RetrogeneDB ID: retro_pabe_2290

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 3:12643466..12644195(-)
• 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_2290
ATGGCATGGTGAGGCTGGGCAGAGAGAGGTTGGGGCAGCGACCAGGCGTGGTTTCCGCCAGTGGGCAGCCGCAGCTGCAA
GGAACTCACTGCGGCCCTAGCCCCGCCACAGCTGCTCAGACGCAGGTTTGGCTTCTTCAGCAAAAATGTGGATTCAGAAA
AGCACCCAGGAAGGCTGAACCTCAAAGATCAGACACAGGCACAAGTGGTGAAGCATACAAGAGAAGTGCTTTGATTCCTC
CTATGGAAGAAACGGCCTTTTATCCTTCTCTGTATCCTATAGGGACTCTCATAAAACCTTTATTTTTTACTGTTGGGTTT
ACAGGCTGTGCATTTGGATCAGCTGCTATTTGGCAATATGAATCACTGAAATCCAGGGTCCAGAGTTATTCTGATGATAT
AAAAGCTGACGGTTGGGATAGCATAAGATCACAAAAAGGAGACTTCAGAAAGGAGATTAACAAGTGGTAGAATAACCTAA
GCGATGGCCACCAGACTGTGACAGGTTATCACAGCTGCAAATGAATGTCTTTGTATTCTGTTTTAGAGAGTACCTTCTCT
GCAGCGGACAATGATCAGGTATTTCACATCTAATCCAGCCTCAAAAGCCCTTTCTTTTCCAATGTTGCTGTCAACATTCA
GTCATTTCTCCTTATTTCACATGGCAGCAAATATCTATGTTTTGTGGAGCTTCGCCTCCAGCACAGTGAACATTCTGGAT
CAAGAGCAG

Alignment

ORF - retro_pabe_2290 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.35 %
• Parental protein coverage: 59.8 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAWRGWAQRGWGCGQAWAASVGGRSCEELTAALTPPRLLGRRFNFF-IQQKCGFRKAPRKVEPRRSDTGT
          MAW.GWA.RGWG..QAW...VG.RSC.ELTAAL..P..L.RR...F..QQKCGFRKAPRK.EP.RSDTGT
Retrocopy MAW*GWAERGWGSDQAWFPPVGSRSCKELTAALA-PPQLLRRRFGF<LQQKCGFRKAPRKAEPQRSDTGT

Parental  SGEAYKRSALIPPVEETVFYPSPYPIRSLIKPLFFTVGFTGCAFGSAAIWQYESLKSRVQSYFDGIKADW
          SGEAYKRSALIPP.EET.FYPS.YPI..LIKPLFFTVGFTGCAFGSAAIWQYESLKSRVQSY.D.IKAD.
Retrocopy SGEAYKRSALIPPMEETAFYPSLYPIGTLIKPLFFTVGFTGCAFGSAAIWQYESLKSRVQSYSDDIKADG

Parental  LDSIRPQKEGDFRKEINKWWNNLSDGQRTVTG-IIAANVLVFCLW-RVPSLQRTMIRYFTSNPASKVLCS
          .DSIR.QK.GDFRKEINKW.NNLSDG..TVTG.I.AAN.....L..RVPSLQRTMIRYFTSNPASK.L..
Retrocopy WDSIRSQK-GDFRKEINKW*NNLSDGHQTVTG>ITAANECLCILF*RVPSLQRTMIRYFTSNPASKALSF

Parental  PMLLSTFSHFSLFHMAANMYVLWSFSSSIVNILGQEQ
          PMLLSTFSHFSLFHMAAN.YVLWSF.SS.VNIL.QEQ
Retrocopy PMLLSTFSHFSLFHMAANIYVLWSFASSTVNILDQEQ

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	36.55 RPM
SRP007412_cerebellum	0.12 RPM	61.04 RPM
SRP007412_heart	0.03 RPM	16.41 RPM
SRP007412_kidney	0.03 RPM	28.17 RPM
SRP007412_liver	0.03 RPM	25.37 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2290 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2290 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2290 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Callithrix jacchus	retro_cjac_1415

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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,