RetrogeneDB ID: retro_ogar_3049

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873705.1:2556713..2557484(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PIM2
• Ensembl ID: ENSOGAG00000009613
• Aliases: None
• Description: pim-2 oncogene [Source:HGNC Symbol;Acc:8987]

Sequence

>retro_ogar_3049
TTATCCCAAGGCAGTTTTAGTTTGTCTTAGAAGCAGCATTTGCTTATCAATGAAAATCAAGTTGCAGATAAGTGATTTCC
CTTAATCGTGTGCTGGGATGGTCCCTCTTGTCAGACTTAGTGAGTTGCCCACTCGAAGTAACAATGCTGTGGAAAGTGGG
TGAAGGTGGAGGGCACCCTGATGTGATCAGCCTGCTTGACTGGTTTGAGACATAAGAGGGCTTTATGCTGGTCCTTGAGT
GGCCTTTGCCTGCCCAGGATCACTTACTACATCACAGAAAAAGGCCTACTGGGTGAAGGCCGAAGCTGCTGCTTCCTTGG
CCAGGTAGTGGCAGCTATCCAACACTGCCATGCCGGTGGAGTTGTCCATCCTGACATCAAGGATGAGAATATTCTGACCG
ACTTCCGCTGGGGATGTATCAGACTCCTTGATTTGGGTTCAGGTGTCCTACTTCATGATGAACCTTATACTGACTTTAAT
GGGACAAGGGTGTACAGCTCTTTGGAATGGATCTCTCGACACCAGTACCACACACTCCCAGCTACTGTGTGATCACTGCG
TATCCTCCTGCGTGATGTAGTGTGTGGGGAAATTCCCTTCGAAAGCGACCAGTATATTCTGGATGCTAAGCTTCACTTCC
CTACCCATGTTTCCCCAGACTGCTGTGCCATAATCTGCTGGTGCCTGCCCCCCAAACTCTCTTCCAGGCCCTCACTGGAA
AAGATCCTGCTGGTCCACCGAATGCAAACACCAGGTCAGGAAACAATTCTC

Alignment

ORF - retro_ogar_3049 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.15 %
• Parental protein coverage: 69.73 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LGKGGFGTVFAGHRVTDRLQVAIK-VIPRNRVLGWSPLSDSVSCPLEVALLWKVGEGGGHPGVIRLLDWF
          L..G.F......H......QVA.K.VI..NRVLGWS.LSD.VSCPLEV..LWKVGEGGGHP.VI.LLDWF
Retrocopy LSQGSFSLS*KQHLLINENQVADK<VISLNRVLGWSLLSDLVSCPLEVTMLWKVGEGGGHPDVISLLDWF

Parental  ETQEGFMLVLERPLPAQDLFDYITEKGPLG-EGRSRCFFGQVVAAVQHCHARGVVHRDIKDENILIDLRR
          ET.EGFMLVLE.PLPAQD.......K.P.G.EGRS.CF.GQVVAA.QHCHA.GVVH.DIKDENIL.D.R.
Retrocopy ET*EGFMLVLEWPLPAQDHLLH-HRKRPTG>EGRSCCFLGQVVAAIQHCHAGGVVHPDIKDENILTDFRW

Parental  GCVKLLDFGSGALLHDEPYTDFDGTRVYSPPEWISRHQYHALPATVWSLGILLYDMVCGDIPFERDQEIL
          GC..LLD.GSG.LLHDEPYTDF.GTRVYS..EWISRHQYH.LPATV.SL.ILL.D.VCG.IPFE.DQ.IL
Retrocopy GCIRLLDLGSGVLLHDEPYTDFNGTRVYSSLEWISRHQYHTLPATV*SLRILLRDVVCGEIPFESDQYIL

Parental  DAELHFPAHVSPDCCALIRRCLAPKPSSRPSLEEILLDPWMQTPAEEAPL
          DA.LHFP.HVSPDCCA.I..CL.PK.SSRPSLE.ILL...MQTP..E..L
Retrocopy DAKLHFPTHVSPDCCAIICWCLPPKLSSRPSLEKILLVHRMQTPGQETIL

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_3049 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 5 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Echinops telfairi	ENSETEG00000007968	1 retrocopy	retro_etel_401,
Mus musculus	ENSMUSG00000031155	2 retrocopies	retro_mmus_2005, retro_mmus_3178,
Oryctolagus cuniculus	ENSOCUG00000015757	1 retrocopy	retro_ocun_1279,
Otolemur garnettii	ENSOGAG00000009613	1 retrocopy	retro_ogar_3049 ,
Sorex araneus	ENSSARG00000008832	3 retrocopies	retro_sara_222, retro_sara_223, retro_sara_395,