGAAAAT
GAGAAAATAAAACTTGAACTACATCAGTTAAAACAAGCAATGGATGAAGTGATCAAAGTCCGAATAGATACCAAGTTAGA
CTTCAATCTAGAAAAGAGCAGAGTAAAAGAACTGTATTCATTGAATGAAAGGAAGCTGTTGGAATTAAGAACAGAAATAG
TGGCACTGCATGCCCAGCAAGATTGGGTCCTTACCCAGACAGACAGGAAGACAGAGACTGAGGTTGCAGGCCTCAAAACC
ATGCTCAAGTCGCACAAGCTTGACAATATTAAATATTTAGCAGGATCTGTATTTACGTGCCCAACAGTAGCTCTGGGATT
CTATCGCCTGTGGGTA

Alignment

ORF - retro_ogar_1819 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.05 %
• Parental protein coverage: 99.55 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LSLSAGYLQLERKRRDFTSSG-SRKLYFDTHALVCLLEENGFTTQQAEIIVSALVKIIEANMDIVYKDMV
          LSLS.GYLQL..KRRDFTSSG.SRKLYFDTHALVCLLEENGFT..Q.EIIVSALVKI.EANMDI.YKDMV
Retrocopy LSLSVGYLQL*LKRRDFTSSG<SRKLYFDTHALVCLLEENGFTAEQEEIIVSALVKIMEANMDIIYKDMV

Parental  TKVQQEITLQQVMSQIANVKKDMIILEKSEFSALRAENEKIKLELHQLKQQVTDEVIKVRTDTKLDFNLE
          T..QQEITLQQ.MSQ.ANVKKDMIILEKSEFSALRAENEKIKLELHQLKQ...DEVIKVR.DTKLDFNLE
Retrocopy TTMQQEITLQQIMSQLANVKKDMIILEKSEFSALRAENEKIKLELHQLKQAM-DEVIKVRIDTKLDFNLE

Parental  KSRVKELYSLNERKLLELRTEIVALHAQQDRALTQTDRKIETEVAGLKTMLESHKLDNIKYLAGSVFTCL
          KSRVKELYSLNERKLLELRTEIVALHAQQD..LTQTDRK.ETEVAGLKTML.SHKLDNIKYLAGSVFTC.
Retrocopy KSRVKELYSLNERKLLELRTEIVALHAQQDWVLTQTDRKTETEVAGLKTMLKSHKLDNIKYLAGSVFTCP

Parental  TVALGFYRLWV
          TVALGFYRLWV
Retrocopy TVALGFYRLWV

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_1819 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 17 parental genes, and 27 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000000395	2 retrocopies	retro_amel_1628, retro_amel_473,
Canis familiaris	ENSCAFG00000009857	3 retrocopies	retro_cfam_1018, retro_cfam_1556, retro_cfam_823,
Callithrix jacchus	ENSCJAG00000016050	1 retrocopy	retro_cjac_2522,
Cavia porcellus	ENSCPOG00000014899	1 retrocopy	retro_cpor_934,
Equus caballus	ENSECAG00000009150	2 retrocopies	retro_ecab_273, retro_ecab_469,
Felis catus	ENSFCAG00000005972	3 retrocopies	retro_fcat_1290, retro_fcat_1405, retro_fcat_1538,
Homo sapiens	ENSG00000050393	1 retrocopy	retro_hsap_1795,
Gorilla gorilla	ENSGGOG00000002632	1 retrocopy	retro_ggor_1320,
Loxodonta africana	ENSLAFG00000003287	2 retrocopies	retro_lafr_1252, retro_lafr_870,
Microcebus murinus	ENSMICG00000000183	2 retrocopies	retro_mmur_280, retro_mmur_580,
Myotis lucifugus	ENSMLUG00000010975	1 retrocopy	retro_mluc_1574,
Mustela putorius furo	ENSMPUG00000000698	1 retrocopy	retro_mputfur_640,
Nomascus leucogenys	ENSNLEG00000000914	1 retrocopy	retro_nleu_2768,
Otolemur garnettii	ENSOGAG00000013458	3 retrocopies	retro_ogar_1587, retro_ogar_1819 , retro_ogar_3178,
Pan troglodytes	ENSPTRG00000017740	1 retrocopy	retro_ptro_1200,
Tarsius syrichta	ENSTSYG00000012562	1 retrocopy	retro_tsyr_810,
Tursiops truncatus	ENSTTRG00000012874	1 retrocopy	retro_ttru_1597,