RetrogeneDB ID: retro_ogar_322

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873520.1:18593236..18594391(+)
• Located in intron of: ENSOGAG00000010597

Retrocopy information

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

Parental gene information

• Parental gene symbol: FH
• Ensembl ID: ENSOGAG00000009936
• Aliases: None
• Description: fumarate hydratase [Source:HGNC Symbol;Acc:3700]

Sequence

>retro_ogar_322
GAGGTGGCTGAAGGTAAATTAAATGATCATTTTCCTCTCGTGGTGTGGCAGACTGGATCCGGAACCCAGACGAATATGAA
TGTGAATGAAGTCATTAGCAATAGAGCAATTGAGATTTTAGGAGGCGAGCTTGGTAGCAAGAGCCCTGTGCATCCCAATG
ATCATGTTAATAAAAGCCAGAGCTCCAACGATACTTTCCCCACAGCAATGCACATTGCTGCTGCAGTCGAGGTTCACGAA
GTGCTGTTACCAGGACTGCAGAAGCTCCATGATGCTCTCCATGCAAAATCCCAAGAGTTTGCGCAGATCATCAAAATTGG
GCGCACTCACACTCAGGACGCTGTTCCCCTTACTCTTGGGCAGGAATTTAGTGGTTATGTTCAACAAGTGGCGTATGCAA
TGGCAAGAATAGAAGCTGCCATGCCACGGATCTACGAGCTCGCAGCTGGAGGCACGGCTGTCGGTACCGGTTTAAATACT
AGAGTCGGCTTCGCAGAAAAAGTTGCTGCCAAAGTGGCTTCACTCACAGGCTTGCCATTTGTCACTGCTCCAAATAAATT
TGAAGCTCTGGCTGCTCACGATGCTCTGGTTGAGCTCAGTGGAGCCATGAACACAACTGCTTGCAGTCTGATGAAGATAG
CAAATGACATCCGCTTTCTGGGTTCTGGTCCTCGGTCAGGTCTAGGTGAACTGATCTTGCCTGAAAATGAACCAGGAAGC
AGTATCATGCCAGGCAAAGTGAACCCTACTCAGTGTGAAGCAATGACCATGGTCGCAGCCCAAGTCATGGGGAATCATGT
CGCTGTAACGGTTGGAGGCAGCAATGGACATTTTGAGTTGAATGTTTTTAAGCCGATGATGATTAAAAATGTGTTACACT
CAGCCAGGCTGCTGGGGGATGCTTCAGTTTCCTTCACAGAAAACTGTGTGGTGGGAATCCAGGCCAACACAGAAAGGATC
AACAAGCTAATGAATGAGTCTCTAATGCTGGTGACAGCTCTCAATCCTCACATAGGGTATGACAAGGCAGCAAAGATTGC
CAAAACAGCACACAAAAATGGATCAACCTTAAAAGAAACTGCCATTGAACTTGGCTATCTCACAGCAGAGCAGTTTGATC
AGTGGGTAAAACCTAAGGACATGCTGGGTCCAAAG

Alignment

ORF - retro_ogar_322 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.29 %
• Parental protein coverage: 75.64 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EPKENKARKDYELLIFAVCSSAYTLVHVYEVISNRAIEILGGELGSKSPVHPNDHVNKSQSSNDTFPTAM
          E..E.K......L......S...T...V.EVISNRAIEILGGELGSKSPVHPNDHVNKSQSSNDTFPTAM
Retrocopy EVAEGKLNDHFPLVVWQTGSGTQTNMNVNEVISNRAIEILGGELGSKSPVHPNDHVNKSQSSNDTFPTAM

Parental  HIAAAVEVHEVLLPGLQKLHDALHAKSQEFAQIIKIGRTHTQDAVPLTLGQEFSGYVQQVAYAMARIEAA
          HIAAAVEVHEVLLPGLQKLHDALHAKSQEFAQIIKIGRTHTQDAVPLTLGQEFSGYVQQVAYAMARIEAA
Retrocopy HIAAAVEVHEVLLPGLQKLHDALHAKSQEFAQIIKIGRTHTQDAVPLTLGQEFSGYVQQVAYAMARIEAA

Parental  MPRIYELAAGGTAVGTGLNTRVGFAEKVAAKVASLTGLPFVTAPNKFEALAAHDALVELSGAMNTTACSL
          MPRIYELAAGGTAVGTGLNTRVGFAEKVAAKVASLTGLPFVTAPNKFEALAAHDALVELSGAMNTTACSL
Retrocopy MPRIYELAAGGTAVGTGLNTRVGFAEKVAAKVASLTGLPFVTAPNKFEALAAHDALVELSGAMNTTACSL

Parental  MKIANDIRFLGSGPRSGLGELILPENEPGSSIMPGKVNPTQCEAMTMVAAQVMGNHVAVTVGGSNGHFEL
          MKIANDIRFLGSGPRSGLGELILPENEPGSSIMPGKVNPTQCEAMTMVAAQVMGNHVAVTVGGSNGHFEL
Retrocopy MKIANDIRFLGSGPRSGLGELILPENEPGSSIMPGKVNPTQCEAMTMVAAQVMGNHVAVTVGGSNGHFEL

Parental  NVFKPMMIKNVLHSARLLGDASVSFTENCVVGIQANTERINKLMNESLMLVTALNPHIGYDKAAKIAKTA
          NVFKPMMIKNVLHSARLLGDASVSFTENCVVGIQANTERINKLMNESLMLVTALNPHIGYDKAAKIAKTA
Retrocopy NVFKPMMIKNVLHSARLLGDASVSFTENCVVGIQANTERINKLMNESLMLVTALNPHIGYDKAAKIAKTA

Parental  HKNGSTLKETAIELGYLTAEQFDQWVKPKDMLGPK
          HKNGSTLKETAIELGYLTAEQFDQWVKPKDMLGPK
Retrocopy HKNGSTLKETAIELGYLTAEQFDQWVKPKDMLGPK

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_322 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 8 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000017359	1 retrocopy	retro_cjac_2339,
Echinops telfairi	ENSETEG00000018721	2 retrocopies	retro_etel_1069, retro_etel_1457,
Microcebus murinus	ENSMICG00000003451	2 retrocopies	retro_mmur_1215, retro_mmur_720,
Mus musculus	ENSMUSG00000026526	1 retrocopy	retro_mmus_3600,
Oryctolagus cuniculus	ENSOCUG00000021494	1 retrocopy	retro_ocun_50,
Otolemur garnettii	ENSOGAG00000009936	1 retrocopy	retro_ogar_322 ,
Rattus norvegicus	ENSRNOG00000003653	1 retrocopy	retro_rnor_2979,
Xenopus tropicalis	ENSXETG00000032112	1 retrocopy	retro_xtro_55,