RetrogeneDB ID: retro_ptro_2375

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 6:106688222..106689384(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CHAF1B
• Ensembl ID: ENSPTRG00000013891
• Aliases: None
• Description: None

Sequence

>retro_ptro_2375
AAAAGTTATGTCCAAGGAGTAAACTGGGACCCTTTAGGTCAATATGTTGCTACTCTGAGCTGTGACACGGTGCTGCAGGT
ATACAGTATACAGAAGAAGCATGTGGTTTTTAATGTTTCAAAGATGCTATCTGGAATAGGGGCTGAAGGAGAGGCAAGAA
GCTACCGCATGTTTCACGATGACAGCATGAAGTTGTTCTTCCATAGACTGAGTTTCACTCCCTATGGATCTTTGCTCCTC
ACACCAGCCGGACGTGTGGAATCCGGTGAAAATGTAATGAACATCACTTACGTTTTCTCCAGGAAGGATCTTAAAAGGCC
CATCGCTCATCTTCCGTGTCCTGGAAAAGCCACTCTTGCTGTTGGCAGCTGTCTGGTCTATTTTGAACTGAGGCCAGTGG
TGGAAACAGGTGCGGAGCTAATGAGTCTGCCCTACTGCCTGGTATTTGCTGTGGCTTAGGAGGACTCTGTGCTTCTGGAC
ACCCAGGAGTCCTTCCCTTTCGGTTATGTGTCTAATATACATTACCACACCCTCAATGACATTTCATGGTCTAGCGATGG
CGCCTTCCTGGCCATTTCTTCCACAGACAGTTACTGCTCGTTTGTGACATTTGAGAAAGGTGAACTTGGAATTCTTTTAA
AAGAGAAGTCAGTTTTGAGCATGAGAACTCCTGATACAGCAAAGAAAACCAAGAGTCAGACACACCAAGGGTCTTTGCCA
GGACCCAGACCCGTAGAGGGAACAACTGCCAGCAGAACCCAAGACCCCAGCAACCCCTGCTCAACCCCCACTCAGGCCAG
ACAGGCCACAGCCCCAACAGCCACCAGGGACCCTCCCTCTATCATTCTGCTGTCAAAAGCTCCTTGCCGAGGCCTTCGGA
GGAGAAGACCCTGCCAGCCAGTAGTTAAAACACAAAAGCCCACCCATCCCGGAGGGTCACTCTGAACACATTGCAATCCT
GGAGCAAGACAACACCCTGGAGAATAAACTCAATACCCTTAAAGACAGACACTCCACCAAAGTCTGTACCAATCAATGTA
ATCTCCACCCCTTCTGCGGAAGAATTTAGTAAGAGACGCCTGGAAACGCTCAGGACAGTCCCGTAAAGCTAAAACAGCCC
AGACTCAATGAAAACAAAGGGGGCACTGAAAGTCTGGAACCT

Alignment

ORF - retro_ptro_2375 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.14 %
• Parental protein coverage: 69.59 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  KSYVQGVTWDPLGQYVATLSCDRVLRVYSIQKKRVAFNVSKMLSGIGAEGEARSYRMFHDDSMKSFFRRL
          KSYVQGV.WDPLGQYVATLSCD.VL.VYSIQKK.V.FNVSKMLSGIGAEGEARSYRMFHDDSMK.FF.RL
Retrocopy KSYVQGVNWDPLGQYVATLSCDTVLQVYSIQKKHVVFNVSKMLSGIGAEGEARSYRMFHDDSMKLFFHRL

Parental  SFTPDGSLLLTPAGCVESGENVMNTTYVFSRKNLKRPIAHLPCPGKATLAVRCCPVYFELRPVVETGVEL
          SFTP.GSLLLTPAG.VESGENVMN.TYVFSRK.LKRPIAHLPCPGKATLAV..C.VYFELRPVVETG.EL
Retrocopy SFTPYGSLLLTPAGRVESGENVMNITYVFSRKDLKRPIAHLPCPGKATLAVGSCLVYFELRPVVETGAEL

Parental  MSLPYRLVFAVASEDSVLLYDTQQSFPFGYVSNIHYHTLSDISWSSDGAFLAISSTDGYCSFVTFEKDEL
          MSLPY.LVFAVA.EDSVLL.DTQ.SFPFGYVSNIHYHTL.DISWSSDGAFLAISSTD.YCSFVTFEK.EL
Retrocopy MSLPYCLVFAVA*EDSVLL-DTQESFPFGYVSNIHYHTLNDISWSSDGAFLAISSTDSYCSFVTFEKGEL

Parental  GIPLKEKPVLNMRTPDTAKKTKSQTHRGSSPGPRPVEGTPASRTQDPSSPGTTPPQARQAPAPTAIRDPP
          GI.LKEK.VL.MRTPDTAKKTKSQTH.GS.PGPRPVEGT.ASRTQDPS.P..TP.QARQA.APTA.RDPP
Retrocopy GILLKEKSVLSMRTPDTAKKTKSQTHQGSLPGPRPVEGTTASRTQDPSNPCSTPTQARQATAPTATRDPP

Parental  SIT-PAVKSPLPGPSEEKTLQPSSQNTKAHPSRRVTLNTLQAWSKTTPRRINLTPLKTDTPPSSVPTSVI
          SI...AVKS.LP.PSEEKTL..SS.NTKAHPSRRVTLNTLQ.WSKTTP.RIN..PLKTDTPP.SVP..VI
Retrocopy SII<SAVKSSLPRPSEEKTLPASS*NTKAHPSRRVTLNTLQSWSKTTPWRINSIPLKTDTPPKSVPINVI

Parental  STPSTEEIQS-ETPGDAQGSPPELKRPRLDENKGGTETLDP
          STPS.EE....ETPG.AQ.SP..LK.PRL.ENKGGTE.L.P
Retrocopy STPSAEEFSK<ETPGNAQDSPVKLKQPRLNENKGGTESLEP

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	0.02 RPM	4.16 RPM
SRP007412_cerebellum	0.00 RPM	15.70 RPM
SRP007412_heart	0.00 RPM	0.99 RPM
SRP007412_kidney	0.00 RPM	1.99 RPM
SRP007412_liver	0.00 RPM	1.70 RPM
SRP007412_testis	0.00 RPM	11.80 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2375 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2375 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2375 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3504
Gorilla gorilla	retro_ggor_2369
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 ,