RetrogeneDB ID: retro_ggor_2821

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 9:97437031..97438868(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PRPF4B
• Ensembl ID: ENSGGOG00000006422
• Aliases: None
• Description: None

Sequence

>retro_ggor_2821
AGCCAATCCTTAGAAGGAAAACGAAGAGAACCAGAGAGAAGACGACTTTCTTCTTCAAGAACACAACCTCAAGATGATAT
CCTCAATAGATGTGAAAGATTAAAAGATGCCAGCCCCATTAATAGGTGGTCTCCAACCCGAAGAAGTAGTAGATCTCCCA
TTAAAAGGAGGTCTCATTCCCCACTCAGGCGTAGCACAAAAATCAGGTCTCCAAGAAGAAGCAGGTCTCCTCAGAAAAGG
GACAGAGGTTGGAGGAGCAGATCATGCTTGAGAAGGTGGCCTCGATCATGGGGTGGTCGTATATGAAGGAGCAGAAGCAA
AGTAAAGGAAGATAAATTTAAAGGAAGTGTTTCTGAAGGAATGAAAGTTGAGCAGGAATCTTCGTCTGATGATAAGCTTG
AAGATTTTGATGTGGAGGAAGAAGATGAAGAAGCCCTAATAGAACAGAGAAGAATCCAAAGGCAGGCAATTGTTCAGAAA
TATAAATATCTTGCTGAAGATAGCAATACGTCCATGTCATCTGAACCAAGCATCCCCCAGAGCAGTATGAAAACATGATC
ACCTTCTCCAGATGACATTCTGGAATGAGTAGCTGCTGATGTTAAAGAGTATGAACGGGAAAATGTTGATACATTTCAGG
CCTCAGTGAAAGCCAAGCATAATCTAATGACAGTTGAACAGAATAATAGTTCATCGCAGAAGAAGTTGTTGGCACTTGAT
AAGTTTTACAGAATCTGATGATGTTTGCTGACTATTTTGATAGTGCTTGCCTTTGGGTTGCTGGCAATGGGTAAGATTCA
AAGAGAATCCCAACCTCAGAGATAACTGGACTGATGCAGAAGGCTATTATCATGTGAACATAGGTGAAGTCCTAGATAAA
TGTTACAATGTGTATGGCTACACTGGGCAAGGTGTATTCAGTAATGTTTTATGAGCCAGAGATAATGCAAGAGCCAACCA
AGAAGTGGCTGTAAAGGTCATCAGAAACAATGAGCTCATGCAAAAGACTGGTTTAAAAGAACTAGATTTCTTGAAAGAAT
TTGATGCTGATCCTGATGACAAACTTCATTGTCTGCGACTCTTCAGGCGCTTCTATCACAAACAGCATCTGTGTCTCATA
TTTGAGCCTCTCAGTATGAACTTATGAGACATGTTAAAAAAATATGATAAATATATTGGTTTTCATATTAAAGCTGTAAG
ATCCCATAGTCAGCAGTTTATCCTGGCATTGAAACTCCTTAAAACATGTGATATCCTACATGCAGACAACAAGCCAGACA
ACATCCTGGTTAATCATCAAAAACTATTTTAAAGCTTTGCAATTTTGGGTTGGCTTCACATGTTGCGGATAATGACATTA
CACCTTATCTTGTCAGTACAGTTTATCGTGCTCTTGAAATCATTATAGGTAAATGCTGTGACTATGGTATAGATATGTGG
TCAGTAGGTTGCACCTTAAACTCTATACTGGAAAAATTTTATTTCCTGGCAAAACCAATAACCATATGTTGAAGCTTGTG
ATGAATCTCAAAGGACAGATGCCAAATGAGATGATTCAAAAGGTGTATTCAAAGATCAGCATTTTGATCAAAATCTCAAC
TTCATGTACATAGAAGTTGATAAAGTAACAGACAGGGAGATAGTTACTGTTATGAGCACAATTAATCCAACTAAGGACCT
ATTGGCCAACTTGATTGGGTGCCAGACACTTCCTGAAGACCAACGTAAAAAAGTATGCTAGCTAAAGGACTTGTTGGACC
AGATTCTAATGTTGGGTCTAGCTAAATGAATTAGCATCAACCAGGCCCTGCAGCATGCCTTCATCCAGGAAAAAATT

Alignment

ORF - retro_ggor_2821 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.74 %
• Parental protein coverage: 63.47 %
• Number of stop codons detected: 8
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  SRSLERKRREPERRRLSSPRKHFCDMALSRSKHYQEIIIINEENTTRRRSRSPIRRRSRSPLRRSRSPR-
          S.SLE.KRREPERRRLSS.R....D..L.R.........IN....TRR.SRSPI.RRS.SPLRRS...R.
Retrocopy SQSLEGKRREPERRRLSSSRTQPQDDILNRCERLKDASPINRWSPTRRSSRSPIKRRSHSPLRRSTKIRS

