RetrogeneDB ID: retro_ptro_2859

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 9:113795545..113797382(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PRPF4B
• Ensembl ID: ENSPTRG00000017683
• Aliases: None
• Description: None

Sequence

>retro_ptro_2859
AGCCGATCCTTAGAAGGAAAACGAAGAGAACCGGAGAGAAGACGACTTTCTTCTTCAAGAACACAACCTCAAGATGATAT
CCTCAATAGATGTGAAAGATTAAAAGATGCCAGCCCCATTAATAGGTGGTCTCCAACCCGAAGAAGTAGTAGATCTCCCA
TTAAAAGGAGATCTTATTCCCCACTCAGACGTAGCACAAAAATCAGGTCTCCAAGAAGAAGCAGGTCTCCTCAGAAAAGG
GACAGAGGTTGGAGGAGCAGATCATGCTTGAGAAGGTGGCCTCGATCATGGGGTGGCCGTAGATGAAGGAGCAGAAGCAA
AGTAAAGGAAGATAAATTTAAAGGAAGTGTTTCTGAAGGAATGAAAATTGAGCAGGAATCTTCGTCTGATGATAAGCTTG
AAGATTTTGATGTGGAGGAAGAAGATGAAGAAGCCCTAATAGAACAGAGAAGAATCCAAAGGCAGGCAATTGTTCAGAAA
TATAAATATCTTGCTGAAGATAGCAATATGTCCATGTCATCTGAACCAAGCATCCCCCAGAGCAGTATGAAAACATGATC
ACCTTCTCCAGATGACATTCTGGAGTGAGTAGCTGCTGACGTTAAAGAGTATGAACGGGAAAATGTTGATACATTTCAGG
CCTCAGTGAAAGCCAAGCACAATCTAATGACAGTTGAACAGAATAATAGTTCATCTCAGAAGAAGTTGTTGGCACTTGAT
AAGTTTTACAGAATCTGATGATGTTTGCTGACTATTTTGTTAGTGCTTGCCTTTGGGTTGCTGGCAATGGGTAAGATTCA
AAGAGAATCCCAACCTCGGAGATAACTGGACTGATGCAGAAGGCTATTATCATGTGAACATAGGTGAAGTCCTAGATAAA
TGTTACAATGTGTATGGCTACACTGAGCAAGGTGTATTCAGTAATGTTTTATGAGCCAGAGATAATGCAAGAGCCAACCA
AGAAGTGGCTGTAAAGGTCATCAGAAACAATGAGCTCATGCAAAAGACTGGTTTAAAAGAACTAGAGTTCTTGAAAGAAT
TTGATGCTGATCCTAATGACAAACTTCATTGTCTGCGACTCTTCAGGCGCTTCTATCACAAACAGCATCTCTGTCTCATA
TTTGAGCCTCTCAGTATGAACTTATGAGAGATGTTAAAGAAATATGATAAAGATATTGGTTTTCGTATTAAAGCTGTAAG
ATCCCATAGTCAGCAGTTTTTCCTGGCATTGAAACTCCTTAAAAGATGCGATATCCTACATGCAGACAACAAGCCAGACA
ATATCCTGGTTAATCATCAAAAACTATTTTAAAGCTTTGCAATTTTGGGTTGGCTTCACATGCTGCGGATAATGACATTA
CACCTTATCTTGTCAGTAGATTTTATCATGCTCTTGAAATCATTATAGGTAAATGTTGTGACTATGGTATAGATATGTGG
TCAGTAGGTTGCACCTTAAACTCTATACTGGAAAAATTTTATTTCCTGGCAAAACCAATAACCATATGTTGAAGCTTGTG
ATGAATCTCAAAGGACAGATGCCAAATGAGATGATTCAAAAGGTGTATTCAAAGATCAGCATTTTGATCAAAATCTCAAC
TTCATGTACATAGAAGTTGATAAAGTAACAGACAGGGAGATAGTTACTGTTATGAGCACAATTAATCCAACTAAGGACCT
ATTGGCCAACTTGATTGGGTGCCAGACACTTCCTGAAGACCAACGTAAAAAAGTATACTAGCTAAAGGACTTGTTGGACC
AGATTCTAATGTTGGGCCTAGCTAAATGAATTAGCATCAACCAGGCCCTGCAGCATGCCTTCATCCAGGAAAAAATT

Alignment

ORF - retro_ptro_2859 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.61 %
• Parental protein coverage: 60.97 %
• Number of stop codons detected: 8
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  SRSLERKRREPERRRLSSPRTRPRDDILSRRERSKDASPINRWSPTRRRSRSPIRRRSRSPLRRSRSPR-
          SRSLE.KRREPERRRLSS.RT.P.DDIL.R.ER.KDASPINRWSPTRR.SRSPI.RRS.SPLRRS...R.
Retrocopy SRSLEGKRREPERRRLSSSRTQPQDDILNRCERLKDASPINRWSPTRRSSRSPIKRRSYSPLRRSTKIRS

