RetrogeneDB ID: retro_ptro_3248

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: X:93264217..93266207(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: AP2B1
• Ensembl ID: ENSPTRG00000009021
• Aliases: None
• Description: None

Sequence

>retro_ptro_3248
ATGACTGACTCCAAGTATTTCACAACCAATAAAAAAGCAGAAATATTTGAACTAAAAGCTGAACTCAACAATGAAAAGAA
AGAAAAGAGAAAGGAGGCTGTGAAGAAAGTGATTGCTGTTATTACCGTGGGGAAGGATGTTAGTTCTGTCTTTCCAGACA
TAGTGAACTGTATGCAGACTGACAATCTGAAACTAAAGAAGCTTGTGTATCTCTACTTGATGAACTATGCCAAGAGTCAG
CCAGACATGGCCATCATAGCTGTAAATAGCTTTGTGAAGGACTGTGAAGATCCTAATCTTTTGATTCGAGCCTTGGCAGT
CAGAACCATGGGGTGCATCTGGGTAGACAAAATTACAGAATATCTCTCTGAGCCCCTCCTCAAGTGCTTAGAGGATGAGG
ATCCCTATGTTCGGAAAACAGCAGCAGTATGCGTGGCAAAACTCCACGATATCAACGCCCAAATGGTGGAAGATCAGGGA
TTTTTGGATTCTCTATGGGGTCTCATAGCAGATTCAAATCCAATGGTGGTGGCTAATGCTGTAGCAGCATTATCTGAAAT
CAGTGAGTCTCACCCAAACAGCAACTTACTCAATCTGAACACACAGAACATTAATAAGCTGCGGACAGCCCTGAATAAGT
GCACTGAAGGGGCCAGATTTTCATGCTGGACTGCCTGTCTAATTACAACCCTAAAAATGATCGGAAGGCTCAGAGCATCT
GTGAGCGGGTAACTCCCCAGCTATCCCATGCCAACTCAGCAGTGGTGCTTTCAGCGGTAAAAGTACTAATGAAGTTTCTA
GAATTGTTATCTAAGGATTCTGACTACTACAATATGCTGCTGAAGAAGTTAGCCCCTCCACTTGTCACTTTGATGTCTGG
GGAGTCAGAAGTGCAGTATGCCTCCCTGAGGAACATCAACTTAATTGTCCAGAAAAGGCCTGAAATCTTGAAGCAGGAAA
TCAAAGTCTTCTTTGTGAAGTACAATGATCCCATCTATATTAAACTAGAGAAGTTGGACATCAGGATTCATTTGGCATCA
CAAGCCAACATTGCTCAGGTTCTGGCAGAACTGAAGGAATATGCCACAGAGGTGAATGTTGACTTTGTTCGAAAAGCTGT
GTGGGCCACTGGACGGTGTGCCATCAAGGTGGAGCAATCTGCAGAGCACTGTGTAAGCACATTGCTTGATCTAATCAAGA
CCAAAGTGAATTATGTGGTCCAAGAAGTGATTGTTGTCAGGGACATCTTCCGCAAATACTCCAACAAGTATGAAAGTATC
ATTGCCACTCTATGTGAGAACTTAGACTTGCTGGATGAGCCAGATGCTCGATCGGCTATGATTTGGATTGTGGGAGAATA
AGCTGAAAGAATTGACAATGCAGATGAGTTACTAGAAAGCTTCCTGGAGGGTTTTCATGATGAAAACACCCAGGTGCAGC
TCACTCTGCTTACTGCCATAATGAAGCTGTTTCTCAAGAAACCACCAAAACACAGGAGCTAGTCCAGCAGATGTTGAATT
TGGCAACACAGGATTCTGATAATCCTGACCTTCGAGAACGGGGCTATACTTATTGGGCTCTTCTCTCAGCTGACCCTGTC
AAGGCTAAAGAAGTAGTCTTGTCTGAGAAGCCACTGATCTCTCAGGAGACGGAACTTATTGAGCCAACTGCGTTGGAGGA
GCTAATCTGCCACATTGGTTCTTTGGCCTCTGTGTATCATAAGCCTTCCAATGCTTTTGTGGAAGGAAGTCATGGAATCC
ATCGTAAACACTTGCCAATTCATCATGGGAGCACTGACGCAGGTGACAGCCCTGTTGGCACCACCACCGCAACGAACCTG
GAACAGCCTCAGGTTATCCCCCCTCAAGGTGATCTTCTGGGGAGTCTTTTAAACCTTGACCTCAGTCTCCCAGTCAATGT
GCCACAGGTGTCCTCCATGCAGATGGGACCAGTGGATCTCCTAGGAGGAGGACTAGATAGTCTGGTGGGA

Alignment

ORF - retro_ptro_3248 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.81 %
• Parental protein coverage: 69.93 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MTDSKYFTTNKKGEIFELKAELNNEKKEKRKEAVKKVIAAMTVGKDVSSLFPDVVNCMQTDNLELKKLVY
          MTDSKYFTTNKK.EIFELKAELNNEKKEKRKEAVKKVIA..TVGKDVSS.FPD.VNCMQTDNL.LKKLVY
Retrocopy MTDSKYFTTNKKAEIFELKAELNNEKKEKRKEAVKKVIAVITVGKDVSSVFPDIVNCMQTDNLKLKKLVY

