RetrogeneDB ID: retro_pabe_3128

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 7:27624993..27625522(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSPPYG00000017277
• Aliases: None
• Description: None

Sequence

>retro_pabe_3128
ATGGTCCAGCACTGGCCTGAGACAGTATGCGAGAAAGTTCAAAACGACTGTAGAGACCCTCCGGATTACTGGACAATACA
TGGGACTATGGCCCGATAAAAGTGAAGGATGTAATGGATCGTGGCACTTAAATGTAGAAGAGATTAAGGATGTTTTGCCG
GAAATGAAGGCATACTGGCCTGATGTAATTCACTCGTTTCCCAATCATAGCCACTTCTGGAAGCATGAGTGGGAGAAGCA
TGGGACCTCTGCCGCCCTGGTGGAGGCACTCAACTCCCAGAAGTACTTTAGCAGAAGCCTGGAACTCTACAGGGAGCTGG
ACAGCAACAGTGTTCTCCTAAAACTGCGGCTAAAACCATCCGTCAATTACTACCAAGTCGCAGATTTTAAAGATGCCCTT
GTCAGAGTGTATGGAGTGATACCCAAAATCCAGTGCCTTCCGCGAAGCCAGGATGGGGAAGTACAGACAATTGGTCAGAC
AGAACTTTGCCTCACTGAGCAAGGCCAGTAGCTGCAAAACTGCACCGAG

Alignment

ORF - retro_pabe_3128 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.27 %
• Parental protein coverage: 69.14 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MVQHWPETVCEKIQNDCRDPPDYWTIHG-LWPDKSEGCNRSWPFNLEEIKDLLPEMKASSPDVIHSFPNR
          MVQHWPETVCEK.QNDCRDPPDYWTIHG.LWPDKSEGCN.SW..N.EEIKD.LPEMKA..PDVIHSFPN.
Retrocopy MVQHWPETVCEKVQNDCRDPPDYWTIHG>LWPDKSEGCNGSWHLNVEEIKDVLPEMKAYWPDVIHSFPNH

Parental  SRFWKHEWEKHGTCAAQVDALSSQKKYFGRSLELYRELDLNSVLLKLGIKPSINYYQVADFKDALARVYG
          S.FWKHEWEKHGT.AA.V.AL.SQK.YF.RSLELYRELD.NSVLLKL..KPS.NYYQVADFKDAL.RVYG
Retrocopy SHFWKHEWEKHGTSAALVEALNSQK-YFSRSLELYRELDSNSVLLKLRLKPSVNYYQVADFKDALVRVYG

Parental  VIPKIQCLPPSQDEEVQTIGQIELCLTKQDQQLQNCTE
          VIPKIQCLP.SQD.EVQTIGQ.ELCLT.Q.Q.LQNCTE
Retrocopy VIPKIQCLPRSQDGEVQTIGQTELCLTEQGQ*LQNCTE

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	14.38 RPM
SRP007412_cerebellum	0.00 RPM	3.28 RPM
SRP007412_heart	0.00 RPM	3.01 RPM
SRP007412_kidney	0.00 RPM	9.35 RPM
SRP007412_liver	0.00 RPM	17.84 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3128 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3128 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3128 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_2529

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Loxodonta africana	ENSLAFG00000003359	1 retrocopy	retro_lafr_764,
Microcebus murinus	ENSMICG00000014184	1 retrocopy	retro_mmur_1544,
Macaca mulatta	ENSMMUG00000005673	1 retrocopy	retro_mmul_1684,
Monodelphis domestica	ENSMODG00000006193	1 retrocopy	retro_mdom_1994,
Nomascus leucogenys	ENSNLEG00000011573	1 retrocopy	retro_nleu_3005,
Pongo abelii	ENSPPYG00000017277	1 retrocopy	retro_pabe_3128 ,
Pan troglodytes	ENSPTRG00000018796	1 retrocopy	retro_ptro_2529,