RetrogeneDB ID: retro_pabe_759

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 11:43540704..43541496(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NAE1
• Ensembl ID: ENSPPYG00000007428
• Aliases: None
• Description: NEDD8 activating enzyme E1 subunit 1 [Source:HGNC Symbol;Acc:621]

Sequence

>retro_pabe_759
ATTCAAGATCTGTGACTGGATAAAGTGTTTTCTGAGCTGAGAGAATATTTCAGTCTTATATTTTGGATCATATGTTGAAA
AAAACTATAGCCATACCCCAAGGATTGTGATCATAGATAAATATTTAGCACAGTAGAGTAGTAAAACAAACGGGTGAATA
TCTAAAATGTATGAAGAAAAAGAGCACTTAAGAGATTTGATTATACAAAAGATTCTAAATAATACAAATAGGACTTCAGA
AGATGAAAAGAATTCTGAAGAAACTATTAAAATATGAACATGGCAATAAATACTACTTAGATACCAAACAATATTTAAGA
TATATTTAATAATAATTTCTGAATAAATATCAGCAAACAGACTTCATCCTTTGGGGTTTTAGCTTATGCCTCAAAGGAAT
TTGTGGCCAAGGAAGGTCATGGAAATTTACCTATTCAAGCACAATTTCTGACACAATTGCCGACTTGAAAAAATATATAA
ATACGCAAAGTATTTACTGTGTGAAAGCAAATGAATATGTTTCTCCTGTGAATAAATCATGCCAACAAAATGCTGCAGTC
CATAGACCAGGCGAACAATGACACTGCAAAGAAAGAATTAAAATTACTCTGTAGCAATTCTTCATTTCTTAGAGTCTTAA
GATGTGAATCCTTTACTGAAGAATATGGTTTGGATACAATTAACAAGAATAAAATCTTTTCCAGCATGGGCACTGCAGAT
AATGAAATAGTATTGTACTTAATATTATGGACTATTGATAGATTTTATATGCAACAATATAGATGTCCAGGA

Alignment

ORF - retro_pabe_759 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.11 %
• Parental protein coverage: 59.15 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  LEDLRLDKPFPELREHF-QSYDLDHMEKK-DHSHTPWIVIIAKYLAQWHSETNGRIPKTYKEKEDFRDLI
          ..DL.LDK.F.ELRE.F.QSY.LDHM.KK...SHTP.IVII.KYLAQ..S.TNG.I.K.Y.EKE..RDLI
Retrocopy IQDL*LDKVFSELREYF<QSYILDHMLKK<NYSHTPRIVIIDKYLAQ*SSKTNG*ISKMYEEKEHLRDLI

Parental  RQGILKNENGAPEDEENFEEAIK-NVNTALNTTQIPSSIEDIFNDDRCINITKQTPSFWILARALKEFVA
          .Q.IL.N.N...EDE.N.EE.IK.N.N.A.NTT.IP..I.DIFN....INI.KQT.SF..LA.A.KEFVA
Retrocopy IQKILNNTNRTSEDEKNSEETIK<NMNMAINTT*IPNNI*DIFNNNF*INISKQTSSFGVLAYASKEFVA

Parental  KEGQGNLPVRG-TIPDMIADSGKYVKLQNVYREKAKKDAAAVG-NHVAKLLQSIGQAPESISEKELKLLC
          KEG.GNLP....TI.D.IAD..KY...Q..Y..KA......V..NH..K.LQSI.QA......KELKLLC
Retrocopy KEGHGNLPIQA<TISDTIADLKKYINTQSIYCVKANEYVSPVN>NHANKMLQSIDQANNDTAKKELKLLC

Parental  SNSAFLRVVRCRSLAEEYGLDTINKDEIISSMDNPDNEIVLYLMLRAVDRFHKQHGRYPG
          SNS.FLRV.RC.S..EEYGLDTINK..I.SSM...DNEIVLYL.L...DRF..Q..R.PG
Retrocopy SNSSFLRVLRCESFTEEYGLDTINKNKIFSSMGTADNEIVLYLILWTIDRFYMQQYRCPG

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	8.63 RPM
SRP007412_cerebellum	0.00 RPM	18.60 RPM
SRP007412_heart	0.00 RPM	7.80 RPM
SRP007412_kidney	0.00 RPM	6.03 RPM
SRP007412_liver	0.00 RPM	5.39 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_759 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_759 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_759 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000021954	1 retrocopy	retro_ecab_942,
Nomascus leucogenys	ENSNLEG00000004047	1 retrocopy	retro_nleu_395,
Otolemur garnettii	ENSOGAG00000014645	1 retrocopy	retro_ogar_1443,
Pongo abelii	ENSPPYG00000007428	2 retrocopies	retro_pabe_3596, retro_pabe_759 ,