RetrogeneDB ID: retro_ogar_1834

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873569.1:5539127..5539795(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOGAG00000033017
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PPM1A
• Ensembl ID: ENSOGAG00000003689
• Aliases: None
• Description: protein phosphatase, Mg2+/Mn2+ dependent, 1A [Source:HGNC Symbol;Acc:9275]

Sequence

>retro_ogar_1834
TTCCTTCAAGATCAGAAACCAAATAATCTGCGGGAGGAAGAACAAATTCCAAATACAAGTGGCTTTGTGATGAGTCAGCC
TGTGACTGAGCCTCTGGCTGTATCCAAAGCCCATGGAGATTTTCACTTCCAAAGTGTCCACGGGAAAGGCCTCACAGAGC
AGCTTGTGTCACCAGAGCCTGAAGCCCGTGACATTGAAAGATGGGAAGAAGTTGAGGAGTTCATTACCCTCGCCTGTGGT
GGTATCCGGGCTGTTCTGGGAAACAAAGAGCTCAGTGATCTTGTGACATCCAGACCCAAAGTCACTGATGACCTTGAGAA
AGTTTGCAAAGAATGGGTCAATGTCTGTTTGTGCAAGGGAAATCCAGACAAGGTGGGTGTGATTTTGATTGGTTTTCCAA
ATGCACCCAAAGTTTTGCCAGAAGCAGTGAAGGAAGGGCAGAGCTGGACAGGTCCCTGGAATGCCCAGGAGAAGAAATCC
TAAGGAAACAGGGGGAAGGCGCCAGGACTCAGTCCGTGTGGTACCTCCGCGAGTGAGTTAGTGAGCGAGATCACCCCCGG
CCTCCCACCAGGGAGTGAATGGGCCAGTGGAGCGCTATTGAAGCCCTTTATGGTAGATTGAATCCTCACAAAAATGACAG
CGCCGACTCTACATTAACTGAGGCTATG

Alignment

ORF - retro_ogar_1834 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.14 %
• Parental protein coverage: 58.12 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  FTQDHKPSNPLEKERIQNAGGSVMIQRVNGSLAVSRALGDFDYKCVHGKGPTEQLVSPEPEVHDIERSEE
          F.QD.KP.N..E.E.I.N..G.VM.Q.V...LAVS.A.GDF....VHGKG.TEQLVSPEPE..DIER.EE
Retrocopy FLQDQKPNNLREEEQIPNTSGFVMSQPVTEPLAVSKAHGDFHFQSVHGKGLTEQLVSPEPEARDIERWEE

Parental  DDQFIILACDGIWDVMGNEELCDFVRSRLEVTDDLEKVCNEVVDTCLYKGSRDNMSVILICFPNAPKVSP
          ...FI.LAC.GI..V.GN.EL.D.V.SR..VTDDLEKVC.E.V..CL.KG..D...VILI.FPNAPKV.P
Retrocopy VEEFITLACGGIRAVLGNKELSDLVTSRPKVTDDLEKVCKEWVNVCLCKGNPDKVGVILIGFPNAPKVLP

Parental  DAVKK-EAELDKYLESRVEEIIKKQGEGV-PDLVHVMRTLASENIPSLPPGGELASKRNVIEAVYNRLNP
          .AVK...AELD..LE...EEI..KQGEG.....V...R...SE.....PP..E.......IEA.Y.RLNP
Retrocopy EAVKE<RAELDRSLECPGEEILRKQGEGARTQSVWYLRE*VSERDHPRPPTRE*MGQWSAIEALYGRLNP

Parental  YKNDDTDSTSTDDM
          .KND..DST.T..M
Retrocopy HKNDSADSTLTEAM

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_1834 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 4 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Mus musculus	ENSMUSG00000021096	2 retrocopies	retro_mmus_2925, retro_mmus_2926,
Otolemur garnettii	ENSOGAG00000003689	1 retrocopy	retro_ogar_1834 ,
Drosophila melanogaster	FBgn0035425	1 retrocopy	retro_dmel_64,
Drosophila melanogaster	FBgn0086361	1 retrocopy	retro_dmel_66,