RetrogeneDB ID: retro_ogar_3345

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873786.1:76668..78192(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOGAG00000031054
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: YAP1
• Ensembl ID: ENSOGAG00000002885
• Aliases: None
• Description: Yes-associated protein 1 [Source:HGNC Symbol;Acc:16262]

Sequence

>retro_ogar_3345
ATGGATCCGGAGCAGCAGCCGCCGCTTCAGCCGGCCCCCCAGGGCCAAAGGCAGCCGCCCGCGCAGAACACCCAGGAGCA
GGCCCCGCCGTCCGGGCTGGAGCAGCCGGCGCCCTCGGCTTCCAAGGAGGCGCCACAGGCACCATTCGCGGGGCACCAGA
TCGTGTGTGTCCAGGGGGACTCGGAGAGCGACCTGGAGGCCCTCTTCAACGCGGTCATCAACCCGAAGACGGCCAACGTG
CCGCAGACCGTGCCCATGAGGCTCCGGAAGCTGCCTGACTCCTTCTTCAAGCCGCCGGAGCCCAAATCCTGCTCCCCACA
GGCCAGTATGGATGCAGGCACTGCAGAAGACTTGACTCCACAGCATGTTCGAGCTCATTCCTCTCCGGCGTCCCTGAAGT
TGGAAGCCGCTTCTCCTGGGACGCTGACCCCCACCGGAGTAGTCTCTGACCCCGCAACCACATCTACAGCTCAACATCTT
CTGCAGTCTTCTTTGGAGATACCTGATGATGTACCTCTGCCAGCAGGCTGGGAGATAGCGGAGACATCTGCTGGTCAGAA
ATACTTCTTAAATCACACCGATCACACAACATCATGGCAGGACCCCAGGGAGGCCATGCTCTTGCAGATGAACGCTACAG
CCTCCACCAGTCCACCAGCGCAGCAGAATATGATGAACTCAGCTTCAGGTCCTCTTCCTGATGGATGGGAACAAGCCGTG
ACTCAGGATGGAGAAATTTACTATATAAACTATAAGAACATGACCGCCCCTTGGCTAGACCCAAGTCTTGACCCTCGTTT
TGGTAAAGCCGTGAACCAGAGAATCAGTCAGAGTGCTCCAGATGAACAGCCACCTCCCCTGACTCCCCAGAGCCCGCAGG
CAGACGTTATGGGTGGCAGCACCTCCAACCAGCAGCAACAGATGCGGCTCCAACTGCAGATGGAAGAAGAGCTCCTGCGC
CTGAAGCAACAAGAACTGCTCTGGCAGGCAATGTGGAGCCTCAGTCCCAGCCTAGCAAATCCTCCAAAATGCCAGGAAGT
AGCTCTCCATGGCCATTTGCCAACACTGGAGCAGGATAGTGGGACTCAAACTCCAGTGTCTTCTCCCAGGATGTTTCAGG
AACTGAGAACAATGACGGCCAACAGCTTCAATCTTCTTTTTAATGGTGGCGCCCATCACTCTCGAGATGAGAGTACAGAC
AGTGGACTAAGCGTGAGCAGCTGCGGTGTCCCTCGAACCCCAGAAGACATACTCAACAGCGTTGATGAAATGGATACAGA
TGACAGCGTTAACCAAAACACCCTGCTGACACTGCAGAACCATTTAAACGACTACCTTGAAAGCATTCCTGGGACCAGTG
TGGACCTTGGAATGGCTGTAGCACTGGAGGGAGATGAAATGTACCTAGAAGGAGAGGAGTTGATGCCAAATATTCAGGAA
GCTTTCAATTCTGACATCCTTAATGACATGGAGTCTGTTTTGGCTGCAGCCAAGCTAGACAAAGACAGTTTTCTTACATG
GTTA

