RetrogeneDB ID: retro_pabe_3596

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: Un:45166942..45167764(-)
• 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_3596
AAGAGTCCAGAAAACCTTCCAAACAGTGATCTTTTGTTTTCCTGTATTTTCACCACTGTGGTTGCAATTTGGCTTCCTGA
AAGTACATTACGATGCTTCCTGATGTCCTCAGGAATTCTCAAATCCCTCTTTTAAACTTTAAGACATATGGACCAGCTGG
CCATAGAAGGATCATTATAAAAGAATATGCAATAATAGAATTTCACCCACATAGTATATTCAAGATCTGTGACTGGATAA
AGTGTTTTCTGAGCTGAGAGAATATTTCAGTCTTATATTTTGGATCATATGTTAAAAAAAACTATAGCCATACCCCAAGG
ATTGTGATCATAGATAAATATTTAGCACAGTAGAGTAGTAAAACAAATGGGTGAATATCTAAAATGTATGAAGAAAAAGA
GCACTTAAGAGATTTGATTATACAAAAGATTCTAAATAATACAAATAGGACTTCAGAAGATGAAAAGAATTCTGAAGAAA
CTATTAAAATATGAACATGGCAATAAATACTACTTAGATACCAAACAATATTTAAGATATATTTAATAATAATTTCTGAA
TAAATATCAGCAAACAGACTTCATCCTTTGGGGGTTTTAGCTTATGCCTCAAAGGAATTTGTGGCCAAGGAAGGTCATGG
AAATTTACCTATTCAAGCACAATTTCTGACACAATTGCCGACTTGAAAAATATATAAATACGCAAAGTATTTACTGTGTG
AAAGCAAATGAATATGTTCTCCTGTGAATAAATCATGCCAACAAAATGCTGCAGTCCATAGACAGGCGACATGACACTGC
AAAGAAAGAATAAATTACTCTG

Alignment

ORF - retro_pabe_3596 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 55.63 %
• Parental protein coverage: 61.61 %
• Number of stop codons detected: 8
• Number of frameshifts detected: 8

Retrocopy - Parental Gene Alignment:

Parental  ESPENLLDNDPSFFCRFTVVVATQLPESTL-LRLADVLWNSQIPLLICRTYGLVGYMRIIIKEHPVIESH
          .SPENL...D..F.C.FT.VVA..LPESTL...L.DVL.NSQIPLL...TYG..G..RIIIKE...IE.H
Retrocopy KSPENLPNSDLLFSCIFTTVVAIWLPESTL<TMLPDVLRNSQIPLLNFKTYGPAGHRRIIIKEYAIIEFH

Parental  PDNA-LEDLRLDKPFPELREHF-QSYDLDHMEKKD-HSHTPWIVIIAKYLAQWHSETNGRIPKTYKEKED
          P......DL.LDK.F.ELRE.F.QSY.LDHM......SHTP.IVII.KYLAQ..S.TNG.I.K.Y.EKE.
Retrocopy PHSI<IQDL*LDKVFSELREYF<QSYILDHMXXXX<YSHTPRIVIIDKYLAQ*SSKTNG*ISKMYEEKEH

Parental  FRDLIRQGILKNENGAPEDEENFEEAIK-NVNTALNTTQIPSSIEDIFNDDRCINITKQTPSF-WILARA
          .RDLI.Q.IL.N.N...EDE.N.EE.IK.N.N.A.NTT.IP..I.DIFN....INI.KQT.SF...LA.A
Retrocopy LRDLIIQKILNNTNRTSEDEKNSEETIK<NMNMAINTT*IPNNI*DIFNNNF*INISKQTSSF>GVLAYA

Parental  LKEFVAKEGQGNLPVR-GTIPDMIAD-SGKYVKLQNVYREKAKKDAAAVGNHVAKLLQSIGQAPESISEK
          .KEFVAKEG.GNLP....TI.D.IAD...KY...Q..Y..KA........NH..K.LQSI..........
Retrocopy SKEFVAKEGHGNLPIQ<STISDTIAD<LEKYINTQSIYCVKANEYVLL*INHANKMLQSIDRRHDTAKKE

Parental  ELKL
          ...L
Retrocopy *ITL

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_3596 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3596 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3596 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,