Parental  LYLMNYAKSQPDMAIMAVNSFVKDCEDPNPLIRALAVRTMGCIRVDKITEYLCEPLRKCLKDEDPYVRKT
          LYLMNYAKSQPDMAI.AVNSFVKDCEDPN.LIRALAVRTMGCI.VDKITEYL.EPL.KCL.DEDPYVRKT
Retrocopy LYLMNYAKSQPDMAIIAVNSFVKDCEDPNLLIRALAVRTMGCIWVDKITEYLSEPLLKCLEDEDPYVRKT

Parental  AAVCVAKLHDINAQMVEDQGFLDSLRDLIADSNPMVVANAVAALSEISESHPNSNLLDLNPQNINKLLTA
          AAVCVAKLHDINAQMVEDQGFLDSL..LIADSNPMVVANAVAALSEISESHPNSNLL.LN.QNINKL.TA
Retrocopy AAVCVAKLHDINAQMVEDQGFLDSLWGLIADSNPMVVANAVAALSEISESHPNSNLLNLNTQNINKLRTA

Parental  LNECTEW-GQIFILDCLSNYNPKDDREAQSICERVTPRLSHANSAVVLSAVKVLMKFLELLPKDSDYYNM
          LN.CTE..GQIF.LDCLSNYNPK.DR.AQSICERVTP.LSHANSAVVLSAVKVLMKFLELL.KDSDYYNM
Retrocopy LNKCTEG<GQIFMLDCLSNYNPKNDRKAQSICERVTPQLSHANSAVVLSAVKVLMKFLELLSKDSDYYNM

Parental  LLKKLAPPLVTLLSGEPEVQYVALRNINLIVQKRPEILKQEIKVFFVKYNDPIYVKLEKLDIMIRLASQA
          LLKKLAPPLVTL.SGE.EVQY..LRNINLIVQKRPEILKQEIKVFFVKYNDPIY.KLEKLDI.I.LASQA
Retrocopy LLKKLAPPLVTLMSGESEVQYASLRNINLIVQKRPEILKQEIKVFFVKYNDPIYIKLEKLDIRIHLASQA

Parental  NIAQVLAELKEYATEVDVDFVRKAVRAIGRCAIKVEQSAERCVSTLLDLIQTKVNYVVQEAIVVIRDIFR
          NIAQVLAELKEYATEV.VDFVRKAV.A.GRCAIKVEQSAE.CVSTLLDLI.TKVNYVVQE...V.RDIFR
Retrocopy NIAQVLAELKEYATEVNVDFVRKAVWATGRCAIKVEQSAEHCVSTLLDLIKTKVNYVVQE-VIVVRDIFR

Parental  KYPNKYESIIATLCENLDSLDEPDARAAMIWIVGEYAERIDNADELLESFLEGFHDESTQVQLTLLTAIV
          KY.NKYESIIATLCENLD.LDEPDAR.AMIWIVGE.AERIDNADELLESFLEGFHDE.TQVQLTLLTAI.
Retrocopy KYSNKYESIIATLCENLDLLDEPDARSAMIWIVGE*AERIDNADELLESFLEGFHDENTQVQLTLLTAIM

Parental  KLFLKKP-SETQELVQQVLSLATQDSDNPDLRDRGYIYWRLLSTDPVTAKEVVLSEKPLISEETDLIEPT
          KLFLKKP...TQELVQQ.L.LATQDSDNPDLR.RGY.YW.LLS.DPV.AKEVVLSEKPLIS.ET.LIEPT
Retrocopy KLFLKKP<TKTQELVQQMLNLATQDSDNPDLRERGYTYWALLSADPVKAKEVVLSEKPLISQETELIEPT

Parental  LLDELICHIGSLASVYHKPPNAFVEGSHGIHRKHLPIHHGSTDAGDSPVGTTTATNLEQPQVIPSQGDLL
          .L.ELICHIGSLASVYHKP.NAFVEGSHGIHRKHLPIHHGSTDAGDSPVGTTTATNLEQPQVIP.QGDLL
Retrocopy ALEELICHIGSLASVYHKPSNAFVEGSHGIHRKHLPIHHGSTDAGDSPVGTTTATNLEQPQVIPPQGDLL

Parental  GDLLNLDLGPPVNVPQVSSMQMGAVDLLGGGLDSLLG
          G.LLNLDL..PVNVPQVSSMQMG.VDLLGGGLDSL.G
Retrocopy GSLLNLDLSLPVNVPQVSSMQMGPVDLLGGGLDSLVG

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	0.25 RPM	302.52 RPM
SRP007412_cerebellum	0.18 RPM	263.88 RPM
SRP007412_heart	0.12 RPM	131.77 RPM
SRP007412_kidney	0.68 RPM	183.77 RPM
SRP007412_liver	0.16 RPM	65.11 RPM
SRP007412_testis	6.22 RPM	860.24 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_3248 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_3248 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_3248 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4875
Macaca mulatta	retro_mmul_2615

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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,