RetrogeneDB ID: retro_pabe_2481

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 4:159449114..159449557(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: WDR45
• Ensembl ID: ENSPPYG00000020333
• Aliases: None
• Description: WD repeat domain 45 [Source:HGNC Symbol;Acc:28912]

Sequence

>retro_pabe_2481
TTGACTCAACAGCCACTTCGAGGAGTGACCAGCCTGCATTTCAACCAAGACCAAAGCTGCTTTTGCTGCGCCATGGAGAC
AGGTGTGCGCATCTACAACGTGGAGCCCTTGATGGAGAAGGGGCATCTGGACCACGAGCAGGTGGCAGCATGGGCTTGGT
GGAGATGCTGCACCGCTGCAACCTTCTGGCCTTGGTGGGCGGTGGTAGTAGCCCCAAGTTCTCAGAGATCTCAGTGCTGA
TCTGGGATGATGCCCGGGAGGGCAAGGACTCCAAGGAGAGGCTGGTGCTGGAGTTCACCTTCACCAAGCCAGTGCTTTCT
GTGTGCATGCGCCATGACAAGATCGTGACCGTGCTGAAGAACCGCATCTATGTATACTCCTTCCCAGACAATCCTCGAAA
GCTGTTTGAGTTTGATACCTGGGTCAACCCCAACAGGCTCTGT

Alignment

ORF - retro_pabe_2481 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.33 %
• Parental protein coverage: 81.87 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MTQQPLRGVTSLRFNQDQSCFCCAMETGVRIYNVEPLMEKGHLDHEQV-GSMGLVEMLHRSNLLALVGGG
          .TQQPLRGVTSL.FNQDQSCFCCAMETGVRIYNVEPLMEKGHLDHEQV.GSMGLVEMLHR.NLLALVGGG
Retrocopy LTQQPLRGVTSLHFNQDQSCFCCAMETGVRIYNVEPLMEKGHLDHEQV<GSMGLVEMLHRCNLLALVGGG

Parental  SSPKFSEISAVLIWDDAREGKDSKEKLVLEFTFTKPVLSVRMRHDKIVIVLKNRIYVYSFPDNPRKLFEF
          SSPKFSEIS.VLIWDDAREGKDSKE.LVLEFTFTKPVLSV.MRHDKIV.VLKNRIYVYSFPDNPRKLFEF
Retrocopy SSPKFSEIS-VLIWDDAREGKDSKERLVLEFTFTKPVLSVCMRHDKIVTVLKNRIYVYSFPDNPRKLFEF

Parental  DTRDNPKAIC
          DT..NP...C
Retrocopy DTWVNPNRLC

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	0.66 RPM	13.55 RPM
SRP007412_cerebellum	0.61 RPM	9.85 RPM
SRP007412_heart	0.15 RPM	8.34 RPM
SRP007412_kidney	1.66 RPM	34.84 RPM
SRP007412_liver	0.55 RPM	15.12 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2481 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2481 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2481 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Echinops telfairi	ENSETEG00000002062	3 retrocopies	retro_etel_1291, retro_etel_688, retro_etel_712,
Gorilla gorilla	ENSGGOG00000000589	1 retrocopy	retro_ggor_2075,
Macaca mulatta	ENSMMUG00000010620	1 retrocopy	retro_mmul_1916,
Pongo abelii	ENSPPYG00000008785	2 retrocopies	retro_pabe_150, retro_pabe_1559,
Pongo abelii	ENSPPYG00000020333	1 retrocopy	retro_pabe_2481 ,