RetrogeneDB ID: retro_pabe_2912

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 6:146284774..146285406(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PARL
• Ensembl ID: ENSPPYG00000014338
• Aliases: PARL, PSARL
• Description: Presenilins-associated rhomboid-like protein, mitochondrial P-beta [Source:UniProtKB/Swiss-Prot;Acc:Q5R5H4]

Sequence

>retro_pabe_2912
TCAGGTATCATAGCTGCAAACGTCCTTGTATTCTGTTTGTAGAGAGTACCTTCTCTGCAGTGGACAGTGATCAGATATTT
CACATCTAATCCAGCCTCAAAGGTCCGTTGTTCTCCAATGTTGCTGTCAACATTCAATCATTTCTCCTTATTTCACATGG
CAGCAAATACGTATGTTTTGTGGAGCTTCTCCTTCAGTATAGTGAACATTCTGGGTCAAGAGCAGTTCATGGCAGTGTAC
CTATCTGCAGGTGTTATTTCCAATTTTGTCAGTTATGTGTGTAAAGTTGCCACACGAAGATATGGACCATCACTTGGTGC
ATCTCGCGCCATCATGATGATCCTCGCAGATGTCCGCACTAAGATCCCAGAAGGGAGGCTTGCCATTATTTTCTTCCAAT
GTTCACATTCACAGCAGGAAATGCCCTAAAATCCATTAATGCCACAGATATGGCAGGAATGATCCTGGGATGGAAATGTT
TTGATTATGCAGCACATCTTCGGGGAGCTCTCTTTGGAATATGATATGTTACTTACAGTCATGAACTGATTTGGAAGAAC
AGGGAGCCTCTAGTGAAAATCTGGCATGAAATGAGGACTAATGCCCCCCCCAAAAAAAGAGGTGGCTCTAAG

Alignment

ORF - retro_pabe_2912 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.85 %
• Parental protein coverage: 55.41 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  TGIIAANVLVFCLWRVPSLQRTMIRYFTSNPASKVLCSPMLLSTFSHFSLFHMAANMYVLWSFSSSIVNI
          .GIIAANVLVFCL.RVPSLQ.T.IRYFTSNPASKV.CSPMLLSTF.HFSLFHMAAN.YVLWSFS.SIVNI
Retrocopy SGIIAANVLVFCL*RVPSLQWTVIRYFTSNPASKVRCSPMLLSTFNHFSLFHMAANTYVLWSFSFSIVNI

Parental  LGQEQFMAVYLSAGVISNFVSYVGKVATGRYGPSLGASGAIMTVLAAVCTKIPEGRLAII-FLPMFTFTA
          LGQEQFMAVYLSAGVISNFVSYV.KVAT.RYGPSLGAS.AIM..LA.V.TKIPEGRLAII.FLPMFTFTA
Retrocopy LGQEQFMAVYLSAGVISNFVSYVCKVATRRYGPSLGASRAIMMILADVRTKIPEGRLAII<FLPMFTFTA

Parental  GNALKAIIAMDTAGMILGWKFFDHAAHLGGALFGIWYVTYGHELIWKNREPLVKIWHEIRTN-GPKKGGG
          GNALK.I.A.D.AGMILGWK.FD.AAHL.GALFGI.YVTY.HELIWKNREPLVKIWHE.RTN...KK.GG
Retrocopy GNALKSINATDMAGMILGWKCFDYAAHLRGALFGI*YVTYSHELIWKNREPLVKIWHEMRTNXXXKKRGG

Parental  SK
          SK
Retrocopy SK

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	1.00 RPM	36.55 RPM
SRP007412_cerebellum	2.31 RPM	61.04 RPM
SRP007412_heart	0.45 RPM	16.41 RPM
SRP007412_kidney	0.83 RPM	28.17 RPM
SRP007412_liver	1.22 RPM	25.37 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2912 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2912 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2912 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3526
Pan troglodytes	retro_ptro_2394

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Dipodomys ordii	ENSDORG00000014935	1 retrocopy	retro_dord_315,
Myotis lucifugus	ENSMLUG00000004507	1 retrocopy	retro_mluc_883,
Mus musculus	ENSMUSG00000033918	2 retrocopies	retro_mmus_1882, retro_mmus_3526,
Oryctolagus cuniculus	ENSOCUG00000007882	1 retrocopy	retro_ocun_541,
Pongo abelii	ENSPPYG00000014338	2 retrocopies	retro_pabe_2290, retro_pabe_2912 ,
Ictidomys tridecemlineatus	ENSSTOG00000023222	1 retrocopy	retro_itri_380,