Alignment

ORF - retro_ogar_3345 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.62 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MDPGQQPPPQPAPPGQGQPPAQTPQGQGQPSGPGQPAPQA---APPAPPAGHQIVHVRGDSETDLEALFN
          MDP.QQPP.QPAP.GQ.QPPAQ..Q.Q..PSG..QPAP.A...AP.AP.AGHQIV.V.GDSE.DLEALFN
Retrocopy MDPEQQPPLQPAPQGQRQPPAQNTQEQAPPSGLEQPAPSASKEAPQAPFAGHQIVCVQGDSESDLEALFN

Parental  AVMNPKTANVPQTVPMRLRKLPDSFFKPPEPKSHSRQASTDAGTAGALTPQHVRAHSSPASLQLGAVSPG
          AV.NPKTANVPQTVPMRLRKLPDSFFKPPEPKS.S.QAS.DAGTA..LTPQHVRAHSSPASL.L.A.SPG
Retrocopy AVINPKTANVPQTVPMRLRKLPDSFFKPPEPKSCSPQASMDAGTAEDLTPQHVRAHSSPASLKLEAASPG

Parental  TLTPTGVVSGPAATSAAQHLRQSSFEIPDDVPLPAGWEMAKTSSGQRYFLNHIDQTTTWQDPRKAMLSQM
          TLTPTGVVS.PA.TS.AQHL.QSS.EIPDDVPLPAGWE.A.TS.GQ.YFLNH.D.TT.WQDPR.AML.QM
Retrocopy TLTPTGVVSDPATTSTAQHLLQSSLEIPDDVPLPAGWEIAETSAGQKYFLNHTDHTTSWQDPREAMLLQM

Parental  NVTAPTSPPVQQSMMNSASGPLPDGWEQAMTQDGEIYYINHKNKTTSWLDPRLDPRF--AMNQRISQSAP
          N.TA.TSPP.QQ.MMNSASGPLPDGWEQA.TQDGEIYYIN.KN.T..WLDP.LDPRF..A.NQRISQSAP
Retrocopy NATASTSPPAQQNMMNSASGPLPDGWEQAVTQDGEIYYINYKNMTAPWLDPSLDPRFGKAVNQRISQSAP

Parental  VKQPPPLAPQSPQGGVMGGSNSNQQQQMRLQQLQMEKERLRLKQQELLRQAMRNINPSTANSPKCQELAL
          ..QPPPL.PQSPQ..VMGGS.SNQQQQMRL.QLQME.E.LRLKQQELL.QAM....PS.AN.PKCQE.AL
Retrocopy DEQPPPLTPQSPQADVMGGSTSNQQQQMRL-QLQMEEELLRLKQQELLWQAMWSLSPSLANPPKCQEVAL

Parental  RSQLPTLEQDGGTQNPVSSPGMSQELRTMTTNSSDPFLNSGTYHSRDESTDSGLSMSSYSVPRTPDDFLN
          ...LPTLEQD.GTQ.PVSSP.M.QELRTMT.NS.....N.G..HSRDESTDSGLS.SS..VPRTP.D.LN
Retrocopy HGHLPTLEQDSGTQTPVSSPRMFQELRTMTANSFNLLFNGGAHHSRDESTDSGLSVSSCGVPRTPEDILN

Parental  SVDEMDTGDTINQSTLPSQQNRFPDYLEAIPGTNVDLG---TLEGDGMNIEGEELMPSLQEALSSDILND
          SVDEMDT.D..NQ.TL...QN...DYLE.IPGT.VDLG....LEGD.M..EGEELMP..QEA..SDILND
Retrocopy SVDEMDTDDSVNQNTLLTLQNHLNDYLESIPGTSVDLGMAVALEGDEMYLEGEELMPNIQEAFNSDILND

Parental  MESVLAATKLDKESFLTWL
          MESVLAA.KLDK.SFLTWL
Retrocopy MESVLAAAKLDKDSFLTWL

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_3345 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
Callithrix jacchus	ENSCJAG00000000627	1 retrocopy	retro_cjac_4112,
Homo sapiens	ENSG00000137693	1 retrocopy	retro_hsap_3531,
Otolemur garnettii	ENSOGAG00000002885	2 retrocopies	retro_ogar_1565, retro_ogar_3345 ,
Pan troglodytes	ENSPTRG00000004211	1 retrocopy	retro_ptro_2399,