RetrogeneDB ID: retro_pabe_2766

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 5:110593864..110594431(-)
• Located in intron of: ENSPPYG00000015675

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSPPYG00000020755
• Aliases: None
• Description: None

Sequence

>retro_pabe_2766
ATGACTGATAAAGCAGAGAAGGCTGCTGTAGAACCTGAAAATGTGTTTAAACGTCCCAGGGAATCTGAGAGTCCTTCATC
TCAGAAAAGGCAGAAGATGGCCCTGTTGTTAAGGAAACAAAGAGCAGGAGACAGTCTTATTGGAGGCTCTGCCATGTCCA
AGGAAAAGAAGCTTATGGCAGTAGATGGTATTCCACCAAGCCAATTGGATTCTCGATTTGATGACTTCAGTGGTTGCAGC
AAAGATGGGCTGATGCAGAAACCTGGTAGAAATGCATCTGTAGGAGGAATCGTTACCAGCAATTTCTCTGGAGATGACCT
AAAAGTCACAGAAATACTCCCTTTTCCAAAATGCCAAGAAGAAATTAATGCTAATATAAAATGTCAATTAGTGAAGGAAA
TTCGACACTTTAGACGAAAATATGAAAAACTCTTCAAATTGCTTGAAGGACTGCAAGGACCTATAGAAGTCAAGAAATGA
TTTTTTGAATCCATCATCAAGGAAGCCACAAGATTTATGAGACGAGACTTAATTCAGCACCTTGAGAAGAAACTGGAATA
AATGATT

Alignment

ORF - retro_pabe_2766 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.49 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MTDKTEKVSVDPETVFKRPRECDSPSYQKRQRMALLARKQGAGDSLIAGSAMSKEKKLMTGGALPPSQLD
          MTDK.EK..V.PE.VFKRPRE..SPS.QKRQ.MALL.RKQ.AGDSLI.GSAMSKEKKLM.....PPSQLD
Retrocopy MTDKAEKAAVEPENVFKRPRESESPSSQKRQKMALLLRKQRAGDSLIGGSAMSKEKKLMAVDGIPPSQLD

Parental  YQIDDFTGFSKDGMMQKPGSNAPVGGNVTSSFSGDDLECRETVPFPKSQEEINADIKCQVVKEIRCIGRK
          ...DDF.G.SKDG.MQKPG.NA.VGG.VTS.FSGDDL...E..PFPK.QEEINA.IKCQ.VKEIR...RK
Retrocopy SRFDDFSGCSKDGLMQKPGRNASVGGIVTSNFSGDDLKVTEILPFPKCQEEINANIKCQLVKEIRHFRRK

Parental  YEKIFKMLEGVQGPTEVRKRFFESIIKEAARCMRRDFVKHLKKKLKRMI
          YEK.FK.LEG.QGP.EV.K.FFESIIKEA.R.MRRD...HL.KKL..MI
Retrocopy YEKLFKLLEGLQGPIEVKK*FFESIIKEATRFMRRDLIQHLEKKLE*MI

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	0.00 RPM
SRP007412_cerebellum	0.12 RPM	0.00 RPM
SRP007412_heart	0.00 RPM	0.00 RPM
SRP007412_kidney	0.10 RPM	0.00 RPM
SRP007412_liver	0.03 RPM	0.00 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2766 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2766 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2766 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3362
Pan troglodytes	retro_ptro_2285
Macaca mulatta	retro_mmul_2100
Callithrix jacchus	retro_cjac_1827

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000014436	2 retrocopies	retro_cfam_441, retro_cfam_444,
Callithrix jacchus	ENSCJAG00000004135	1 retrocopy	retro_cjac_1827,
Dipodomys ordii	ENSDORG00000008443	1 retrocopy	retro_dord_354,
Homo sapiens	ENSG00000242284	1 retrocopy	retro_hsap_3362,
Macaca mulatta	ENSMMUG00000021984	1 retrocopy	retro_mmul_2100,
Nomascus leucogenys	ENSNLEG00000002303	1 retrocopy	retro_nleu_961,
Pongo abelii	ENSPPYG00000005381	1 retrocopy	retro_pabe_2727,
Pongo abelii	ENSPPYG00000020755	1 retrocopy	retro_pabe_2766 ,
Pan troglodytes	ENSPTRG00000041730	1 retrocopy	retro_ptro_2285,