RetrogeneDB ID: retro_pabe_2753

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 5:79138053..79138669(-)
• Located in intron of: ENSPPYG00000015584

Retrocopy information

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

Parental gene information

• Parental gene symbol: IMPACT
• Ensembl ID: ENSPPYG00000009071
• Aliases: None
• Description: impact RWD domain protein [Source:HGNC Symbol;Acc:20387]

Sequence

>retro_pabe_2753
CAGAATATTGGTGAAAGTATTCTTTGCCTGTGAGAGGAGAAAATAAGAGATGTTCCAATACAAAAACCTCAGATGACAGA
ACCAGGCCCAGATGTAAAGAAAGAAACTGAAGAGGAAGATGTTGAATGTGAAGATGATCTCATTTTTGCATGTCAGCCAG
AAAGTTCGGTGGAAGCACTGGATTTTGATATCAGTGAAAATCAAAGAGAAATAGAATGATCTCCAATTGATCATGGCATT
TCTGTTACAGACCAAATAAGTACTTTTCGGGCAGACTTTGATCCAGTAGTTTGTCCCAAACAGGTGAAAATGGTTCTTTC
CAACTTGTATGAGAATAAGAAAATAGCTAGTACCACCCACAGCATCTGTGCCTACAGAGTATGTTGTGAGAATAAACAGA
CCTTCTTACAGGATTGTGAGGATGATGGGGAAAGAGCAGCTGGTGGGCATCTTCTTCATCTCATGGAGATTTTAAATGTG
AGGAATATCATGGTGGTGGTATCACGCTGGTATGGAGAGATTCTGTAGGACCAGATCACTTTAAACATAACTGTGCCAGA
AACATACTAGTGGAGAAGAACAACACACATTCACCTGAAAATCATCTAAGGCTTTG

Alignment

ORF - retro_pabe_2753 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.93 %
• Parental protein coverage: 65.94 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  QNIGESILYLWVEKIRDVLIQKSQMTEPGPDVKKKTEEEDVECEDDLILACQPESLVKALDFDISETRTE
          QNIGESIL.L..EKIRDV.IQK.QMTEPGPDVKK.TEEEDVECEDDLI.ACQPES.V.ALDFDISE...E
Retrocopy QNIGESILCL*EEKIRDVPIQKPQMTEPGPDVKKETEEEDVECEDDLIFACQPESSVEALDFDISENQRE

Parental  VEVEELPPIDHGIPITDRRSTFQAHLAPVVCPKQVKMVLSKLYENKKIASATHNIYAYRIYCEDKQTFLQ
          ....E..PIDHGI..TD..STF.A...PVVCPKQVKMVLS.LYENKKIAS.TH.I.AYR..CE.KQTFLQ
Retrocopy I---E*SPIDHGISVTDQISTFRADFDPVVCPKQVKMVLSNLYENKKIASTTHSICAYRVCCENKQTFLQ

Parental  DCEDDGETAAGGRLLHLMEILNVKNVMVVVSRWYGGIL-LGPDRFKHINNCARNILVEKNYTNSPE-ESS
          DCEDDGE.AAGG.LLHLMEILNV.N.MVVVSRWYG.IL..GPD.FKH..NCARNILVEKN.T.SPE..SS
Retrocopy DCEDDGERAAGGHLLHLMEILNVRNIMVVVSRWYGEIL<VGPDHFKH--NCARNILVEKNNTHSPE<KSS

Parental  KAL
          KAL
Retrocopy KAL

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	0.06 RPM	18.91 RPM
SRP007412_cerebellum	0.00 RPM	15.08 RPM
SRP007412_heart	0.03 RPM	9.18 RPM
SRP007412_kidney	0.73 RPM	13.52 RPM
SRP007412_liver	2.23 RPM	6.49 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2753 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2753 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2753 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3341
Pan troglodytes	retro_ptro_2141

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000013068	1 retrocopy	retro_chof_2523,
Erinaceus europaeus	ENSEEUG00000003962	1 retrocopy	retro_eeur_409,
Homo sapiens	ENSG00000154059	1 retrocopy	retro_hsap_3341,
Macaca mulatta	ENSMMUG00000004664	1 retrocopy	retro_mmul_1041,
Nomascus leucogenys	ENSNLEG00000006582	1 retrocopy	retro_nleu_1166,
Pongo abelii	ENSPPYG00000009071	1 retrocopy	retro_pabe_2753 ,
Pan troglodytes	ENSPTRG00000009927	1 retrocopy	retro_ptro_2141,
Sorex araneus	ENSSARG00000002836	1 retrocopy	retro_sara_719,