RetrogeneDB ID: retro_pabe_356

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 1:1985272..1986076(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PRIM1
• Ensembl ID: ENSPPYG00000004672
• Aliases: None
• Description: primase, DNA, polypeptide 1 (49kDa) [Source:HGNC Symbol;Acc:9369]

Sequence

>retro_pabe_356
TTTGACCCCACCAAGCTGTCTGAGCTATTCAAATGTTATTACCAGAGGCTCTTTCCCTATTCTCTGTACTGTTACTGGCT
CAACTACAGCAGAGTGATAAAGAATTACTCCCAACACTGTGAATTTTCATTCACACTGAAAGATGACATTACATTCGATA
CCAATCCTTCAACAACCAGAGTGATCTGGAAAAGGAGATGCAGAAAATGAATCCATACAAGATTGATATAGGTGCAGTAT
ATTCCCACAGACCCAATCAACACAATACAATGAAGCTGGGAGCTTTCCAGGCTCAGGAAAAAGAACTGGTGTTTGACACT
GACATGACAGACTGTGACAATGTGAGGAGATGCTGTAGTTCTGCAGATACATGTTCTAAGTGCTGGACCCTCATGACAAG
GGCCATACGCATCACCGACACTGCACTGAAGGAGGACTGTGGATTTAAGCATCGTCTCTGGGTATATTCTGGAAGGAGGG
GTGTACATTGTTCGGTCTGTGATAAATCACTTAGAAAACTGTCTTCGGTGGTATATTCTGGGATAGTTGAGTATTTGAGT
CTTGTAAAGCGTGGTCAAGATGTTAAAAAGAAAGTTCACCTAACTGAAAAAATTCACCCTTTTGTCAGAAAATCTATAAA
CATAATAAAAAAAAAACTTTGAAGAATATGCCTTGGTTAATCAAGATATTCTCAAAAATAACAAAAGCTGGGGTAAGATT
TTAGCCCTTGTTCCTGAAACAATTCAGGATGAACTTCAACAAAGCTTCCAAAAGTCTCACAATTCACTTCAGCATTGGGA
GCAC

Alignment

ORF - retro_pabe_356 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.44 %
• Parental protein coverage: 63.81 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  FDPTELPELLKLYYRRLFPYSQYYRWLNYGGVIKNYFQHREFSFTLKDDI-YIRYQSFNNQSDLEKEMQK
          FDPT.L.EL.K.YY.RLFPYS.Y..WLNY..VIKNY.QH.EFSFTLKDDI.YIRYQSFNNQSDLEKEMQK
Retrocopy FDPTKLSELFKCYYQRLFPYSLYCYWLNYSRVIKNYSQHCEFSFTLKDDI<YIRYQSFNNQSDLEKEMQK

Parental  MNPYKIDIGAVYSHRPNQHNTVKLGAFQAQEKELVFDIDMTDYDDVRRCCSSADICPKCWTLMTMAIRII
          MNPYKIDIGAVYSHRPNQHNT.KLGAFQAQEKELVFD.DMTD.D.VRRCCSSAD.C.KCWTLMT.AIRI.
Retrocopy MNPYKIDIGAVYSHRPNQHNTMKLGAFQAQEKELVFDTDMTDCDNVRRCCSSADTCSKCWTLMTRAIRIT

Parental  DRALKEDFGFKHRLWVYSGRRGVHCWVCDESVRKLSSAVRSGIVEYLSLVKGGQDVKKKVHLSEKIHPFI
          D.ALKED.GFKHRLWVYSGRRGVHC.VCD.S.RKLSS.V.SGIVEYLSLVK.GQDVKKKVHL.EKIHPF.
Retrocopy DTALKEDCGFKHRLWVYSGRRGVHCSVCDKSLRKLSSVVYSGIVEYLSLVKRGQDVKKKVHLTEKIHPFV

Parental  RKSINI-IKKYFEEYALVNQDILENKESWDKILALVPETIHDELQQSFQKSHNSLQRWEH
          RKSINI.....FEEYALVNQDIL.N..SW.KILALVPETI.DELQQSFQKSHNSLQ.WEH
Retrocopy RKSINI>XXXXFEEYALVNQDILKNNKSWGKILALVPETIQDELQQSFQKSHNSLQHWEH

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	3.26 RPM
SRP007412_cerebellum	0.12 RPM	10.34 RPM
SRP007412_heart	0.03 RPM	1.29 RPM
SRP007412_kidney	0.00 RPM	2.75 RPM
SRP007412_liver	0.03 RPM	2.85 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_356 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_356 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_356 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_339
Pan troglodytes	retro_ptro_271

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000015297	1 retrocopy	retro_ecab_447,
Homo sapiens	ENSG00000198056	1 retrocopy	retro_hsap_339,
Mustela putorius furo	ENSMPUG00000001603	1 retrocopy	retro_mputfur_587,
Nomascus leucogenys	ENSNLEG00000017443	1 retrocopy	retro_nleu_1780,
Oryctolagus cuniculus	ENSOCUG00000003458	1 retrocopy	retro_ocun_1265,
Procavia capensis	ENSPCAG00000007103	1 retrocopy	retro_pcap_174,
Pongo abelii	ENSPPYG00000004672	1 retrocopy	retro_pabe_356 ,
Pan troglodytes	ENSPTRG00000022987	1 retrocopy	retro_ptro_271,
Pteropus vampyrus	ENSPVAG00000008017	2 retrocopies	retro_pvam_153, retro_pvam_703,
Sus scrofa	ENSSSCG00000000408	1 retrocopy	retro_sscr_499,
Tupaia belangeri	ENSTBEG00000012998	1 retrocopy	retro_tbel_2255,
Tursiops truncatus	ENSTTRG00000002153	1 retrocopy	retro_ttru_352,