RetrogeneDB ID: retro_pabe_2051

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 2b:32096947..32097382(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSPPYG00000007263
• Aliases: None
• Description: None

Sequence

>retro_pabe_2051
CAGGATCCAAATAATCCTGCCATCATCAAGTGAGCTGCTGGAAATTATATTAGAAGCTCTTTGGCAAGAGCTAAATTCAC
TCCTCTCATTACAACTATAAAATCATGCCTAGGTCTTTCGGTAAACTGGTTGTACAAATACCTTAATAACCGGGATCTGA
GAACGAAGCCTTTTTGTGATATTGCTCTCCATCAAACATTTTACTCAGCCTTCCAAGCTGTGTTCCACACCTTTGTTTTT
AGACACAAGCAGCTTTTAAGCGTAAACCTGAAAGAAGGTTTGAGATGTCTTCAGTGCCTACATTTTTAAGGGATAGTGAC
TAGGCAGCTAAATCCTCTGAATATTTGCCTGCCTTCAGTGGTTAACTTATTTGCTGCTGTCATGAATAAATATCAGCTAG
TCTGCTACACTATCATTGAGAGGAACAACGGCCAG

Alignment

ORF - retro_pabe_2051 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.32 %
• Parental protein coverage: 65.62 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  QDPSNPAIIRQAAGNYIGSFLARAKFIPLIT-VRSCLDLLVNWLHIYLNNQDSGTKAFCDVALHGPFYSA
          QDP.NPAII..AAGNYI.S.LARAKF.PLIT...SCL.L.VNWL..YLNN.D..TK.FCD.ALH..FYSA
Retrocopy QDPNNPAIIK*AAGNYIRSSLARAKFTPLITTIKSCLGLSVNWLYKYLNNRDLRTKPFCDIALHQTFYSA

Parental  CQAVFYTFVFRHKQLLSGNLKEAKGLRYLQSLNFERIVMSQLNPLKICLPSVVNFFAAITNKYQLVFCYT
          .QAVF.TFVFRHKQLLS.NLKE..GLR.LQ.L.F..IV..QLNPL.ICLPSVVN.FAA..NKYQLV.CYT
Retrocopy FQAVFHTFVFRHKQLLSVNLKE--GLRCLQCLHF*GIVTRQLNPLNICLPSVVNLFAAVMNKYQLV-CYT

Parental  IIERNNRQ
          IIERNN.Q
Retrocopy IIERNNGQ

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	6.14 RPM
SRP007412_cerebellum	0.00 RPM	7.54 RPM
SRP007412_heart	0.00 RPM	2.11 RPM
SRP007412_kidney	0.00 RPM	2.95 RPM
SRP007412_liver	0.00 RPM	5.02 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2051 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2051 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2051 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Gorilla gorilla	ENSGGOG00000023418	1 retrocopy	retro_ggor_1719,
Pongo abelii	ENSPPYG00000007263	1 retrocopy	retro_pabe_2051 ,