RetrogeneDB ID: retro_pabe_2894

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 6:102083431..102084127(+)
• Located in intron of: ENSPPYG00000016869

Retrocopy information

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

Parental gene information

• Parental gene symbol: DCUN1D2
• Ensembl ID: ENSPPYG00000005527
• Aliases: None
• Description: DCN1, defective in cullin neddylation 1, domain containing 2 [Source:HGNC Symbol;Acc:20328]

Sequence

>retro_pabe_2894
AAAAAAACCGCAGTAAGTTGTCTATCTTAAAATGACTGGAAGTTAGATGTTGCAACAGATAATTTTTTCAAAAACCTGAA
CTTTACGTACGAGCGAGTGTAAAAGGATCACTGGAAAGGAAGAAGTTAGAACAACTGTACAATAGAGACAAAGATCCTCA
AAATGAGAATAAAATTGGAATAGATGGTATATAGCAGTTCTGCGATGGCCTGGCACTCAATCCAGCCAGCATTAGTGAGT
TGATTATTGCATGGATGTTCAGAGCAGCTAACACAGTGCGAGTTCTCCAAACAGGAGTTCATGAATGGCATGACAGAATT
AGGATGTGACAGCATAGAAAAACTAAAGGCCCAGATACCCAAGATGGAACAACAATTGAAAGAACCAGGACAATTCAAGG
ATTTTTACCAGTTTACTTTTAATTTTGCAAAGAATCTAAGACAAAAAGGATTAGATCTAGAAATGGCCATTGCCTACTGG
AACTTAGTGCTTAATAGAAGATTTAAATTCTTAGACTTATGGAATAAATTTTTGTTGGAACATCACAAACAATCAATACC
AAAAGACACTTGGAATCTTCTTTTAGACTTCAGTAGGGTGATTGCAGATCACGTGTCTAATTATGATGAAGGAGCATGGC
CTGTTCTTATTGATGACTTTGTGGAATTTGCATGCCCTCACACTGCTGGGACAAAA

Alignment

ORF - retro_pabe_2894 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.36 %
• Parental protein coverage: 95.49 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  ERTAIYCLTQNEWRLDEATDSFFQN-PDSFHRESMRNAVDKKKLERLYGRYKDPQDENKIGIDGIQQFCD
          ..TA..CL..N.W.LD.ATD.FF.N.P....R.S.......KKLE.LY.R.KDPQ.ENKIGIDGI.QFCD
Retrocopy KKTAVSCLS*NDWKLDVATDNFFKN<PELYVRASVKGSLERKKLEQLYNRDKDPQNENKIGIDGI*QFCD

Parental  DLSLDPASISVLVIAWKFRAA-TQCEFSRKEFLDGMTELGCDSMEKLKALLPRLEQELKDTAKFKDFYQF
          .L.L.PASIS.L.IAW.FRAA.TQCEFS..EF..GMTELGCDS.EKLKA..P..EQ.LK....FKDFYQF
Retrocopy GLALNPASISELIIAWMFRAA>TQCEFSKQEFMNGMTELGCDSIEKLKAQIPKMEQQLKEPGQFKDFYQF

Parental  TFTFAKNPGQKGLDLEMAVAYWKLVLSGRFKFLDLWNTFLLEHHKRSIPRDTWNLLLDFGNMIADDMSNY
          TF.FAKN..QKGLDLEMA.AYW.LVL..RFKFLDLWN.FLLEHHK.SIP.DTWNLLLDF...IAD..SNY
Retrocopy TFNFAKNLRQKGLDLEMAIAYWNLVLNRRFKFLDLWNKFLLEHHKQSIPKDTWNLLLDFSRVIADHVSNY

Parental  DEEGAWPVLIDDFVEYARPVVTGGK
          D.EGAWPVLIDDFVE.A.P...G.K
Retrocopy D-EGAWPVLIDDFVEFACPHTAGTK

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	0.83 RPM	13.49 RPM
SRP007412_cerebellum	0.97 RPM	23.59 RPM
SRP007412_heart	0.36 RPM	27.91 RPM
SRP007412_kidney	0.33 RPM	6.63 RPM
SRP007412_liver	0.34 RPM	2.78 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2894 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2894 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2894 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3502
Pan troglodytes	retro_ptro_2374
Gorilla gorilla	retro_ggor_2368
Macaca mulatta	retro_mmul_1782

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000007821	4 retrocopies	retro_chof_1022, retro_chof_1937, retro_chof_461, retro_chof_771,
Mus musculus	ENSMUSG00000038506	1 retrocopy	retro_mmus_2204,
Pongo abelii	ENSPPYG00000005527	1 retrocopy	retro_pabe_2894 ,