RetrogeneDB ID: retro_ogar_2657

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873644.1:489262..489741(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOGAG00000034138
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: YIPF5
• Ensembl ID: ENSOGAG00000001543
• Aliases: None
• Description: Yip1 domain family, member 5 [Source:HGNC Symbol;Acc:24877]

Sequence

>retro_ogar_2657
GTGTCAGGCTTTGAAAACTTAAACCCGGATTTCTACCAGACAAGTTACAGCATCGATGACCAGTCACACCAGTCCTACGA
TTATGGAGGAAGTGGAGGACCCTATAGCAAACAATATGCCGGCTGTGACTACTCACAGCAGGGCCGATTTGTCCCACCAG
ACATGAGGCAGCCACAGCAGCCATACACTGGGCAGATTTTCCAGCCAGCTCAGGCATATACTCCAACTTCACCTTCGCCA
TTCTATGGAATCAACTTAGAGGATGAGCCACCTTTATTAGTAGTGTTAGGTATCAATTTTGACCACATCTGGCAAAAAAC
CCTGACAGTGTTACATCCATTAAAAGTGGCAGATGCAGCATCATGAAGGAAACTGATCTGGCAGGACCAATGGTTCTTTG
CCTTGCCTTTGGAGCCACATTATTGCTGGCTGGCAAAATCCAGTTTTGTTGTGCATATGGGATCAGTGCAGTTGGATGT

Alignment

ORF - retro_ogar_2657 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.71 %
• Parental protein coverage: 61.39 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSGFENLNTDFYQTSYSIDDQSQQSYDYGGSGGPYSKQYASYDYSQQGRFVPPDMMQPQQPYTGQIFQPT
          .SGFENLN.DFYQTSYSIDDQS.QSYDYGGSGGPYSKQYA..DYSQQGRFVPPDM.QPQQPYTGQIFQP.
Retrocopy VSGFENLNPDFYQTSYSIDDQSHQSYDYGGSGGPYSKQYAGCDYSQQGRFVPPDMRQPQQPYTGQIFQPA

Parental  QTYTP-SPQPYYGNNFEDEPPLLEELGINFDHIWQKTLTVLHPLKVADG-SIMNETDLAGPMVFCLAFGA
          Q.YTP.SP.P.YG.N.EDEPPLL..LGINFDHIWQKTLTVLHPLKVAD..SIM.ETDLAGPMV.CLAFGA
Retrocopy QAYTPTSPSPFYGINLEDEPPLLVVLGINFDHIWQKTLTVLHPLKVADA<SIMKETDLAGPMVLCLAFGA

Parental  TLLLAGKIQFGYVYGISAIGC
          TLLLAGKIQF...YGISA.GC
Retrocopy TLLLAGKIQFCCAYGISAVGC

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_2657 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 6 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000010135	1 retrocopy	retro_amel_489,
Dasypus novemcinctus	ENSDNOG00000014497	1 retrocopy	retro_dnov_16,
Felis catus	ENSFCAG00000031350	1 retrocopy	retro_fcat_177,
Myotis lucifugus	ENSMLUG00000011143	3 retrocopies	retro_mluc_2549, retro_mluc_521, retro_mluc_750,
Otolemur garnettii	ENSOGAG00000001543	2 retrocopies	retro_ogar_2657 , retro_ogar_2803,
Tarsius syrichta	ENSTSYG00000008071	1 retrocopy	retro_tsyr_16,