RetrogeneDB ID: retro_pabe_3347

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 8:79290321..79290941(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MRPL9
• Ensembl ID: ENSPPYG00000000857
• Aliases: None
• Description: mitochondrial ribosomal protein L9 [Source:HGNC Symbol;Acc:14277]

Sequence

>retro_pabe_3347
TGGAAGGTACCACTGGTCAGTGAGGGCCAGAAGCTGCGCCTGCACAAGCGACACTATATCGACAAGCTGGTGGAGGACAC
AAAGCACTGGCCCAAAGAAAACCTGGAGATCATCTTCACACAGTCTGTGGAGACACTTGGAGTCCGGGGTGACCTGGCCT
CAGTAAAGAAATCTATGGATCGGAATCAACTCCTTCCTCAGAGACTGGCTGCATATGCATCACCTGAAAACAAGAAGCTG
TTTGAAGAGGAGAAATTGCTGAGACCAGGAGGAAAGTCAGAGAAGATCCAGACCAAGGCAGGTGAGGCAACAGTGACATT
TCTGAAAAGCTGTCACCTGGAGGTAGGGATGAAGAACAATGTCAAATGGGAGCTGAACCCTGAAACAGTTGCCCGCCACT
TCTTCAAGAATCTTGGTGTTGTGGTCACCCCCCATACATTAAAGTTACCAGAAGAGCCCCTCACTCGGTGAGGCAAGTAC
TGTTGTGAGGTGATGGTAAATGGGCTTGGTACTGTGAGGGTGCCTATGTCTCTGGTAAACTTTGAGAGGCCCAAACTCAA
AAGTAGAAGTACTGGTTAGCCCAGCAAGCTGCCAACGGCATGGCCCCACCAGCCCCTAGA

Alignment

ORF - retro_pabe_3347 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.85 %
• Parental protein coverage: 77.53 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  WKVPLAGEGRKPRLHRRHRVYKLVEDTKHRPKENLELILTQSVENVGVRGDLVSVKKSLGRNRLLPQGLA
          WKVPL..EG.K.RLH.RH...KLVEDTKH.PKENLE.I.TQSVE..GVRGDL.SVKKS..RN.LLPQ.LA
Retrocopy WKVPLVSEGQKLRLHKRHYIDKLVEDTKHWPKENLEIIFTQSVETLGVRGDLASVKKSMDRNQLLPQRLA

Parental  VYASPENRKLFEEEKLLRQEGKLEKIQTKAGEATVKFLKSCRLEVGMKNNVKWELNPEIVARHFFKNLGV
          .YASPEN.KLFEEEKLLR..GK.EKIQTKAGEATV.FLKSC.LEVGMKNNVKWELNPE.VARHFFKNLGV
Retrocopy AYASPENKKLFEEEKLLRPGGKSEKIQTKAGEATVTFLKSCHLEVGMKNNVKWELNPETVARHFFKNLGV

Parental  VVAPHTLKLPEEPITRWGEYWCEVTVNGLDTVRVPMSVVNFEKPK-TKRYKYWLAQQAAKAMAPTSPQ
          VV.PHTLKLPEEP.TR.G.Y.CEV.VNGL.TVRVPMS.VNFE.PK.T...KYWLAQQAA..MAP..P.
Retrocopy VVTPHTLKLPEEPLTR*GKYCCEVMVNGLGTVRVPMSLVNFERPK<TQK*KYWLAQQAANGMAPPAPR

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	42.41 RPM
SRP007412_cerebellum	0.00 RPM	27.48 RPM
SRP007412_heart	0.00 RPM	18.57 RPM
SRP007412_kidney	0.00 RPM	41.76 RPM
SRP007412_liver	0.00 RPM	32.47 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3347 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3347 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3347 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4078
Pan troglodytes	retro_ptro_2765
Gorilla gorilla	retro_ggor_2735

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000000258	1 retrocopy	retro_chof_10,
Dasypus novemcinctus	ENSDNOG00000011403	1 retrocopy	retro_dnov_1989,
Homo sapiens	ENSG00000143436	1 retrocopy	retro_hsap_4078,
Gorilla gorilla	ENSGGOG00000001902	1 retrocopy	retro_ggor_2735,
Loxodonta africana	ENSLAFG00000006271	2 retrocopies	retro_lafr_498, retro_lafr_563,
Nomascus leucogenys	ENSNLEG00000010275	1 retrocopy	retro_nleu_2045,
Oryctolagus cuniculus	ENSOCUG00000001383	1 retrocopy	retro_ocun_725,
Otolemur garnettii	ENSOGAG00000030456	1 retrocopy	retro_ogar_159,
Pongo abelii	ENSPPYG00000000857	1 retrocopy	retro_pabe_3347 ,
Pan troglodytes	ENSPTRG00000001295	2 retrocopies	retro_ptro_2765, retro_ptro_2996,