RetrogeneDB ID: retro_ogar_3480

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873897.1:123125..124244(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOGAG00000033235
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: SPOP
• Ensembl ID: ENSOGAG00000012793
• Aliases: None
• Description: speckle-type POZ protein [Source:HGNC Symbol;Acc:11254]

Sequence

>retro_ogar_3480
AAACTGATGAGTTCTTCACCCACAGCAGAGATGTCAAGTGTCCCTGTAACTGAGAGCTGGTGCTACACACAGATCAAGGT
AGTGAAATTCTCCTACATATGGGCCATCAATAACTTTAGCTTTTACCTGGGGGAAGTGGGTGAGTTCATTAAAAGTTCAA
CCTTTTCGTCAGGAGCCAGTGATAAACTAAAATGGTGTTTGCGAGTAAACCCAAAAGGGCTAGATGAAGAAAGCAAAGAT
TACCTGTCACTTTACCTGTTACTGGTCAGCCGTCCAAAGAAGGAAGTTCAGGCAAGATTCAAATTCTCCATCCTTAATAC
TAAGAGAGAAGAGACCAGAGCTATGGAGAGCCAGCGGGCATATAGGTTTGTGCAAGGCAAAGACTGGGGATTCAAAAAAT
TCATCCGTAGAGATTTTCTCTTGGATGAGGCCCACGGGCTTCTGCCTGATGACAAGCTTACTATCTTTTGTGAGGTGAAT
TTGGTGCAAGATTCTGTCAACATTTCTGGCCGGAATACTATGACTAGGGTGAAGGTTCCTGAGTGCCGGTTTACAGATGA
GATAGGAGGACTGTGGGAGAATTCTCGGTTCACAGACTGCTGCTTATGTGTTGCTGGCCAGGAATTCCAGGCTCACAAAG
CTATCTTAGCAGCGCGTTCTCCAGTTTTTAGTGCCATGTTTGAACATGAAATGAAGGAGAGCAAAAAAAATCGAGTTGAA
ATCAATGACATGGAGCTTGAAGTTTTTAAGGAAATGATGTCCTTCATTTACACGGGGAAGGCTCCAAACCTCTGCAAAAT
GGCTGTTGATTTGCTGGCAGCTGCTGACAAGTACACCCTGGAGCGTTTGAAGGTCATGTGTGAGAATGCCCTCTCCAATA
ACCTGTCTGTGGAGAATGCTGCTGAGATCCTTATCCTGGCGGACCTCCACAGTGCAGATCAGCTGAAAACTCAGGCAGTG
AATTTCATCAGCTATCACGCTTCAGAAGTCTTGGAGACCTGTGAATGGAAGTCGATGGTGGTGTCACATCCCCACTTGGT
GGCTGAAGCATACCGCTCTCTGGCTTCAGCACAGCGCCCTTTTCTTAGACTCTGTCGACCCAAACGCCTGAAGCAATCC

Alignment

ORF - retro_ogar_3480 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.99 %
• Parental protein coverage: 99.47 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RVPSPPPPAEMSSGPVAESWCYTQIKVVKFSYMWTINNFSFCREEMGEVIKSSTFSSGANDKLKWCLRVN
          ...S..P.AEMSS.PV.ESWCYTQIKVVKFSY.W.INNFSF...E.GE.IKSSTFSSGA.DKLKWCLRVN
Retrocopy KLMSSSPTAEMSSVPVTESWCYTQIKVVKFSYIWAINNFSFYLGEVGEFIKSSTFSSGASDKLKWCLRVN

Parental  PKGLDEESKDYLSLYLLLVSCPKSEVRAKFKFSILNAKGEETKAMESQRAYRFVQGKDWGFKKFIRRDFL
          PKGLDEESKDYLSLYLLLVS.PK.EV.A.FKFSILN.K.EET.AMESQRAYRFVQGKDWGFKKFIRRDFL
Retrocopy PKGLDEESKDYLSLYLLLVSRPKKEVQARFKFSILNTKREETRAMESQRAYRFVQGKDWGFKKFIRRDFL

Parental  LDEANGLLPDDKLTLFCEVSVVQDSVNISGQNTMNMVKVPECRLADELGGLWENSRFTDCCLCVAGQEFQ
          LDEA.GLLPDDKLT.FCEV..VQDSVNISG.NTM..VKVPECR..DE.GGLWENSRFTDCCLCVAGQEFQ
Retrocopy LDEAHGLLPDDKLTIFCEVNLVQDSVNISGRNTMTRVKVPECRFTDEIGGLWENSRFTDCCLCVAGQEFQ

Parental  AHKAILAARSPVFSAMFEHEMEESKKNRVEINDVEPEVFKEMMCFIYTGKAPNLDKMADDLLAAADKYAL
          AHKAILAARSPVFSAMFEHEM.ES...RVEIND.E.EVFKEMM.FIYTGKAPNL.KMA.DLLAAADKY.L
Retrocopy AHKAILAARSPVFSAMFEHEMKESXXXRVEINDMELEVFKEMMSFIYTGKAPNLCKMAVDLLAAADKYTL

Parental  ERLKVMCEDALCSNLSVENAAEILILADLHSADQLKTQAVDFINYHASDVLETSGWKSMVVSHPHLVAEA
          ERLKVMCE.AL..NLSVENAAEILILADLHSADQLKTQAV.FI.YHAS.VLET..WKSMVVSHPHLVAEA
Retrocopy ERLKVMCENALSNNLSVENAAEILILADLHSADQLKTQAVNFISYHASEVLETCEWKSMVVSHPHLVAEA

Parental  YRSLASAQCPFLGPPR-KRLKQS
          YRSLASAQ.PFL...R.KRLKQS
Retrocopy YRSLASAQRPFLRLCRPKRLKQS

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_3480 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 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Myotis lucifugus	ENSMLUG00000011013	1 retrocopy	retro_mluc_2589,
Otolemur garnettii	ENSOGAG00000012793	1 retrocopy	retro_ogar_3480 ,
Rattus norvegicus	ENSRNOG00000004686	2 retrocopies	retro_rnor_1677, retro_rnor_534,
Rattus norvegicus	ENSRNOG00000042221	1 retrocopy	retro_rnor_2748,
Rattus norvegicus	ENSRNOG00000047767	2 retrocopies	retro_rnor_1675, retro_rnor_26,