RetrogeneDB ID: retro_pabe_3793

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: X:91895164..91897158(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: AP2B1
• Ensembl ID: ENSPPYG00000008188
• Aliases: None
• Description: AP-2 complex subunit beta [Source:RefSeq peptide;Acc:NP_001126334]

Sequence

>retro_pabe_3793
ATGACTGACTCCAAGTATTTCACAACCAATAAAAAAGCAGAAATATTTGAACTAAAAGCTGAACTCAACAATGAAAAGAA
ATAAAAGAGAAAGGAGGCTGTGAAGAAAGTGACTGCTGTTATGACCATGGGGAAGGATGCTAGTTCTGTCTTTCCAGACA
TAGTGAACTGTATGCAGACTGACAATCTGAAACTAAAGAAGCTTGTGTGTCTCTACTTGATGAACTATGCCAAGAGTCAG
CCAGACATGGCCATCATAGATGTAAATAGCTTTGTGAAGGACTGTGAAGGTCCTAATCCTTTGATTCGAGCCTTGGCAGT
CAGAACCATGGGGTGCATCTGGGTAGACAAAATTACAGAATATCTCTGTGAGCCCCTCCTCAAGTGCTTGGAGGATGAGG
ATGCCTATGTTCGGAAAACAGCAGCAGTATGCGTGGCAAAACTCCATGATATCAACGCCCAAATGGTGGAAGATCAGGGA
TTTTTGGATTCTCTACGGGGTCTCATAGCAGATTCAAATCCAGTGGTGGTGGCTAATGCTGTAGCAGCATTATCTGAAAT
CAGTGAGTCTCACCCAAACAGCGACTTACTCAATCTGAACACACAGAACATTAATAAGCTGCGGACAGCCCTGAAGAAGT
GCACTGAAGGGGCCAGATTTTCATCCTGGACTGCCTGTCTAATTATAACCCTAAAGATGATCGGAAGGCTCAGAGCATCT
GTGAGCGGGTAACTCCCCAGCTATCCCATGCCAACTCAGCAGTGGTGCTTTCAGCGGTAAAAGTCCTAATGAAGTTTCTA
GAATTGTTACCTAAGGATTCTGACTACTACAATATGCTGCTGAAGAATTTAGCCCCTCCACTTGTCACTTTGATGTCTGG
GGAGTCCGAAGTGCAGTGTGTCTCCCTGAGGAACATCAACTGAATTGTCCAGAAAAGTCCTGAAATCTTGAAGCAGGAAA
TCAAAGTCTTCTTTGTGAAGTACAATGATCCCATCTATGTTAAACTAGAGAAGTTGGACATCAGGTTTCATTTGGCATCA
CAAGCCAACATTGCTCAGGTTCTGGCAGAACTGAAGGAATATGCCACAGAGGTGAATGTTGACTTTGTTCGAAAAGCAGT
GTGGGCCATTGGACGGTGTGCCATCAAGGTGGAGCAATCTGCAGAGCACTGTGTAAGCACATTGCTTGATCTAATCAAGA
CCAAAGTGAATTATGTGGTCCAAGAAGTGATTGTTGTCATCAGGGACATCTCCCGCAAATACTCCAACAAGTATGAAAGT
AACATTGCCACTCTATGTGAGAACTTAGACTCGCTGGATGAGCCAGATGCTTGAGTGGCTATGATTTGGATTGTGGGAGA
ATATGCTGAAAGAATTGACAATGCAGATGAGTTACTAGAAAGCTTCCTGGAGGGTTTTCAGGATGAAAGCACCCAGGTGC
AACTCACTCTGCTTACTGCCATAATGAAGCTGTTTCTCAAGAAACCACCAGACACACAGGAGCTAGTCCATCAGATGTTG
ACTTTGGCAACACAGGATTCTGATAATCCTGACCTTCGAGAATAGGGCTATACTTATTGGGCTCTTCTCTCAACTGACCC
TGTCACGGCTAAAGAAGTAGTCTTGTCTGAGAAGCCACTGATCTCTCAGGAGACGGAACTTATTGAGCCAACTGCGTTGG
AGGAGCTAATCTGCCACATTGGTTCTTTGGCCTCTGTGTATCATAAGTCTTCCAATGCTTTTGTGGAAGGACGTCATGGA
ATCCATCGTAAACACTTGCCAATTCATCATGGGAGCACTAATGCAGGTGACAGCCCTGTTGGCACCACCACCGCAATGAA
CCTGGAACAGCCTCAGGTTATCCCCTCTCAAGGTGATCTTCTGGGGAGTCTTTTAAACCTTGACCTCAGTTTCCCAGTCA
ATGTGCCACAGGTGTCCTCCCTGCAGATGGGAGCAGTGGATCTCTTAGGAGGAGGACTAGATAGTCTGGTGGGA

Alignment

ORF - retro_pabe_3793 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.74 %
• Parental protein coverage: 69.93 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MTDSKYFTTNKKGEIFELKAELNNEKKEKRKEAVKKVIAAMTVGKDVSSLFPDVVNCMQTDNLELKKLVY
          MTDSKYFTTNKK.EIFELKAELNNEKK.KRKEAVKKV.A.MT.GKD.SS.FPD.VNCMQTDNL.LKKLV.
Retrocopy MTDSKYFTTNKKAEIFELKAELNNEKK*KRKEAVKKVTAVMTMGKDASSVFPDIVNCMQTDNLKLKKLVC

