RetrogeneDB ID: retro_pabe_508

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 10:25150461..25151151(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NUP35
• Ensembl ID: ENSPPYG00000012998
• Aliases: None
• Description: nucleoporin 35kDa [Source:HGNC Symbol;Acc:29797]

Sequence

>retro_pabe_508
CAGGTGCCCACATTAAGATCTGAACCCATGATGCTGGCTTCAACTCCAAAGCCAGGAGTTAATGCCTGGTTCTTAACCTG
GATTTTGAATGTGGAATTTTCCAGCTCTGGTGACTCCTCAACCTCGATCAATTAATGGCCCTTCGGTAGGAGTAGTGGAA
ATGAGATCACCTTTACTTGCAGGTCGGTCACCACCACAACCAGTTGTACTAGCTCGGAAAGATAAAAGTGGCGCTCCACA
AGTTAGAAGTATATATGATGACATTTCTAGCCTGGGACTTGGATCAGCACCTTTAACTTCAAGAAGACAGCCAAACATTT
CATAATGCAGAGTCCTCTTACTGGAGTTACATCGACTCCTGGAACAGGGCAAAGTATGTTTAGTCCAGCAAATATCGGTC
AGCCATGAAAGATGACATTATCTCCTTCCCAGTTGGATCCTTTTTATACTCAAGGAGATTCTTTGACTTCAGAAGATCAC
CTTGATGACACTTGGGTGACTGTGTTTGGGTTTTCTCAAGCCTCTGCTTCCTATATATTATTACAATTTGCACAGTATGG
GAATATCTTAAAACACGTGATGTCTAACACAGGAAATTGAATGTATATTCATTATCAGTCTAAACTGCAGGCTCGGAAAG
CCTTAACCAAAGATGGGAGGATTTTTAGAGAATTCATCATGATTGGTGTA

Alignment

ORF - retro_pabe_508 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.76 %
• Parental protein coverage: 56.86 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  QGPASGSEPMMLGSPTSPKPGVNAQFL-PGFLMGDLPAPVTPQPRSISGPSVGVMEMRSPLLAGGSPPQP
          Q.P...SEPMML.S...PKPGVNA.FL.PGF.M...PA.VTPQPRSI.GPSVGV.EMRSPLLAG.SPPQP
Retrocopy QVPTLRSEPMMLAS--TPKPGVNAWFL>PGF*MWNFPALVTPQPRSINGPSVGVVEMRSPLLAGRSPPQP

Parental  VVPAHKDKSGAPPVRSIYDDISSPGLGSTPLTSRRQPNIS-VMQSPLVGVTSTPGTGQSMFSPASIGQPR
          VV.A.KDKSGAP.VRSIYDDISS.GLGS.PLTSRRQPNIS..MQSPL.GVTSTPGTGQSMFSPA.IGQP.
Retrocopy VVLARKDKSGAPQVRSIYDDISSLGLGSAPLTSRRQPNIS<IMQSPLTGVTSTPGTGQSMFSPANIGQP*

Parental  KTTLSPAQLDPFYTQGDSLTSEDHLDDSWVTVFGFPQASASYILLQFAQYGNILKHVMSNTGNWMHIRYQ
          K.TLSP.QLDPFYTQGDSLTSEDHLDD.WVTVFGF.QASASYILLQFAQYGNILKHVMSNTGN.M.I.YQ
Retrocopy KMTLSPSQLDPFYTQGDSLTSEDHLDDTWVTVFGFSQASASYILLQFAQYGNILKHVMSNTGN*MYIHYQ

Parental  SKLQARKALSKDGRIFGESIMIGV
          SKLQARKAL.KDGRIF.E.IMIGV
Retrocopy SKLQARKALTKDGRIFREFIMIGV

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	4.31 RPM
SRP007412_cerebellum	0.00 RPM	4.62 RPM
SRP007412_heart	0.00 RPM	3.13 RPM
SRP007412_kidney	0.00 RPM	3.81 RPM
SRP007412_liver	0.00 RPM	3.98 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_508 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_508 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_508 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_551
Pan troglodytes	retro_ptro_414
Macaca mulatta	retro_mmul_2387

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Erinaceus europaeus	ENSEEUG00000008469	1 retrocopy	retro_eeur_666,
Homo sapiens	ENSG00000163002	1 retrocopy	retro_hsap_551,
Gorilla gorilla	ENSGGOG00000009919	1 retrocopy	retro_ggor_500,
Macaca mulatta	ENSMMUG00000004140	1 retrocopy	retro_mmul_2387,
Nomascus leucogenys	ENSNLEG00000006423	1 retrocopy	retro_nleu_2019,
Pongo abelii	ENSPPYG00000012998	1 retrocopy	retro_pabe_508 ,
Pan troglodytes	ENSPTRG00000012711	1 retrocopy	retro_ptro_414,
Ictidomys tridecemlineatus	ENSSTOG00000000711	2 retrocopies	retro_itri_755, retro_itri_760,