Parental  -RRSRSPRRRDRGRRSRSRLRRRSRSRGGRRRRSRSKVKEDKFKGSLSEGMKVEQESSSDDNLEDFDVEE
          .RRSRSP..RDRG.RSRS.LRR..RS.GGR..RSRSKVKEDKFKGS.SEGMKVEQESSSDD.LEDFDVEE
Retrocopy PRRSRSPQKRDRGWRSRSCLRRWPRSWGGRI*RSRSKVKEDKFKGSVSEGMKVEQESSSDDKLEDFDVEE

Parental  EDEEALIEQRRIQRQAIVQKYKYLAEDSNMSVPSEPSSPQSSTRTRSPSPDDILERVAADVKEYERENVD
          EDEEALIEQRRIQRQAIVQKYKYLAEDSN.S..SEPS.PQSS..T.SPSPDDILE.VAADVKEYERENVD
Retrocopy EDEEALIEQRRIQRQAIVQKYKYLAEDSNTSMSSEPSIPQSSMKT*SPSPDDILE*VAADVKEYERENVD

Parental  TFEASVKAKHNLMTVEQNNGSSQKKLLAPDMF-TESDDMFAAYFDSARLRAAGIGKD-FKENPNLRDNWT
          TF.ASVKAKHNLMTVEQNN.SSQKKLLA.D.F......MFA.YFDSA.L..AG.G.D.FKENPNLRDNWT
Retrocopy TFQASVKAKHNLMTVEQNNSSSQKKLLALDKF<LQNLMMFADYFDSACLWVAGNG*D<FKENPNLRDNWT

Parental  DAEGYYRVNIGEVLDKRYNVYGYTGQGVFSNVVRARDNARANQEVAVKIIRNNELMQKTGLKELEFLKKL
          DAEGYY.VNIGEVLDK.YNVYGYTGQGVFSNV..ARDNARANQEVAVK.IRNNELMQKTGLKEL.FLK..
Retrocopy DAEGYYHVNIGEVLDKCYNVYGYTGQGVFSNVL*ARDNARANQEVAVKVIRNNELMQKTGLKELDFLKEF

Parental  NDADPDDKFHCLRLFRHFYHKQHLCLVFEPLRSMNLREVLKKYGKDVGLHIKAVRSYSQQLFLALKLLKR
          .DADPDDK.HCLRLFR.FYHKQHLCL.FEPL.SMNL...LKKY.K..G.HIKAVRS.SQQ..LALKLLK.
Retrocopy -DADPDDKLHCLRLFRRFYHKQHLCLIFEPL-SMNL*DMLKKYDKYIGFHIKAVRSHSQQFILALKLLKT

Parental  CNILHADIKPDNILVN-ESKTILKLCDFGSASHVADNDITPYLVSRFYRAPEIIIGKSYDYGIDMWSVGC
          C.ILHAD.KPDNILVN..SKTILKLC.FG.ASHVADNDITPYLVS..YRA.EIIIGK..DYGIDMWSVGC
Retrocopy CDILHADNKPDNILVN<SSKTILKLCNFGLASHVADNDITPYLVSTVYRALEIIIGKCCDYGIDMWSVGC

Parental  TLYELYTGKILF-PGKTNNHMLKLAMDLKGKMPNKMIR-KGVFKDQHFDQNLNFMYIEVDKVTEREKVTV
          TL......K..F.PGKTNNHMLKL.M.LKG.MPN.MI..KGVFKDQHFDQNLNFMYIEVDKVT.RE.VTV
Retrocopy TLNSILE-KFYF<PGKTNNHMLKLVMNLKGQMPNEMIQ<KGVFKDQHFDQNLNFMYIEVDKVTDREIVTV

Parental  MSTINPTKDLLADLIGCQRLPEDQRKKVHQLKDLLDQILMLDPAKRISINQALQHAFIQEKI
          MSTINPTKDLLA.LIGCQ.LPEDQRKKV..LKDLLDQILML..AK.ISINQALQHAFIQEKI
Retrocopy MSTINPTKDLLANLIGCQTLPEDQRKKVC*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	0.10 RPM	30.07 RPM
SRP007412_cerebellum	0.04 RPM	41.01 RPM
SRP007412_heart	0.00 RPM	8.54 RPM
SRP007412_kidney	0.08 RPM	44.77 RPM
SRP007412_liver	0.08 RPM	33.21 RPM
SRP007412_testis	0.52 RPM	75.01 RPM

ChIP-Seq

Gorilla gorilla was not studied using ChIP-Seq data.

EST

Gorilla gorilla was not studied using EST data.

TSS

Gorilla gorilla was not studied using FANTOM5 data.

Lab

retro_ggor_2821 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_2821 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4212
Pan troglodytes	retro_ptro_2859

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000112739	1 retrocopy	retro_hsap_4212,
Gorilla gorilla	ENSGGOG00000006422	1 retrocopy	retro_ggor_2821 ,
Gorilla gorilla	ENSGGOG00000009438	1 retrocopy	retro_ggor_2575,
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	ENSPTRG00000017683	1 retrocopy	retro_ptro_2859,