RetrogeneDB ID: retro_pabe_1645

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 19:54386796..54387391(+)
• Located in intron of: ENSPPYG00000010341

Retrocopy information

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

Parental gene information

• Parental gene symbol: PABPN1
• Ensembl ID: ENSPPYG00000005663
• Aliases: None
• Description: poly(A) binding protein, nuclear 1 [Source:HGNC Symbol;Acc:8565]

Sequence

>retro_pabe_1645
GCCGGGGCGGCGGCGCCATCTTGTGCCCGGGGCCGGTGGGGAGGCCGGGGAGGTTGCCCCGGGGGGCGCAGGGGACGATG
GGAATGGCCTGGAATCTGAGGAACTGGAGCCTGAGGAGCTGCTGTTGGAGCCCGAGCCGGAAGAGGAGCCGCTCCAGCCC
CGCGCCGCATGCCCAGGAGCTCCAGGCCCTAGGCCTCCTTCAGGAGCCACCGGCAGCCAAGAGGAGGGGGAGGAGCCGGG
ACTGGTCGAGGGTGACCCGGGGGACGGTGCCATTGAGGACCCGGTGCCGGAAGCTATCAAAGCTGGAGTCAGGGAGATGG
AGGAAGAAGCTGAGAAGCTAAAGGAGCTACAGAACGACGTAGAGAAGCAGATGAATATGAGTCCACCTCCAGGCGATGTT
GGCCCAGTGATCACGTCCATTGAGGAGAAGATGGAGGCTGATGCCCGTTCCATCGGTGCTGGCAATGTGGACTACGGTGC
AACAGCAGAAGAGCTGGAAGCTCACTTTCATGGCTGTGGTTCAGTCAACCATGTTACCATACTCTGTGACAAATTTAGTG
GCCATTCCAAAAGGTTTGCATATATAGAGTCCTCA

Alignment

ORF - retro_pabe_1645 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.25 %
• Parental protein coverage: 71.53 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  AAAAATGAARRR-GETGEGAPGGAGDYGNGLESEELEPEELLLEPEPEPEPEEEPPRPRAP-PGAPGPGP
          A.AAA...AR.R.GE.GE.APGGAGD.GNGLESEELEPEELLL....EPEPEEEP..PRA..PGAPGP.P
Retrocopy AGAAAPSCARGR>GEAGEVAPGGAGDDGNGLESEELEPEELLL----EPEPEEEPLQPRAACPGAPGPRP

Parental  GSGAPGSQEEEEEPGLVEGDPGDGAIEDPELEAIKARVREMEEEAEKLKELQNEVEKQMNMSPPPGNAGP
          .SGA.GSQEE.EEPGLVEGDPGDGAIEDP..EAIKA.VREMEEEAEKLKELQN.VEKQMNMSPPPG..GP
Retrocopy PSGATGSQEEGEEPGLVEGDPGDGAIEDPVPEAIKAGVREMEEEAEKLKELQNDVEKQMNMSPPPGDVGP

Parental  VIMSIEEKMEADARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFS
          VI.SIEEKMEADARSI..GNVDYGATAEELEAHFHGCGSVN.VTILCDKFSGH.K.FAYIE.S
Retrocopy VITSIEEKMEADARSIGAGNVDYGATAEELEAHFHGCGSVNHVTILCDKFSGHSKRFAYIESS

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	39.04 RPM
SRP007412_cerebellum	0.24 RPM	62.87 RPM
SRP007412_heart	0.00 RPM	11.71 RPM
SRP007412_kidney	0.13 RPM	48.23 RPM
SRP007412_liver	0.12 RPM	23.96 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1645 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1645 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1645 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000006884	1 retrocopy	retro_btau_693,
Callithrix jacchus	ENSCJAG00000007960	4 retrocopies	retro_cjac_1263, retro_cjac_2291, retro_cjac_3278, retro_cjac_3836,
Dipodomys ordii	ENSDORG00000002873	1 retrocopy	retro_dord_606,
Homo sapiens	ENSG00000100836	1 retrocopy	retro_hsap_4855,
Gorilla gorilla	ENSGGOG00000022683	2 retrocopies	retro_ggor_1454, retro_ggor_3030,
Mustela putorius furo	ENSMPUG00000006775	1 retrocopy	retro_mputfur_496,
Mus musculus	ENSMUSG00000022194	1 retrocopy	retro_mmus_403,
Nomascus leucogenys	ENSNLEG00000015009	2 retrocopies	retro_nleu_2066, retro_nleu_3023,
Otolemur garnettii	ENSOGAG00000008710	1 retrocopy	retro_ogar_797,
Pongo abelii	ENSPPYG00000005663	2 retrocopies	retro_pabe_1645 , retro_pabe_3773,
Pan troglodytes	ENSPTRG00000006168	2 retrocopies	retro_ptro_1339, retro_ptro_3232,
Sus scrofa	ENSSSCG00000002023	1 retrocopy	retro_sscr_625,