RetrogeneDB ID: retro_pabe_1232

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 15:33499302..33499992(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DKFZP469K0123
• Ensembl ID: ENSPPYG00000012353
• Aliases: None
• Description: RNA-binding protein PNO1 [Source:RefSeq peptide;Acc:NP_001125677]

Sequence

>retro_pabe_1232
GGTGGCCGGCGGGCAAAGAAACAATAGGCTGAACAGCTGTCCGCAGCAGAAGAGGGTGGGGATGCGGGCCGCATGGACAC
AGAGGAGGCCAGGCCAGCGAAGAGGCCCGTCTTCCCGCCTCTCTGAGTGGACGGGCTCCTGAGTGGGAAAGAAGAAAGAA
GGAAAATTCCAGTCCCAGCTAAAAGATACACACCATTAAAAGAAAACTGGATGAAAATATTTACTCCTATTGTCGCACAT
TTGGGACTTTAGATACGCTTTAACTTGAAATCTAAGAATGTAGAAGTCAGGACTTGTAAAGAAACCAAGGATGTTAGCGC
TCTGACAGAAGCAACTGATTTTGTGAAAGCCTTTATTCTCGGCTTTCAAGTGGAGGATGGGCTTGCCCTCATCAGGTTGA
ATGACCCCTTCCTAGAGTCTTTTGAAATTATAGATACTAAACCCCCAAAGGGAGACCATCTATCCAGGGCAATAGGAAGA
ATCGCTGGCGAAGGAGGAAAACCCGAATTCATCATAGAGAATGTGACACGGGCGCGGACAGTTTTGGCTGATATGGAAGT
TCACATCCTTGGCTCCTTCCAAAACATCAAGATGGCAAGAACTGCCATTTGCAACCTAATCTTGGGAAATCCTCCTTCCA
AGGTTTATGGCAATATTCGAGCTGTGGCTAGCAGATCAGCAGATCGATTC

Alignment

ORF - retro_pabe_1232 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.96 %
• Parental protein coverage: 91.27 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GGRRAKKRQAEQLSAAGESGDADRMDTEEARPAKRPVFPPLCGDGLLSGKEETRTIPVPANRYTPLKENW
          GGRRAKK..AEQLSAA.E.GDA.RMDTEEARPAKRPVFPPL..DGLLSGKEE.R.IPVPA.RYTPLKENW
Retrocopy GGRRAKKQ*AEQLSAAEEGGDAGRMDTEEARPAKRPVFPPL*VDGLLSGKEERRKIPVPAKRYTPLKENW

Parental  MKIFTPIVEHLGLQIRFNLKSRNVEIRTCKETKDVSALTKAADFVKAFILGFQVEDALALIRLDDLFLES
          MKIFTPIV.HLGL.IRFNLKS.NVE.RTCKETKDVSALT.A.DFVKAFILGFQVED.LALIRL.D.FLES
Retrocopy MKIFTPIVAHLGL*IRFNLKSKNVEVRTCKETKDVSALTEATDFVKAFILGFQVEDGLALIRLNDPFLES

Parental  FEITDVKPLKGDHLSRAIGRIAGKGGKTKFTIENVTRTRIVLADVKVHILGSFQNIKMARTAICNLILGN
          FEI.D.KP.KGDHLSRAIGRIAG.GGK..F.IENVTR.R.VLAD..VHILGSFQNIKMARTAICNLILGN
Retrocopy FEIIDTKPPKGDHLSRAIGRIAGEGGKPEFIIENVTRARTVLADMEVHILGSFQNIKMARTAICNLILGN

Parental  PPSKVYGNIRAVASRSADRF
          PPSKVYGNIRAVASRSADRF
Retrocopy PPSKVYGNIRAVASRSADRF

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	4.81 RPM
SRP007412_cerebellum	0.00 RPM	5.72 RPM
SRP007412_heart	0.00 RPM	5.12 RPM
SRP007412_kidney	0.00 RPM	6.93 RPM
SRP007412_liver	0.00 RPM	7.90 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1232 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1232 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1232 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000003256	1 retrocopy	retro_cfam_1886,
Callithrix jacchus	ENSCJAG00000006564	3 retrocopies	retro_cjac_2615, retro_cjac_273, retro_cjac_4127,
Felis catus	ENSFCAG00000025330	2 retrocopies	retro_fcat_1521, retro_fcat_864,
Loxodonta africana	ENSLAFG00000000046	1 retrocopy	retro_lafr_419,
Microcebus murinus	ENSMICG00000010897	1 retrocopy	retro_mmur_516,
Myotis lucifugus	ENSMLUG00000010850	1 retrocopy	retro_mluc_1719,
Macaca mulatta	ENSMMUG00000017461	2 retrocopies	retro_mmul_102, retro_mmul_352,
Nomascus leucogenys	ENSNLEG00000009993	1 retrocopy	retro_nleu_2389,
Oryctolagus cuniculus	ENSOCUG00000006100	1 retrocopy	retro_ocun_47,
Otolemur garnettii	ENSOGAG00000016637	1 retrocopy	retro_ogar_3025,
Pongo abelii	ENSPPYG00000012353	1 retrocopy	retro_pabe_1232 ,
Rattus norvegicus	ENSRNOG00000005524	1 retrocopy	retro_rnor_712,
Sus scrofa	ENSSSCG00000008352	2 retrocopies	retro_sscr_114, retro_sscr_352,
Tarsius syrichta	ENSTSYG00000004007	1 retrocopy	retro_tsyr_1625,