RetrogeneDB ID: retro_ptro_2399

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 6:148949416..148950390(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: YAP1
• Ensembl ID: ENSPTRG00000004211
• Aliases: None
• Description: None

Sequence

>retro_ptro_2399
ATGGATCCCGGGCAGCAGCAACCGCCTCAACCGGCCCCCCAGGGCCAAGGACAGCCACCGGCGCAGCGCCCCCCAGGGGC
AGGGCTCGCGGTCCAGACCAGGGCAGCCGGTGCCCACGGCGACCCAGGCGGCGCCACAGGCACCCCCCACCGGGCATCAG
ATCCTGCACGTCCACGGGGACTGGGAGAGGAACCTGGAGGCGCTCTTCAACGCCGTCATGAACCCCAAGATGGCCAAGGT
GCACCAGACCATGCCCATGAGGCTCCGGAAGCTGCCCGACTCTTTCAAGCCACTCGAGCCCAAGTCCAACTCCCAACGGG
TCAGTACTGAGGCAGGCACCGCAGGAGCCCTGACTCCACAGCACGTTCGAGCTCATTCCTCTCCAGCTTCTCTGCAGTTG
GGAGCTGTTTCTCCTGGGACACTGACCCCCACTGGAGTAGTTTCTGGCCCAGCAGCTACACCCACAGCTCAGCATTTTCA
CAGTCTTCTTTTGAGATACCTGATGGTGTACCTCTACCAGCAGTTTGGGAGATGGCGAAGGCATCTTCTGGTCAGAGATA
CTTCTTAAATCACATCGATCAGAAAACAACACAGCAGGACCCCCAGGAAGACCATGCTGTCTCAGATGAATGTTATAGCC
AATCCACCAGTGCAGCAGAATATGATGAACTCGGCTTCAGGTCCTCTTCCTGATGGATGGGAACAAGCCATGACTCAGGA
TGGAGAAATTTACTGTATAAACCATAAGAACAAGACCGCCTCTTGGCTAGACTCAAGGCTTGACCCTCGTTTTGCCAGGA
ACCTGAGAATCAGAGTGCTCCAGTGAAACAGCCACCACCCCTGGTTCCCCAGAGCCCACAAGGAGGCGTCATAGTGGCAG
CAACTCCAACCAGCAGCGACAGATGCGACCGCAGCAACTGCAGATGGAGGAGAGGCTGCAGCTGAAACAGCAATAACTGC
TTCGGCAGGAGTTA

Alignment

ORF - retro_ptro_2399 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.3 %
• Parental protein coverage: 65.48 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  MDPGQQPPPQPAPQGQGQPPSQ-PPQGQGPPSGPGQPAPAATQAAPQAPPAGHQIVHVRGDSETDLEALF
          MDPGQQ.PPQPAPQGQGQPP.Q..PQGQG..S.PGQP.P.ATQAAPQAPP.GHQI.HV.GD.E..LEALF
Retrocopy MDPGQQQPPQPAPQGQGQPPAQ>APQGQGSRSRPGQPVPTATQAAPQAPPTGHQILHVHGDWERNLEALF

Parental  NAVMNPKTANVPQTVPMRLRKLPDSFFKPPEPKSHSRQASTDAGTAGALTPQHVRAHSSPASLQLGAVSP
          NAVMNPK.A.V.QT.PMRLRKLPDS.FKP.EPKS.S...ST.AGTAGALTPQHVRAHSSPASLQLGAVSP
Retrocopy NAVMNPKMAKVHQTMPMRLRKLPDS-FKPLEPKSNSQRVSTEAGTAGALTPQHVRAHSSPASLQLGAVSP

Parental  GTLTPTGVVSGPAATPTAQHLR-QSSFEIPDDVPLPAGWEMAKTSSGQRYFLNHIDQTTTWQD-PRKAML
          GTLTPTGVVSGPAATPTAQH...QSSFEIPD.VPLPA.WEMAK.SSGQRYFLNHIDQ.TT.QD.PRK.ML
Retrocopy GTLTPTGVVSGPAATPTAQHFH<QSSFEIPDGVPLPAVWEMAKASSGQRYFLNHIDQKTTQQD>PRKTML

Parental  SQMNVTAPTSPPVQQNMMNSASGPLPDGWEQAMTQDGEIYYINHKNKTTSWLDPRLDPRFAMNQRI-SQS
          SQMNV.A...PPVQQNMMNSASGPLPDGWEQAMTQDGEIY.INHKNKT.SWLD.RLDPRFA.N.RI....
Retrocopy SQMNVIA--NPPVQQNMMNSASGPLPDGWEQAMTQDGEIYCINHKNKTASWLDSRLDPRFARNLRI<QSA

Parental  APVKQPPPLAPQSPQGGVM-GGSNSNQQQQMRLQQLQMEKERLRLKQQELLRQAM
          .....PP.L.PQSPQGGV...GSNSNQQ.QMR.QQLQME.ERL.LKQQ.LLRQ..
Retrocopy PVKQPPP-LVPQSPQGGVI<SGSNSNQQRQMRPQQLQME-ERLQLKQQ*LLRQEL

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP007412_brain_prefrontal_cortex	0.00 RPM	6.76 RPM
SRP007412_cerebellum	0.07 RPM	7.38 RPM
SRP007412_heart	0.06 RPM	52.96 RPM
SRP007412_kidney	0.05 RPM	61.88 RPM
SRP007412_liver	0.07 RPM	43.21 RPM
SRP007412_testis	0.53 RPM	20.66 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2399 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2399 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2399 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3531

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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 ,