RetrogeneDB ID: retro_pabe_17

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: X:41191129..41191453(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPPYG00000020252
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: MPC1
• Ensembl ID: ENSPPYG00000017166
• Aliases: None
• Description: mitochondrial pyruvate carrier 1 [Source:HGNC Symbol;Acc:21606]

Sequence

>retro_pabe_17
AGGGTGGCGGTACTGTGGCGGAAGATGAGAGATAACTTCCAGAGCAAGGAGTTCCGGGAATACGTGAGCAGCACTCACTT
CTGGGGTCCCGCGTTCAACTGGGGCCTTCCGCTGGCTGCCTTTAAAGATATGAAGGCGTCGCCAGAGATCATCAGTGGCC
GCATGACAACAGCGCTCATCTTGTACTCGGCGATCTTCATGCGCTTCGCCTACCTCGTACAGCCTCGAAACCTGCTGCTG
ATGGCGTGCCACTGTACCAACGTGATGGCGCAGAGTGTGCAGGCCAGTCGCTACCTACTCTACTACTACGGCGGCGGCGC
CGAG

Alignment

ORF - retro_pabe_17 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.26 %
• Parental protein coverage: 87.16 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LVRKAADYVRSKDFRDYLMSTHFWGPVANWGLPIAAINDMKKSPEIISGRMTFALCCYSLTFMRFAYKVQ
          L.RK..D...SK.FR.Y..STHFWGP..NWGLP.AA..DMK.SPEIISGRMT.AL..YS..FMRFAY.VQ
Retrocopy LWRKMRDNFQSKEFREYVSSTHFWGPAFNWGLPLAAFKDMKASPEIISGRMTTALILYSAIFMRFAYLVQ

Parental  PRNWLLFACHATNEVAQLIQGGRLI
          PRN.LL.ACH.TN..AQ..Q..R..
Retrocopy PRNLLLMACHCTNVMAQSVQASRYL

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	16.92 RPM
SRP007412_cerebellum	0.00 RPM	26.87 RPM
SRP007412_heart	0.00 RPM	67.04 RPM
SRP007412_kidney	0.00 RPM	72.79 RPM
SRP007412_liver	0.03 RPM	23.99 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_17 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_17 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_17 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4675

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000027879	1 retrocopy	retro_btau_43,
Callithrix jacchus	ENSCJAG00000012552	2 retrocopies	retro_cjac_2102, retro_cjac_4053,
Dasypus novemcinctus	ENSDNOG00000001205	1 retrocopy	retro_dnov_2139,
Homo sapiens	ENSG00000060762	1 retrocopy	retro_hsap_4675,
Myotis lucifugus	ENSMLUG00000000583	1 retrocopy	retro_mluc_28,
Mus musculus	ENSMUSG00000023861	3 retrocopies	retro_mmus_2037, retro_mmus_3420, retro_mmus_979,
Ornithorhynchus anatinus	ENSOANG00000004153	1 retrocopy	retro_oana_45,
Pongo abelii	ENSPPYG00000017166	1 retrocopy	retro_pabe_17 ,
Rattus norvegicus	ENSRNOG00000012415	3 retrocopies	retro_rnor_1111, retro_rnor_2632, retro_rnor_296,
Tursiops truncatus	ENSTTRG00000004456	1 retrocopy	retro_ttru_663,