RetrogeneDB ID: retro_pabe_1876

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 22:18321262..18322181(+)
• Located in intron of: ENSPPYG00000011622

Retrocopy information

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

Parental gene information

• Parental gene symbol: FBXW4
• Ensembl ID: ENSPPYG00000002586
• Aliases: None
• Description: F-box and WD repeat domain containing 4 [Source:HGNC Symbol;Acc:10847]

Sequence

>retro_pabe_1876
GCTCGGGCTGGGCTCCGCATCGGGCCGGCCCCGCGGCCGCTCTTGGGCAGCCAGGGCCGCTGGGTGGGGGGCTCCCGGGA
ACTGCCGTCCCGGGTGAGGGCGGGGGCGGACAGGCGAGGAAGCTGCAGGAAAGGCGGGTGGCGAGGGGGAAGCAAAGGAA
GGGGAAGAGGAAGAGAAAAGCTAGCGAGAGGGGCAAGGCGGAAGAGGAAGCAGGGTGGAAGGGAAGTCCGGGCCGCAGAC
GGCGAAGGAGGCAGCGGGGCCGGGGGCTGAGGCGGGAGCGAGGGCATGCCCAAGAGAGGAAGCAGAGGGAGGCGGAAGCG
TGGAGGAAGGGGCGAGAAGCATAGCATCATCAAAGATGAGGGGAGCGCAGGGGCCGGGAAGGAGGCACAAGGAAGAGTAT
GGGAAGAAGGAGGAATGGAGGGTCAGGGCTAGGCGGCTGGAGGGCGCCAGGCCGGGAAGAGCACAAGGACAAGGGGGTCA
GGCTTGGGCCTACATCCCGGGTACAGGGGCGGCCGTGGCGGCGGCAGCCAGTGGGGAGGAGGAGGAGGCGGCTCGGGAGG
CGGCCGCCTGCCCGGCTGCGGGGCCAGCGCTCTGGCGCCTGCCGGAAGTGCTGCTGCTGCTCATCTGCTCCTACCTCGAC
ATGCCGGACCTCAGCCGCCTGGCCCAGGTGTGCCGCTGGCTGCGGCGCTTCACCAACTGCGACCTGCTTCGGCGCCAGAT
AGCCCGGGCCTCGCTGAACTCTGGCTTCACGCGGCTCGGCACCAACCTGATGACCAGTGTCCCAGTGAAGGTGTCTCAGA
AGTGGATACTGGGGCGCTGCCGAGAGGGGATTCTGCTGAAGTGGAGATGCAGTCAGATGCCTTGGATGCAGCTAGAGGAT
GATGCTTTGTACATATCCCAGGCTAATTTCATCCTGGCC

Alignment

ORF - retro_pabe_1876 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.67 %
• Parental protein coverage: 52.2 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  ARAGLRVGPAPRPL-MGSQGR--SGPPGNGGPGEGEGGEARKLQEGRVARGKRRKGK-GKGKA-RAGQGG
          ARAGLR.GPAPRPL..G..G....G.PG...PGEG.GG.ARKLQE.RVARGK.RKGK.G..K..R.GQGG
Retrocopy ARAGLRIGPAPRPL<LGQPGPLGGGLPGTAVPGEGGGGQARKLQERRVARGKQRKGK>GREKL>REGQGG

Parental  RGSGAEGKPGPQTAKEAAGPGADAGARACPREEAEGGGSAEEGARGIVKG-VEGS-AGAGKEAQGREY-G
          RGS..EGK.GPQTAKEAAGPGA.AGARACPREEAEGGGS.EEGAR.I......G..AGAGKEAQGR...G
Retrocopy RGSRVEGKSGPQTAKEAAGPGAEAGARACPREEAEGGGSVEEGARSIASSKMRGA<AGAGKEAQGRVW<G

Parental  KK-EEWRVRARRREGARPGRAQGRRGQAWADIAGTGVAMAAAAGEEEKEEAARESAARLAAGPALWRLPE
          ...EEWRVRARR.EGARPGRAQG..GQAWA.I.GTG.A.AAAA..EE.EEAARE.AA..AAGPALWRLPE
Retrocopy RR<EEWRVRARRLEGARPGRAQGQGGQAWAYIPGTGAAVAAAASGEE-EEAAREAAACPAAGPALWRLPE

Parental  ELLLLICSYLDMRALGRLAQVCRWLRRFTSCDLLWRRIARASLNSGFTRLGTDLMTSVPVKERVKVSQNW
          .LLLLICSYLDM..L.RLAQVCRWLRRFT.CDLL.R.IARASLNSGFTRLGT.LMTSVPVK....VSQ.W
Retrocopy VLLLLICSYLDMPDLSRLAQVCRWLRRFTNCDLLRRQIARASLNSGFTRLGTNLMTSVPVK----VSQKW

Parental  RLGRCREGILLKWRCSQMPWMQLEDDSLYISQANFILA
          .LGRCREGILLKWRCSQMPWMQLEDD.LYISQANFILA
Retrocopy ILGRCREGILLKWRCSQMPWMQLEDDALYISQANFILA

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	0.77 RPM	45.95 RPM
SRP007412_cerebellum	0.85 RPM	47.55 RPM
SRP007412_heart	0.84 RPM	33.44 RPM
SRP007412_kidney	0.40 RPM	37.02 RPM
SRP007412_liver	0.15 RPM	14.14 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1876 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1876 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1876 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
Macaca mulatta	ENSMMUG00000006753	1 retrocopy	retro_mmul_615,
Pongo abelii	ENSPPYG00000002586	1 retrocopy	retro_pabe_1876 ,