RetrogeneDB ID: retro_ptro_181

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 1:106748355..106750133(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MATR3
• Ensembl ID: ENSPTRG00000017294
• Aliases: None
• Description: Pan troglodytes matrin 3 (MATR3), transcript variant 2, mRNA. [Source:RefSeq mRNA;Acc:NM_001205233]

Sequence

>retro_ptro_181
ATGTCCAAGTCATTCCAGCAGTCATCTCTCAGTAGGGACTAACAGGGTCATGGGTGTGACCTGTCTGCGGCAGGCATAGG
CCTTCCTGCTGCTGTTACCCAGTCTTTAAGTATGCCAGCATCTCTTAGGAAGGATGAACCAGGGTACTGCACGCCTTGCT
AGTTGAATGAATCTTGGAACGAATTCTTCATTGAATCAAAAAGGAGCTCATAGTGCACGGTCTTCTGCTAGTACTTCTTC
CTATAATTTACAGTCTATATTTAACATTGGAAGTAGAGGTCCACTCCCTTTATCTTCTCAACGCTGTGGAGATGCAGACC
AGGACAGTAACATTTTGGCCAGCTTTGGTCTGTCTGCTAGAGACTTAGATGAACTGAGTCGTTATCCAGAGGACAAGATG
ACTCCTGAGAATTTGCCCCAAATCCTTCTACAGCTTAAAAGGAGGAGAACTGAAGAAGGCCCTACTTTGAGTAATGGTAG
AGATGACAGATCTGCTGCATGGGAGCCACCATACAGAGTACCTAGGGATGATTTGGAAGAAAAAAGGCACTTTAGAAGAG
ATAGTTTTGATGATCATGGTCCTAGTCTCAACCTGGTGCTTGATTATGATCATGGAAGTCATTCTCAAGAATCTGGCTAT
TATGACAGAATGGATTATGAAGATGACAGATTACGAGATGGAAAAAAGGTGTAGGGATGATACTTTTTTTGGTGAGACCT
CGCGTAACTATCATAAATTTGACAGTGAGTATGAAAGAATGGGACTTGGTCATGGTCCTGACCCTTTACAAGAGAGATCT
CTCTTTGAGAAAAAGAGGGGCGCTCCTCCAAGTAGCAATATTGAAGACTTTCATGGACTCTTACTGAAAGGTTATACCCA
TCTGTGCTCTATATGTGATTTGCCAGTTCATTCTAATGAGGAGTTGAGTCAACATATCAATAGAGCAAGCCACAGTCGTC
GATGCCAGCTTCTTCTTGAAATCTACCCAGAATGGGATCCTGACAATGATACAGAACACACAGTGGGTGATCCATTCATG
TCTCAGCAGTCTACAAACCCAGCACCAGGAATTCTGGGATCTCCACCTCCCTCGTTTCATCTTGGAGGACCAGCAATTGG
ACCAAGAGGAAATCTGGGTGCTGGAAATGGAAACCTGCAAAGAACTAGACACATACAAAATGGCAGAGTGGAAACGAGCA
GAGTTGTTCACATCATGGATTTTCAGTGAGGGAAAAACTTGAGATACCAGCTATTACAGCTGGTAGAACCATTTGGAGTC
ATTTCAAATCATCTGATTCTAAATAAAATTAATGAGGCATTTATTGAAAGGGCAACCACAGAGGATGCTCAGGCTGCAGT
GGATTATTATACAACCACACCAGCGTTAGTATTAAGCAAGCCAGTGAGAGTTCATTTATCCCAGAAGTATAAAAGAATAA
AGAAACCTGAAGGAAAGCCAGATCAGAAGTTTGATCGAAGGCAAGAGCTTGGATGTGTGATACATCACAGCAATTTGCCC
CATTCTGCCTATTCTGATAGTGCTGTTCTCAAGCTTGCTGAGCCTTATGGGAAAATAAAGAATTACATATTGATGAGGAT
GAAAAGTCAGGCTTTTATTGAGATGGAGACAAGAGAAGATGCAATGGCAATGGTTGACCATTGTTTGAAAAAAGCCCTTT
AGTTTCAGGGGAGATGTGTGAAGGTAGACCTGTCTGAGAAATATAAAAATCTAGTACTGAGGATTCCAAACAGAGGCATT
GATTTACTGAAAAAAGAT

Alignment

ORF - retro_ptro_181 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.4 %
• Parental protein coverage: 69.66 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MSKSFQQSSLSRDSQGHGRDLSAAGIGLLAAATQSLSMPASL-GRMNQGTARLASLMNLGMSSSLNQQGA
          MSKSFQQSSLSRD.QGHG.DLSAAGIGL.AA.TQSLSMPASL.GRMNQGTARLAS.MNLG..SSLNQ.GA
Retrocopy MSKSFQQSSLSRD*QGHGCDLSAAGIGLPAAVTQSLSMPASL>GRMNQGTARLAS*MNLGTNSSLNQKGA

