RetrogeneDB ID: retro_pabe_2764

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 5:100524699..100525119(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CENPO
• Ensembl ID: ENSPPYG00000012596
• Aliases: None
• Description: centromere protein O [Source:HGNC Symbol;Acc:28152]

Sequence

>retro_pabe_2764
CTAGAAGAAACAGCTGCAGAACACTTACAGACTGATATTCAGCATTTCCTTCTCAGCTTCTGCAAGTACCTAACTGCTCA
CTCTGGGAGAAAGTGGCAGGCACACTGACTACAGAGTGACTGCAGGCTTTCTTTCTGATGGCCCCTTGCAGAGAAACTCA
CTGTGAAACTTTTCGTCATTTACTTACAAACTGGATCCAATGGGTAACCTTTCTCATTTGGTGCTAGATTGATGGAAAAG
AATTTCACAATAACTCTTCCCACTGACCTCACCGTTACATATCAAGGAATAGAAGTGTCATTCACTTCATGGGAGGCACA
GGAAGCATCCCATGAAACTTTGTTCTGTATGAAGTGCCTACATCAAGACTTCCCTTCATTTGCAAGAAAAGGAAAAATGT
TTGATATGAACCTGGTCTCT

Alignment

ORF - retro_pabe_2764 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.49 %
• Parental protein coverage: 57.38 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LEEIAAKYLQTNIQHFLFSLCEYLNAYSGRKYQADRLQSDFAA-LLTGPLQRNPLCNLLSFTYKLDPGGQ
          LEE.AA..LQT.IQHFL.S.C.YL.A.SGRK.QA..LQSD....L..GPLQRN.L.N..SFTYKLDP.G.
Retrocopy LEETAAEHLQTDIQHFLLSFCKYLTAHSGRKWQAH*LQSDCRL>LSDGPLQRNSL*NFSSFTYKLDPMGN

Parental  -SFPFCARLLYKDLTATLPTDVTVTCQGVEALSTSWEEQRASHETLFCTKPLHQVFASFARKGEKLDMSL
          ..F.F.ARL..K..T.TLPTD.TVT.QG.E...TSWE.Q.ASHETLFC.K.LHQ.F.SFARKG...DM.L
Retrocopy <PFSFGARLMEKNFTITLPTDLTVTYQGIEVSFTSWEAQEASHETLFCMKCLHQDFPSFARKGKMFDMNL

Parental  VS
          VS
Retrocopy VS

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	4.92 RPM
SRP007412_cerebellum	0.00 RPM	4.50 RPM
SRP007412_heart	0.00 RPM	0.75 RPM
SRP007412_kidney	0.00 RPM	2.32 RPM
SRP007412_liver	0.00 RPM	1.10 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2764 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2764 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2764 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Macropus eugenii	ENSMEUG00000010491	1 retrocopy	retro_meug_568,
Pongo abelii	ENSPPYG00000012596	1 retrocopy	retro_pabe_2764 ,
Rattus norvegicus	ENSRNOG00000050111	1 retrocopy	retro_rnor_1069,
Sarcophilus harrisii	ENSSHAG00000005861	1 retrocopy	retro_shar_388,