RetrogeneDB ID: retro_pabe_1269

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 15:89580627..89581083(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ASB9
• Ensembl ID: ENSPPYG00000020140
• Aliases: None
• Description: ankyrin repeat and SOCS box containing 9 [Source:HGNC Symbol;Acc:17184]

Sequence

>retro_pabe_1269
ATGGATGGCAAACAAGGGGGCATGGATGGGAGCAAGCCCACGGGGCCAGGAGACTCTCCTGACACCAGGCTTCTTTCAAA
CCCATTGATGGGTGATTCTGTGTCTGATTGGTCTCTTACGCCTGCAGCTGCAATCCACGGACATCAGCTGTCTCTGAGGA
ACCTCATCAGCCAGAGGTGGCTTGTGAACATCATCACGGCAGATCGTGTTTCCCCACTCCATGAAGCCTGTCTCAGAGGT
CATCCCTCTTGTGTAAAGATTTTATTAAAGCATGGAGCTCAGGTGAATGGTGTGACAACAGATTGGCACACTCCACTGTT
TAATGTTTGTGTCAGCAGCAGCCGGGATTATGTGAATTTGCTTCTGCAGTATGAGGCCAGCGTTCAACCTGAGTGTGATC
TGGCATCCCCCATCCATGAAGCTGCTGGGAGAGACCACGTGGAGTGTGTCGACTCT

Alignment

ORF - retro_pabe_1269 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.84 %
• Parental protein coverage: 58.02 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MDGKQGGMDGSKPAGPRDSPDIRLLSNPLMGDAVSDWSPMHEAAIHGHQLSLRNLISQGWPVNIITADHV
          MDGKQGGMDGSKP.GP.DSPD.RLLSNPLMGD.VSDWS....AAIHGHQLSLRNLISQ.W.VNIITAD.V
Retrocopy MDGKQGGMDGSKPTGPGDSPDTRLLSNPLMGDSVSDWSLTPAAAIHGHQLSLRNLISQRWLVNIITADRV

Parental  SPLHEACLGGHPSCVKILLKHGAQVNGVTTDWHTPLFNACVSGSRDCVNLLLQHGASVQPESDLASPIHE
          SPLHEACL.GHPSCVKILLKHGAQVNGVTTDWHTPLFN.CVS.SRD.VNLLLQ..ASVQPE.DLASPIHE
Retrocopy SPLHEACLRGHPSCVKILLKHGAQVNGVTTDWHTPLFNVCVSSSRDYVNLLLQYEASVQPECDLASPIHE

Parental  AARRGHVECVDS
          AA.R.HVECVDS
Retrocopy AAGRDHVECVDS

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	0.22 RPM
SRP007412_cerebellum	0.00 RPM	0.12 RPM
SRP007412_heart	0.06 RPM	0.12 RPM
SRP007412_kidney	0.13 RPM	20.12 RPM
SRP007412_liver	0.09 RPM	2.82 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1269 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1269 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1269 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
Macropus eugenii	ENSMEUG00000002950	1 retrocopy	retro_meug_1676,
Pongo abelii	ENSPPYG00000020140	1 retrocopy	retro_pabe_1269 ,