Parental  HSALSSASTSSHNLQSIFNIGSRGPLPLSSQHRGDADQASNILASFGLSARDLDELSRYPEDKITPENLP
          HSA.SSASTSS.NLQSIFNIGSRGPLPLSSQ..GDADQ.SNILASFGLSARDLDELSRYPEDK.TPENLP
Retrocopy HSARSSASTSSYNLQSIFNIGSRGPLPLSSQRCGDADQDSNILASFGLSARDLDELSRYPEDKMTPENLP

Parental  QILLQLKRRRTEEGPTLSYGRDGRSATREPPYRVPRDDWEEKRHFRRDSFDDRGPSLNPVLDYDHGSRSQ
          QILLQLKRRRTEEGPTLS.GRD.RSA..EPPYRVPRDD.EEKRHFRRDSFDD.GPSLN.VLDYDHGS.SQ
Retrocopy QILLQLKRRRTEEGPTLSNGRDDRSAAWEPPYRVPRDDLEEKRHFRRDSFDDHGPSLNLVLDYDHGSHSQ

Parental  ESGYYDRMDYEDDRLRDGE-RCRDDSFFGETSHNYHKFDSEYERMG--RGPGPLQERSLFEKKRGAPPSS
          ESGYYDRMDYEDDRLRDG..RCRDD.FFGETS.NYHKFDSEYERMG...GP.PLQERSLFEKKRGAPPSS
Retrocopy ESGYYDRMDYEDDRLRDGK>RCRDDTFFGETSRNYHKFDSEYERMGLGHGPDPLQERSLFEKKRGAPPSS

Parental  NIEDFHGLLPKGYPHLCSICDLPVHSNKEWSQHINGASHSRRCQLLLEIYPEWNPDNDTGHTMGDPFMLQ
          NIEDFHGLL.KGY.HLCSICDLPVHSN.E.SQHIN.ASHSRRCQLLLEIYPEW.PDNDT.HT.GDPFM.Q
Retrocopy NIEDFHGLLLKGYTHLCSICDLPVHSNEELSQHINRASHSRRCQLLLEIYPEWDPDNDTEHTVGDPFMSQ

Parental  QSTNPAPGILGPPPPSFHLGGPAVGPRGNLGAGNGNLQGPRHMQKGRVETSRVVHIMDFQRGKNLRYQLL
          QSTNPAPGILG.PPPSFHLGGPA.GPRGNLGAGNGNLQ..RH.Q.GRVETSRVVHIMDFQ.GKNLRYQLL
Retrocopy QSTNPAPGILGSPPPSFHLGGPAIGPRGNLGAGNGNLQRTRHIQNGRVETSRVVHIMDFQ*GKNLRYQLL

Parental  QLVEPFGVISNHLILNKINEAFIEMATTEDAQAAVDYYTTTPALVFGKPVRVHLSQKYKRIKKPEGKPDQ
          QLVEPFGVISNHLILNKINEAFIE.ATTEDAQAAVDYYTTTPALV..KPVRVHLSQKYKRIKKPEGKPDQ
Retrocopy QLVEPFGVISNHLILNKINEAFIERATTEDAQAAVDYYTTTPALVLSKPVRVHLSQKYKRIKKPEGKPDQ

Parental  KFDQKQELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRMKSQAFIEMETREDAMAMVDHCLKKA
          KFD..QELG.VIH.SNLPHS.YSDSAVLKLAEPYGKIKNYILMRMKSQAFIEMETREDAMAMVDHCLKKA
Retrocopy KFDRRQELGCVIHHSNLPHSAYSDSAVLKLAEPYGKIKNYILMRMKSQAFIEMETREDAMAMVDHCLKKA

Parental  LWFQGRCVKVDLSEKYKKLVLRIPNRGIDLLKKD
          L.FQGRCVKVDLSEKYK.LVLRIPNRGIDLLKKD
Retrocopy L*FQGRCVKVDLSEKYKNLVLRIPNRGIDLLKKD

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	0.29 RPM	256.68 RPM
SRP007412_cerebellum	1.36 RPM	321.63 RPM
SRP007412_heart	0.29 RPM	165.49 RPM
SRP007412_kidney	0.24 RPM	170.72 RPM
SRP007412_liver	0.10 RPM	65.44 RPM
SRP007412_testis	0.32 RPM	281.37 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_181 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_181 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_181 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_199
Gorilla gorilla	retro_ggor_276

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000006888	1 retrocopy	retro_cjac_3950,
Homo sapiens	ENSG00000015479	1 retrocopy	retro_hsap_199,
Gorilla gorilla	ENSGGOG00000007308	2 retrocopies	retro_ggor_276, retro_ggor_421,
Nomascus leucogenys	ENSNLEG00000009093	1 retrocopy	retro_nleu_1849,
Oryctolagus cuniculus	ENSOCUG00000026311	1 retrocopy	retro_ocun_652,
Otolemur garnettii	ENSOGAG00000010607	1 retrocopy	retro_ogar_3417,
Pongo abelii	ENSPPYG00000015835	2 retrocopies	retro_pabe_1722, retro_pabe_438,
Pan troglodytes	ENSPTRG00000017294	1 retrocopy	retro_ptro_181 ,
Rattus norvegicus	ENSRNOG00000019875	2 retrocopies	retro_rnor_1124, retro_rnor_475,