Parental  LYLMNYAKSQPDMAIMAVNSFVKDCEDPNPLIRALAVRTMGCIRVDKITEYLCEPLRKCLKDEDPYVRKT
          LYLMNYAKSQPDMAI..VNSFVKDCE.PNPLIRALAVRTMGCI.VDKITEYLCEPL.KCL.DED.YVRKT
Retrocopy LYLMNYAKSQPDMAIIDVNSFVKDCEGPNPLIRALAVRTMGCIWVDKITEYLCEPLLKCLEDEDAYVRKT

Parental  AAVCVAKLHDINAQMVEDQGFLDSLRDLIADSNPMVVANAVAALSEISESHPNSNLLDLNPQNINKLLTA
          AAVCVAKLHDINAQMVEDQGFLDSLR.LIADSNP.VVANAVAALSEISESHPNS.LL.LN.QNINKL.TA
Retrocopy AAVCVAKLHDINAQMVEDQGFLDSLRGLIADSNPVVVANAVAALSEISESHPNSDLLNLNTQNINKLRTA

Parental  LNECTEW-GQIFILDCLSNYNPKDDREAQSICERVTPRLSHANSAVVLSAVKVLMKFLELLPKDSDYYNM
          L..CTE..GQIFILDCLSNYNPKDDR.AQSICERVTP.LSHANSAVVLSAVKVLMKFLELLPKDSDYYNM
Retrocopy LKKCTEG<GQIFILDCLSNYNPKDDRKAQSICERVTPQLSHANSAVVLSAVKVLMKFLELLPKDSDYYNM

Parental  LLKKLAPPLVTLLSGEPEVQYVALRNINLIVQKRPEILKQEIKVFFVKYNDPIYVKLEKLDIMIRLASQA
          LLK.LAPPLVTL.SGE.EVQ.V.LRNIN.IVQK.PEILKQEIKVFFVKYNDPIYVKLEKLDI...LASQA
Retrocopy LLKNLAPPLVTLMSGESEVQCVSLRNIN*IVQKSPEILKQEIKVFFVKYNDPIYVKLEKLDIRFHLASQA

Parental  NIAQVLAELKEYATEVDVDFVRKAVRAIGRCAIKVEQSAERCVSTLLDLIQTKVNYVVQEAIVVIRDIFR
          NIAQVLAELKEYATEV.VDFVRKAV.AIGRCAIKVEQSAE.CVSTLLDLI.TKVNYVVQE.IVVIRDI.R
Retrocopy NIAQVLAELKEYATEVNVDFVRKAVWAIGRCAIKVEQSAEHCVSTLLDLIKTKVNYVVQEVIVVIRDISR

Parental  KYPNKYESIIATLCENLDSLDEPDARAAMIWIVGEYAERIDNADELLESFLEGFHDESTQVQLTLLTAIV
          KY.NKYES.IATLCENLDSLDEPDA..AMIWIVGEYAERIDNADELLESFLEGF.DESTQVQLTLLTAI.
Retrocopy KYSNKYESNIATLCENLDSLDEPDA*VAMIWIVGEYAERIDNADELLESFLEGFQDESTQVQLTLLTAIM

Parental  KLFLKKPSETQELVQQVLSLATQDSDNPDLRDRGYIYWRLLSTDPVTAKEVVLSEKPLISEETDLIEPTL
          KLFLKKP..TQELV.Q.L.LATQDSDNPDLR..GY.YW.LLSTDPVTAKEVVLSEKPLIS.ET.LIEPT.
Retrocopy KLFLKKPPDTQELVHQMLTLATQDSDNPDLRE*GYTYWALLSTDPVTAKEVVLSEKPLISQETELIEPTA

Parental  LDELICHIGSLASVYHKPPNAFVEGSHGIHRKHLPIHHGSIDAGDSPVGTTTATNLEQPQVIPSQGDLLG
          L.ELICHIGSLASVYHK..NAFVEG.HGIHRKHLPIHHGS..AGDSPVGTTTA.NLEQPQVIPSQGDLLG
Retrocopy LEELICHIGSLASVYHKSSNAFVEGRHGIHRKHLPIHHGSTNAGDSPVGTTTAMNLEQPQVIPSQGDLLG

Parental  DLLNLDLGPPVNVPQVSSMQMGAVDLLGGGLDSLLG
          .LLNLDL..PVNVPQVSS.QMGAVDLLGGGLDSL.G
Retrocopy SLLNLDLSFPVNVPQVSSLQMGAVDLLGGGLDSLVG

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	2.99 RPM	406.39 RPM
SRP007412_cerebellum	2.19 RPM	255.00 RPM
SRP007412_heart	0.90 RPM	53.70 RPM
SRP007412_kidney	0.89 RPM	133.91 RPM
SRP007412_liver	0.58 RPM	62.67 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3793 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3793 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3793 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000014853	1 retrocopy	retro_cjac_1850,
Loxodonta africana	ENSLAFG00000015777	1 retrocopy	retro_lafr_446,
Myotis lucifugus	ENSMLUG00000002837	1 retrocopy	retro_mluc_2443,
Mus musculus	ENSMUSG00000035152	1 retrocopy	retro_mmus_2503,
Nomascus leucogenys	ENSNLEG00000013939	2 retrocopies	retro_nleu_1925, retro_nleu_2554,
Pongo abelii	ENSPPYG00000008188	1 retrocopy	retro_pabe_3793 ,
Pan troglodytes	ENSPTRG00000009021	1 retrocopy	retro_ptro_3248,
Rattus norvegicus	ENSRNOG00000009988	2 retrocopies	retro_rnor_1267, retro_rnor_574,