RetrogeneDB ID: retro_ogar_2535

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873632.1:5612665..5613211(+)
• Located in intron of: ENSOGAG00000005019

Retrocopy information

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

Parental gene information

• Parental gene symbol: FRG1
• Ensembl ID: ENSOGAG00000005749
• Aliases: None
• Description: FSHD region gene 1 [Source:HGNC Symbol;Acc:3954]

Sequence

>retro_ogar_2535
AGTAAGAAGAAAAAAGCAAAGACAGGAAGAGAAACAGAGAAGAGGATGAAAAAACCCAACTGGATCTTGTTGGAATCTGG
TGGACAGTAACAAACTTCAGTGAAATTTCAGGAACCACAGCCATCGAAATGGATAAAGGAACCTACATACATGCACTTGA
CAATGGTCTTTTCACACTGGGGGCCCCACATAAAGAAGCTGATGAGGGCCCCAGTCCTCCCGAACAGTGTACGGCTGTCA
AATTGTCCAATTCCAGAATTGCCTGAAATCTGGTTATGGAAAACATCTTGGTATAAATTCAGATGGACTTGTTGGGTGGT
CAGACACAATTAGACGGAGAGAACAGTGGGAACCAGTCTTTCAAGATGGAAAATGGCTTTACTGGCCTCAACTAGCTGCT
TTATTAGATGCAATGAAGCAGGTGACATAGAAGCAAAAAGTCAAACAGCAGGAGAAGAAGAAGTGACAAAGATTCAGTCC
TGTGCTGAAAGGGAAACCAGGAAAAGAGACGACGTCCCACAAGGAGACAAAGGCAACGTAAAGCAG

Alignment

ORF - retro_ogar_2535 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.56 %
• Parental protein coverage: 71.32 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  SKKKK-SKDRTRTREEDEKTQLDIVGIWWTVTNFGEISGTIAIEMDKGTYIHALDNGLFTLGAPHKEVDE
          SKKKK.SKDR.R.REEDEKTQLD.VGIWWTVTNF.EISGT.AIEMDKGTYIHALDNGLFTLGAPHKE.DE
Retrocopy SKKKK<SKDRKRNREEDEKTQLDLVGIWWTVTNFSEISGTTAIEMDKGTYIHALDNGLFTLGAPHKEADE

Parental  GPSPPEQFTAVKLSDSRIA-LKSGYGKYLGINSDGLVVGRSDAIGPREQWEPVFQDG-KMALLASNSCFI
          GPSPPEQ.TAVKLS.SRIA.LKSGYGK.LGINSDGL.VG.SD.I..REQWEPVFQDG.KMALLAS.SCFI
Retrocopy GPSPPEQCTAVKLSNSRIA<LKSGYGKHLGINSDGL-VGWSDTIRRREQWEPVFQDG<KMALLASTSCFI

Parental  RCNEAGDIEAKSKTAGEEEMIKIRSCAERETKKKDDIPEEDKGNVKQ
          RCNEAGDIEAKS.TAGEEE..KI.SCAERET.K.DD.P..DKGNVKQ
Retrocopy RCNEAGDIEAKSQTAGEEEVTKIQSCAERETRKRDDVPQGDKGNVKQ

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_2535 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 7 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000022277	7 retrocopies	retro_cpor_1349, retro_cpor_1350, retro_cpor_1359, retro_cpor_1361, retro_cpor_1362, retro_cpor_1363, retro_cpor_864,
Felis catus	ENSFCAG00000025737	1 retrocopy	retro_fcat_464,
Otolemur garnettii	ENSOGAG00000005749	2 retrocopies	retro_ogar_1523, retro_ogar_2535 ,
Pan troglodytes	ENSPTRG00000016671	1 retrocopy	retro_ptro_2930,
Rattus norvegicus	ENSRNOG00000009846	1 retrocopy	retro_rnor_88,
Tupaia belangeri	ENSTBEG00000014491	2 retrocopies	retro_tbel_1202, retro_tbel_3435,
Tarsius syrichta	ENSTSYG00000010985	2 retrocopies	retro_tsyr_1347, retro_tsyr_1778,