Parental  -RRSRSPRRRDRGRRSRSRLRRRSRSRGGRRRRSRSKVKEDKFKGSLSEGMKVEQESSSDDNLEDFDVEE
          .RRSRSP..RDRG.RSRS.LRR..RS.GGRR.RSRSKVKEDKFKGS.SEGMK.EQESSSDD.LEDFDVEE
Retrocopy PRRSRSPQKRDRGWRSRSCLRRWPRSWGGRR*RSRSKVKEDKFKGSVSEGMKIEQESSSDDKLEDFDVEE

Parental  EDEEALIEQRRIQRQAIVQKYKYLAEDSNMSVPSEPSSPQSSTRTRSPSPDDILERVAADVKEYERENVD
          EDEEALIEQRRIQRQAIVQKYKYLAEDSNMS..SEPS.PQSS..T.SPSPDDILE.VAADVKEYERENVD
Retrocopy EDEEALIEQRRIQRQAIVQKYKYLAEDSNMSMSSEPSIPQSSMKT*SPSPDDILE*VAADVKEYERENVD

Parental  TFEASVKAKHNLMTVEQNNGSSQKKLLAPDMF-TESDDMFAAYFDSARLRAAGIGKD-FKENPNLRDNWT
          TF.ASVKAKHNLMTVEQNN.SSQKKLLA.D.F......MFA.YF.SA.L..AG.G.D.FKENPNL.DNWT
Retrocopy TFQASVKAKHNLMTVEQNNSSSQKKLLALDKF<LQNLMMFADYFVSACLWVAGNG*D<FKENPNLGDNWT

Parental  DAEGYYRVNIGEVLDKRYNVYGYTGQGVFSNVVRARDNARANQEVAVKIIRNNELMQKTGLKELEFLKKL
          DAEGYY.VNIGEVLDK.YNVYGYT.QGVFSNV..ARDNARANQEVAVK.IRNNELMQKTGLKELEFLK..
Retrocopy DAEGYYHVNIGEVLDKCYNVYGYTEQGVFSNVL*ARDNARANQEVAVKVIRNNELMQKTGLKELEFLKEF

Parental  NDADPDDKFHCLRLFRHFYHKQHLCLVFEPLSMNLREVLKKYGKDVGLHIKAVRSYSQQLFLALKLLKRC
          .DADP.DK.HCLRLFR.FYHKQHLCL.FEPLSMNL.E.LKKY.KD.G..IKAVRS.SQQ.FLALKLLKRC
Retrocopy -DADPNDKLHCLRLFRRFYHKQHLCLIFEPLSMNL*EMLKKYDKDIGFRIKAVRSHSQQFFLALKLLKRC

Parental  NILHADIKPDNILVN-ESKTILKLCDFGSASHVADNDITPYLVSRFYRAPEIIIGKSYDYGIDMWSVGCT
          .ILHAD.KPDNILVN..SKTILKLC.FG.ASH.ADNDITPYLVSRFY.A.EIIIGK..DYGIDMWSVGCT
Retrocopy DILHADNKPDNILVN<SSKTILKLCNFGLASHAADNDITPYLVSRFYHALEIIIGKCCDYGIDMWSVGCT

Parental  LYELYTGKILF-PGKTNNHMLKLAMDLKGKMPNKMIR-KGVFKDQHFDQNLNFMYIEVDKVTEREKVTVM
          L......K..F.PGKTNNHMLKL.M.LKG.MPN.MI..KGVFKDQHFDQNLNFMYIEVDKVT.RE.VTVM
Retrocopy LNSILE-KFYF<PGKTNNHMLKLVMNLKGQMPNEMIQ<KGVFKDQHFDQNLNFMYIEVDKVTDREIVTVM

Parental  STINPTKDLLADLIGCQRLPEDQRKKVHQLKDLLDQILMLDPAKRISINQALQHAFIQEKI
          STINPTKDLLA.LIGCQ.LPEDQRKKV..LKDLLDQILML..AK.ISINQALQHAFIQEKI
Retrocopy STINPTKDLLANLIGCQTLPEDQRKKVY*LKDLLDQILMLGLAK*ISINQALQHAFIQEKI

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	40.95 RPM
SRP007412_cerebellum	0.00 RPM	63.60 RPM
SRP007412_heart	0.00 RPM	44.19 RPM
SRP007412_kidney	0.00 RPM	64.31 RPM
SRP007412_liver	0.00 RPM	29.33 RPM
SRP007412_testis	0.00 RPM	43.94 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2859 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2859 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2859 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4212
Gorilla gorilla	retro_ggor_2821

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000112739	1 retrocopy	retro_hsap_4212,
Gorilla gorilla	ENSGGOG00000006422	1 retrocopy	retro_ggor_2821,
Myotis lucifugus	ENSMLUG00000005901	1 retrocopy	retro_mluc_259,
Monodelphis domestica	ENSMODG00000009756	1 retrocopy	retro_mdom_1114,
Nomascus leucogenys	ENSNLEG00000011291	1 retrocopy	retro_nleu_1453,
Pan troglodytes	ENSPTRG00000001419	1 retrocopy	retro_ptro_2604,
Pan troglodytes	ENSPTRG00000007278	1 retrocopy	retro_ptro_405,
Pan troglodytes	ENSPTRG00000017683	1 retrocopy	retro_ptro_2859 ,