RetrogeneDB ID: retro_pabe_3594

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: Un:43652196..43652976(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPPYG00000020054
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PPID
• Ensembl ID: ENSPPYG00000015159
• Aliases: None
• Description: peptidylprolyl isomerase D [Source:HGNC Symbol;Acc:9257]

Sequence

>retro_pabe_3594
AAGCATGATCGGGAGGGTTTACTGAGCATGGGAAACGCAGGCCGCAACACAAATGGTTCTCAGTTTTTTATCACAACAGT
TCCAACTCCTCATTTGGATGGGAAACTTGTGCTGTTTGGCCAAGTAAGTAAAGGAATAGGAGTGGCAAGGATATTGGAAA
ATGCGGAAGTGAAAGGTGAAAAACCTGCTAAATTGTGTGTTATTGCAGAATGTGGAGAATTGAAGGAAGGAGATGATTGG
GGAATATTCCCAAAAGATGGCTCTGGCGACAGTCATCCAGATTTCCCTGAGGATGCGGCTATAGATTTAAAAGATGTAGA
TAAAATTTTATTAATAACAGAAGACTTAAAAAACATTGGAAATACTTTTTTCAAATCCCAGAACTGGGAGATGGCCATTA
AAAAATATGCAAAAGTTTTAAGATACGTGGACAGGTCAAAGGCTGTTATTGAGACAGCAGATAGAGCCAAGCTGCAACCT
ATAGCTTTAAGCTGTGTACTGAATATTGGTGCTTGTAAACTGAAGATGTCAAATTGGCAGGGAGCAATTGACAGTTGTTT
AGAGGCTCTTGAAATAGACCCATCAAATACCAAAGCATTGTACCGCAGAGCTCAAGGATGGCAAGGATTAAAAGAATATG
ATCAAGCATTGGCTGATCTTAAGAAAGCTCAGGAGATAGCACCAGAAGATAAAGCTATCCAGGCAGAATTGCTGAAAGTC
AAACAAAAGATAAAGGCACAGAAAGATATAGAGAAGGCAGTATATGCAAAAATGTTTGCT

Alignment

ORF - retro_pabe_3594 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.54 %
• Parental protein coverage: 70.27 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KHDQEGLLSMANAGRNTNGSQFFITTVPTPHLDGKHVVFGQVIKGIGVARILENVEVKGEKPAKLCVIAE
          KHD.EGLLSM.NAGRNTNGSQFFITTVPTPHLDGK.V.FGQV.KGIGVARILEN.EVKGEKPAKLCVIAE
Retrocopy KHDREGLLSMGNAGRNTNGSQFFITTVPTPHLDGKLVLFGQVSKGIGVARILENAEVKGEKPAKLCVIAE

Parental  CGELKEGDDWGIFPKDGSGDSHPDFPEDADIDLKDVDKILLITEDLKNIGNTFFKSQNWEMAIKKYAKVL
          CGELKEGDDWGIFPKDGSGDSHPDFPEDA.IDLKDVDKILLITEDLKNIGNTFFKSQNWEMAIKKYAKVL
Retrocopy CGELKEGDDWGIFPKDGSGDSHPDFPEDAAIDLKDVDKILLITEDLKNIGNTFFKSQNWEMAIKKYAKVL

Parental  RYVDSSKAVIETADRAKLQPIALSCVLNIGACKLKMSNWQGAIDSCLEALEIDPSNTKALYRRAQGWQGL
          RYVD.SKAVIETADRAKLQPIALSCVLNIGACKLKMSNWQGAIDSCLEALEIDPSNTKALYRRAQGWQGL
Retrocopy RYVDRSKAVIETADRAKLQPIALSCVLNIGACKLKMSNWQGAIDSCLEALEIDPSNTKALYRRAQGWQGL

Parental  KEYDQALADLKKAQEIAPEDKAIQAELLKVKQKIKAQKDKEKAVYAKMFA
          KEYDQALADLKKAQEIAPEDKAIQAELLKVKQKIKAQKD.EKAVYAKMFA
Retrocopy KEYDQALADLKKAQEIAPEDKAIQAELLKVKQKIKAQKDIEKAVYAKMFA

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	0.11 RPM	17.20 RPM
SRP007412_cerebellum	0.00 RPM	16.42 RPM
SRP007412_heart	0.06 RPM	7.50 RPM
SRP007412_kidney	0.03 RPM	10.84 RPM
SRP007412_liver	0.06 RPM	9.21 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3594 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3594 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3594 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000016680	1 retrocopy	retro_btau_1672,
Choloepus hoffmanni	ENSCHOG00000012069	1 retrocopy	retro_chof_1533,
Callithrix jacchus	ENSCJAG00000001437	2 retrocopies	retro_cjac_2321, retro_cjac_4162,
Echinops telfairi	ENSETEG00000012655	2 retrocopies	retro_etel_10, retro_etel_633,
Felis catus	ENSFCAG00000028926	2 retrocopies	retro_fcat_494, retro_fcat_559,
Myotis lucifugus	ENSMLUG00000009317	1 retrocopy	retro_mluc_1667,
Macaca mulatta	ENSMMUG00000017768	2 retrocopies	retro_mmul_281, retro_mmul_348,
Mustela putorius furo	ENSMPUG00000018108	1 retrocopy	retro_mputfur_1415,
Oryctolagus cuniculus	ENSOCUG00000006602	1 retrocopy	retro_ocun_1625,
Otolemur garnettii	ENSOGAG00000003317	2 retrocopies	retro_ogar_2355, retro_ogar_2680,
Pongo abelii	ENSPPYG00000015159	1 retrocopy	retro_pabe_3594 ,
Rattus norvegicus	ENSRNOG00000027408	1 retrocopy	retro_rnor_188,
Ictidomys tridecemlineatus	ENSSTOG00000001552	1 retrocopy	retro_itri_1422,