RetrogeneDB ID: retro_pabe_2898

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 6:107596177..107597309(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CHAF1B
• Ensembl ID: ENSPPYG00000011403
• Aliases: None
• Description: chromatin assembly factor 1, subunit B (p60) [Source:HGNC Symbol;Acc:1911]

Sequence

>retro_pabe_2898
CCTTTAGGTCAATATGTTGCTACTCTGAGCTGTGACAGGGTGCTGCGGGTATACAGTATACAGAAGAAGCATGTGGTTTT
TAATGTTTCAAAGATGCTATCTGGAATAGGGGCTGAAGGAGAGGCAAGAAGCTACAGGATGTTTCATGACAACAGCATGA
AGTTGTTCTTCCGTAGACTGAGTTTCACTCCTGATGGATCTTTGCTCCTCACACCAGCTGGATGTGTGGAATCTGGTGAA
AATGTAATGAACACCACTTACGTTTTCTCCAGGAAGAATCTTAAAAGGCCCATCGCTCATCTTCCATGTCCTGGAAAAGC
CACTCTTGCTGTTGGCAGCTGTCTGGTCTACTTTGAACTGAGGCCGGTGGTGGAAACAGGTGTGGAGCTAATGAGTCTGC
CCTACCGCCTGGTATTTGCTGTGGCTTAGGAGGACTCTGTGCTTCTGGACACCCAGGAATCCTTCCCTTTCGGTTACGTG
TCTAATATACATTACCACACCCTCAGTGACATTTCATGATCTAGCGATGGCGCCTTCATGGCCATTTCTTCCACAGACAG
TTACTGCTCGTTCGTGACATTTGAGAAAGGTGAACTTGGAATACTTTTAAAAGAGAAGTCAGTTTTGAGCACAAGAACTC
CTGATACAGCAAAGAAAACCAAGAGTCAGACACACCGAGGGTCTTTGCCAGGACCCAGACCAGTAGAGGGAACAACTGCC
AGCAGAACCCAAGATCCCAGCAACCCCTGCTCGACCCCCACTCAGGCCAGACAGGCCCCAGCCCCAGCAGCCATCAGGAA
CCCTCCCTCTATCATTCTGCTGTCAAAAGCTCCTTGCCGAGGCCTTCGGAGGAGAAGACCCTGCCGCCCAGTAGTTAAAA
CACAAAAGCCCACCCATCCCGGAGGGTCACTCTGAACACATTGCAATCCTGGAGCAAGACAATACCCTGGAGAATAAACT
TAATACCCTTAAAGACAGACACTCCACCAAAGTCTGTACCAATCAATGTAATTTCCACCCCTTCTGCAGAAGAATTTAGT
AAGAGATGCCTGGAAACACTCAGGGCAGTCCCGCAGAGCTAAAACAGCCCAGACTCAATGAAAACAAAGGGGGCACTGAA
AGTCTGGAACCT

Alignment

ORF - retro_pabe_2898 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.3 %
• Parental protein coverage: 67.8 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  PLGQYVATLSCDRVLRVYSIQKKRVAFNVSKMLSGIGAEGEARSYRMFHDDSMKSFFRRLSFTPDGSLLL
          PLGQYVATLSCDRVLRVYSIQKK.V.FNVSKMLSGIGAEGEARSYRMFHD.SMK.FFRRLSFTPDGSLLL
Retrocopy PLGQYVATLSCDRVLRVYSIQKKHVVFNVSKMLSGIGAEGEARSYRMFHDNSMKLFFRRLSFTPDGSLLL

Parental  TPAGCVESGENVMNTTYVFSRKNLKRPIAHLPCPGKATLAVRCCPVYFELRPVVETGVELMSLPYRLVFA
          TPAGCVESGENVMNTTYVFSRKNLKRPIAHLPCPGKATLAV..C.VYFELRPVVETGVELMSLPYRLVFA
Retrocopy TPAGCVESGENVMNTTYVFSRKNLKRPIAHLPCPGKATLAVGSCLVYFELRPVVETGVELMSLPYRLVFA

Parental  VASEDSVLLYDTQQPFPFGYVSNIHYHTLSDISWSSDGAFLAISSTDGYCSFVTFEKDELGIPLKEKPVL
          VA.EDSVLL.DTQ..FPFGYVSNIHYHTLSDIS.SSDGAF.AISSTD.YCSFVTFEK.ELGI.LKEK.VL
Retrocopy VA*EDSVLL-DTQESFPFGYVSNIHYHTLSDIS*SSDGAFMAISSTDSYCSFVTFEKGELGILLKEKSVL

Parental  SMRTPDTAKKTKSQTHRGSSPGPRPVEGTPASRTQDPSSPGTTPPQARQAPAPTAIRDPPSIT-PAVRSP
          S.RTPDTAKKTKSQTHRGS.PGPRPVEGT.ASRTQDPS.P..TP.QARQAPAP.AIR.PPSI...AV.S.
Retrocopy STRTPDTAKKTKSQTHRGSLPGPRPVEGTTASRTQDPSNPCSTPTQARQAPAPAAIRNPPSII<SAVKSS

Parental  LPGPSEEKSLQPSSQNTKVHPSRRVTLNTLQAWSKTTPRRMNLTPLKTDTPPSSVPTSVISTPSTEEIQS
          LP.PSEEK.L.PSS.NTK.HPSRRVTLNTLQ.WSKT.P.R.NL.PLKTDTPP.SVP..VISTPS.EE...
Retrocopy LPRPSEEKTLPPSS*NTKAHPSRRVTLNTLQSWSKTIPWRINLIPLKTDTPPKSVPINVISTPSAEEFSK

Parental  -ETPGDAQGSPPELKRPRLDENKGGTESLDP
          .E.PG..QGSP.ELK.PRL.ENKGGTESL.P
Retrocopy <EMPGNTQGSPAELKQPRLNENKGGTESLEP

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	7.91 RPM
SRP007412_cerebellum	0.00 RPM	7.78 RPM
SRP007412_heart	0.00 RPM	1.78 RPM
SRP007412_kidney	0.00 RPM	1.56 RPM
SRP007412_liver	0.00 RPM	0.80 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2898 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2898 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2898 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3504
Pan troglodytes	retro_ptro_2375
Gorilla gorilla	retro_ggor_2369

---

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,