RetrogeneDB ID: retro_pabe_1808

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 20:15935400..15935865(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MRPS11
• Ensembl ID: ENSPPYG00000006751
• Aliases: None
• Description: mitochondrial ribosomal protein S11 [Source:HGNC Symbol;Acc:14050]

Sequence

>retro_pabe_1808
AAAGTCATGGCCAGGATGCTGGTGCAGACCATCCACACAGGCACCCAGAAGCTCCAAGACATTGAGGCCAAGCAGAACAT
TGAAGAGAAGATGGTAGCTCCCAGCTACACCAGCTTTAGCATTTACCCTCCCATTACAGAAGAAAAAAGCTCTCTGAGGT
GGGCAGGAAAGAAATTTGAGGAGATCCCAACTGCACACATTAAAGCATCCTACAACAACACACAGATCCAGGTAATCTCT
GCCACTAATCAGCCCCTTGCCCATACTTCCTGTGGCACAGAGGAATTTCTGAATGCCAAGAAGGGCACAGGCATTGATGC
ACAGACAGCAGGCATAGCAGCCGTGACGAAAGCTACAGGAAAGGGTGTTACCCACATCTGAGTTGTGGTGAAGGGCCAGG
GGCCAGGACACTTGTCTGCCATCCAGGGACTGACTGTGGGGGGCCTGGAAGTGATCTCAATCACA

Alignment

ORF - retro_pabe_1808 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.68 %
• Parental protein coverage: 79.38 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RVVARTPAGTIHTGARQLQDAAAKQKVEVK-AAPSHTKFSIYPPIPGEENSLRWAGKKFEEIPIAHIKAS
          .V.AR....TIHTG...LQD..AKQ..E.K..APS.T.FSIYPPI..E..SLRWAGKKFEEIP.AHIKAS
Retrocopy KVMARMLVQTIHTGTQKLQDIEAKQNIEEKMVAPSYTSFSIYPPITEEKSSLRWAGKKFEEIPTAHIKAS

Parental  HNNTLIQVVSASNEPLALASCGTEGFRNAKKGTGVAAQTAGIAAAARAKQKGVIHIRVVVKGLGPGRLSA
          .NNT.IQV.SA.N.PLA..SCGTE.F.NAKKGTG..AQTAGIAA...A..KGV.HI.VVVKG.GPG.LSA
Retrocopy YNNTQIQVISATNQPLAHTSCGTEEFLNAKKGTGIDAQTAGIAAVTKATGKGVTHI*VVVKGQGPGHLSA

Parental  MHGLIMGGLEVISIT
          ..GL..GGLEVISIT
Retrocopy IQGLTVGGLEVISIT

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	24.44 RPM
SRP007412_cerebellum	0.00 RPM	14.47 RPM
SRP007412_heart	0.00 RPM	12.46 RPM
SRP007412_kidney	0.00 RPM	26.15 RPM
SRP007412_liver	0.00 RPM	21.57 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1808 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1808 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1808 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000013012	2 retrocopies	retro_cjac_2601, retro_cjac_2989,
Felis catus	ENSFCAG00000014967	1 retrocopy	retro_fcat_282,
Homo sapiens	ENSG00000181991	1 retrocopy	retro_hsap_2458,
Gorilla gorilla	ENSGGOG00000015152	1 retrocopy	retro_ggor_1531,
Macaca mulatta	ENSMMUG00000013659	1 retrocopy	retro_mmul_637,
Nomascus leucogenys	ENSNLEG00000011441	1 retrocopy	retro_nleu_1902,
Ochotona princeps	ENSOPRG00000008247	1 retrocopy	retro_opri_540,
Pongo abelii	ENSPPYG00000006751	2 retrocopies	retro_pabe_1808 , retro_pabe_2583,
Pan troglodytes	ENSPTRG00000007420	1 retrocopy	retro_ptro_1419,