RetrogeneDB ID: retro_ogar_648

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873525.1:6431395..6432160(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOGAG00000029913
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PARL
• Ensembl ID: ENSOGAG00000006126
• Aliases: None
• Description: presenilin associated, rhomboid-like [Source:HGNC Symbol;Acc:18253]

Sequence

>retro_ogar_648
GGGTATGCTTTTGGATCAGCTGCTATTTGGCAATATGAATCACTGAAATCCAGGGTCCAGAGTTATTTTGATGGTATAAA
AGCTGATTGGTCGGATAGCATAAAACCACAGAAAGAAGGAGACTTCAGAAAGGAGATTAACAAGTGGTGGAATAACCTTA
GTGACGGCCAGCAGACTGTGACAGGTATCATAGCTGCAGATATCTTCGTATTCTGTGTATGGAGAGTACCTTCTCTACAG
AGAACAATGATCAGATATTTCACATCCAATCCGGCCTCAAAGGTCCTTTGTTCTCCAATGTTGCTGTCAACATTCAGTCA
TTTCTCCATTTTTTCATATGGCAGCAAATATGTCTGTGTTGTGGAGCTTCTCCCCCAGCAAAGTGAACATTCGGGTCAAG
AGCAGTTCATGGCAGTGTATCTGTCTGCAGGCGTTATTTCCAATTTTGTCAGTTACATGTGTAAAGTTGCCACAGGAAGA
TATGGACCATCACTTGGTGCATCTGGTGCGATCATGACTCTCCTGGCCGCTGTCTGCACTAAGATCCAAGAAGGGAGGCT
CGTTATTATCTTCCCTCTAATGTTCACCTTCACAGCAGAGAATGCCCTAAAAGCCAGTATTGCCATGGACACAGTGGGGA
TGATCCTGAGATGGAAATTTTTTGATCATGCAGCACATCTTGGGGGAGGTCTCTTGGGAATATGGTATGTTACTTGTGGT
CATGAACTCATTTGGAAGAATAGAGAGCCTCTAGTGAAAATCTGG

Alignment

ORF - retro_ogar_648 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.27 %
• Parental protein coverage: 75.22 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  GCAFGSAAIWQYESLKSRVQSYFDGIKADWLDSIKPQKEGDFRKEINKWWNNLSDGQRTVTGIIAANVFV
          G.AFGSAAIWQYESLKSRVQSYFDGIKADW.DSIKPQKEGDFRKEINKWWNNLSDGQ.TVTGIIAA..FV
Retrocopy GYAFGSAAIWQYESLKSRVQSYFDGIKADWSDSIKPQKEGDFRKEINKWWNNLSDGQQTVTGIIAADIFV

Parental  FCLWRVPSLQRTMIRYFTSNPASKVLCSPMLLSTFSHFSL-FHMAANMYVLWSFSSSIVNI-LGQEQFMA
          FC.WRVPSLQRTMIRYFTSNPASKVLCSPMLLSTFSHFS..FHMAANM.VLWSFS.S.VNI..GQEQFMA
Retrocopy FCVWRVPSLQRTMIRYFTSNPASKVLCSPMLLSTFSHFSI>FHMAANMSVLWSFSPSKVNI<SGQEQFMA

Parental  VYLSAGVISNFVSYVCKVATGRYGPSLGASGAIMTVLAAVCTKIPEGRLAIIFLPMFTFTAGNALKAIIA
          VYLSAGVISNFVSY.CKVATGRYGPSLGASGAIMT.LAAVCTKI.EGRL.IIF..MFTFTA.NALKA.IA
Retrocopy VYLSAGVISNFVSYMCKVATGRYGPSLGASGAIMTLLAAVCTKIQEGRLVIIFPLMFTFTAENALKASIA

Parental  MDTVGMILGWKFFDHAAHLGGALFGIWYVTYGHELIWKNREPLVKIW
          MDTVGMIL.WKFFDHAAHLGG.L.GIWYVT.GHELIWKNREPLVKIW
Retrocopy MDTVGMILRWKFFDHAAHLGGGLLGIWYVTCGHELIWKNREPLVKIW

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_648 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 9 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000021241	2 retrocopies	retro_cjac_1415, retro_cjac_2384,
Dipodomys ordii	ENSDORG00000014935	1 retrocopy	retro_dord_315,
Homo sapiens	ENSG00000175193	1 retrocopy	retro_hsap_3526,
Gorilla gorilla	ENSGGOG00000000416	1 retrocopy	retro_ggor_2384,
Mus musculus	ENSMUSG00000033918	2 retrocopies	retro_mmus_1882, retro_mmus_3526,
Nomascus leucogenys	ENSNLEG00000006072	1 retrocopy	retro_nleu_491,
Otolemur garnettii	ENSOGAG00000006126	1 retrocopy	retro_ogar_648 ,
Pan troglodytes	ENSPTRG00000015673	1 retrocopy	retro_ptro_2394,
Ictidomys tridecemlineatus	ENSSTOG00000023222	1 retrocopy	retro_itri_380,