RetrogeneDB ID: retro_ggor_2369

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 6:105706368..105707533(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CHAF1B
• Ensembl ID: ENSGGOG00000015726
• Aliases: None
• Description: None

Sequence

>retro_ggor_2369
CATAAAAGTTATGTCCAAGGAGTAAACTGGGACCCTTTAGGTCAATATGTTGCTACTCTGAGCTGTGACAGGGTGCTGCA
GGTATACAGTATACAGAAGAAGCATGTGGTTTTTAATGTTTCAAAGACGCTATCTGGAATAGGGGCTGAAGGAGAGGCAA
GAAGCTACCGCATGTTTCACGATGACAGCATGAAGTTGTTCTTCCGTAGACTGAGTTTCACTCCCAATGGATCTTTGCTC
CTCACACCAGCCGGATGTGTGGAATCCGGTGAAAATGTAATGAACACCACTTACGTTTTCTCCAGGAAGAGTCTTAAAAG
GCCCATCGCTCATCTTCCGTGTCCTGGAAAAGCCACTCTTGCTGTTGGCAGCTGTCTGGTCTATTTTGAACTGAGACCAG
TGGTGGAAACAGGTGCGGAGCTAATGAGTCTGCCCTACTGCCTGGTATTTGCTGTGGCTTAGGAGGACTCTGTGCTTCTG
GACACCCAGGAGTCCTTCCGTTTCGGTTACGTGTCTAATATACATTACCACACCCTCAATGACATTTCCTGGTCTAGCGA
TGGCGCCTTCCTGGCCATTTCTTCCACAGACAGTTACTGCTCGTTTGTGACATTTGAGAAAGGTGAACTTGGAATTCTTT
TAAAAGAGAAGTCAGTTTTGAGCATGAGAACTCCTGATACAGCAAAGAAAACCAAGAGTCAGACACACCGAGGTTCTTTG
CCAGGACCCAGACCCGTAGAGGGAACAACTGCCAGCAGAACCCAAGACCCCAGCAACCCCTGGTCAACCTCAACTCAGGC
CAGACAGGCCGCAGCCCCAACAGCCACCAGGGACCCTCCCTCTATCATTCTGCTGTCAAAAGCTCCTTGTCAAGGCCTTC
GGAGGAGAAGACCCTGCCGCCCAGTAGTTAAAACACAAAAGCCCACCCATCCCGGAGGGTCACTCTGAACACATTGCAAT
CCTGGAGCAAGACAACACCCTGGAGAATAAACTCAATACCCTTAAAGACAGACACTCCACCAAAGTCTGTACCAATCAAT
GTAATTTCCACCCCTTCTGCAGAACAATTTAGTAAGAGATGCCTGGAAACGCTCAGGACAGTCCCGTAGAGCTAAAACAG
CCCAGACTCAATGAAAACAAAGGGGGCACTGAAAGTCTGGAACCT

Alignment

ORF - retro_ggor_2369 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.76 %
• Parental protein coverage: 69.88 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  HKSYVQGVTWDPLGQYVATLSCDRVLRVYIIQKKRVAFNVSKMLSGVGAEGEARSYRMFHDDSMKSFFRR
          HKSYVQGV.WDPLGQYVATLSCDRVL.VY.IQKK.V.FNVSK.LSG.GAEGEARSYRMFHDDSMK.FFRR
Retrocopy HKSYVQGVNWDPLGQYVATLSCDRVLQVYSIQKKHVVFNVSKTLSGIGAEGEARSYRMFHDDSMKLFFRR

Parental  LSFTPDGSLLLTPAGCVESGENVMNTTYVFSRKNLKRPIAHLPCPGKATLAVRCCPVYFELRPVVETGVE
          LSFTP.GSLLLTPAGCVESGENVMNTTYVFSRK.LKRPIAHLPCPGKATLAV..C.VYFELRPVVETG.E
Retrocopy LSFTPNGSLLLTPAGCVESGENVMNTTYVFSRKSLKRPIAHLPCPGKATLAVGSCLVYFELRPVVETGAE

Parental  LMSLPYRLVFAVASEDSVLLYDTQQSFPFGYVSNIHYHTLSDISWSSDGAFLAISSTDGYCSFVTFEKDE
          LMSLPY.LVFAVA.EDSVLL.DTQ.SF.FGYVSNIHYHTL.DISWSSDGAFLAISSTD.YCSFVTFEK.E
Retrocopy LMSLPYCLVFAVA*EDSVLL-DTQESFRFGYVSNIHYHTLNDISWSSDGAFLAISSTDSYCSFVTFEKGE

Parental  LGIPLKEKPVLSMRTPDTAKKTKSQTHRGSSPGPRPVEGTPASRTQDPSSPGTTPPQARQAPAPTVIRDP
          LGI.LKEK.VLSMRTPDTAKKTKSQTHRGS.PGPRPVEGT.ASRTQDPS.P..T..QARQA.APT..RDP
Retrocopy LGILLKEKSVLSMRTPDTAKKTKSQTHRGSLPGPRPVEGTTASRTQDPSNPWSTSTQARQAAAPTATRDP

Parental  PSIT-PAVKSPLPGPSEEKTLQPSSQNTKAHPSRRVTLNTLQAWSKTTPRSRRINLTPLKTDTPPSSVPT
          PSI...AVKS.L..PSEEKTL.PSS.NTKAHPSRRVTLNTLQ.WSKTTP...RIN..PLKTDTPP.SVP.
Retrocopy PSII<SAVKSSLSRPSEEKTLPPSS*NTKAHPSRRVTLNTLQSWSKTTP--WRINSIPLKTDTPPKSVPI

Parental  SVISTPSTEEIQS-ETPGDAQGSPPELKRPRLDENKGGTESLDP
          .VISTPS.E.....E.PG.AQ.SP.ELK.PRL.ENKGGTESL.P
Retrocopy NVISTPSAEQFSK<EMPGNAQDSPVELKQPRLNENKGGTESLEP

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	7.48 RPM
SRP007412_cerebellum	0.00 RPM	7.60 RPM
SRP007412_heart	0.00 RPM	0.59 RPM
SRP007412_kidney	0.00 RPM	1.39 RPM
SRP007412_liver	0.00 RPM	1.58 RPM
SRP007412_testis	0.00 RPM	7.77 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_2369 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_2369 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3504
Pan troglodytes	retro_ptro_2375
Pongo abelii	retro_pabe_2898

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000159259	1 retrocopy	retro_hsap_3504,
Gorilla gorilla	ENSGGOG00000015726	1 retrocopy	retro_ggor_2369 ,
Nomascus leucogenys	ENSNLEG00000004429	1 retrocopy	retro_nleu_797,
Pongo abelii	ENSPPYG00000011403	1 retrocopy	retro_pabe_2898,
Pan troglodytes	ENSPTRG00000013891	1 retrocopy	retro_ptro_2375,