RetrogeneDB ID: retro_nleu_2554

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397371.1:1107424..1109415(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: AP2B1
• Ensembl ID: ENSNLEG00000013939
• Aliases: None
• Description: None

Sequence

>retro_nleu_2554
ATGACTGACTCCAAGTATTTTGCAACCAATAAAAAAGCAGAAATATTTGAACTAAAAGCTGAACTCAACAATGAAAAGAA
AGAAAAGAGAAAGGAGGCTGTGAAGAAAGTGATTGCTGTTATGACCGTGGGGAAGGATGTTAGTGCTGTCTTTCCAGACA
TAGTGAACTGTACGCAGACTGACAATCTGAAACTAACGAAGCTTGTGTATCTCTACTTGATGAACTATGCCAAGAGTCAG
CCAGACATGGCCATCATAGCTGTAAATAGCTTTGTGAAGGACTGTGAAGATGCTAATCATTTGATTCGAGCCTTGGCAGT
CAGAACCACGGGGTGCATCTGGGTAGACAAAATTACAGAATATCTCTGTGAGCCCCTCCTCAAGTGCTTGGAGGATGAGG
ATCCCTATGTTCGGAAAACAGCAGCAGTATGCGTGGCAAAACTCCATGATATCAACGCCCAAATGGTGGACGATCAGGGA
TTTTTGGATTCTCTACGGGGTCTCATAGCAGATTCAAATCCAATGGTGGTGGCTAATGCTGTAGCAGCATTATCTGAAAT
CAGGGAGTCTCACCCAAACAGCAATTTACACAATCTGAACACACAGAACATTAATAAGCTGCTGACAGCCCTGAATAAGT
GCACTGAAGGGGCCAGATTTTCATCCTGGACTGCCTGTCTAATTACAACCCTAAAGATGATCGGAAGGCTCAGAGAATCT
GTGAGCAGGTAACTCCCCAGCTATCCCATGCCAACTCAGCAGTGGTGCTTTCAGCGGTAAAAGTCCTAATGAAGTTTCTA
GAATTGTTACCTAAGGATTCTGACTACTACAATATGCTGCTGAAGAAGTTAGCCCCTCCACTTGTCACTTTGATGTCTGG
GGAGTCAGAAGCGCAGTATGTCTCCCTGAGGAACATCAACTTGATTGTCCAGTAAAGGCCTGAAATCTTGAAGCAGGAAA
TCGAAGTCTTCTTTGTGAAGTACAATGATCCCATCTACGTTAAACTAGAGAAGTTGGACATCAGGATTCTTTTGGCATCA
CAAGCCAACATTGCTCAGGTTCTGGCAGAACTGAAGGAATATGCCACAGAGGTGAGTGTTGACTTTGTTCGAAAAGCTGT
GCGGGCCATTGGACGGTGTGCCATCAAGGTGGAGCAATCTGCAGAGCACTGTGTAAGCACAATGCTTGATCTAATCAAGA
CCAAAGTGAATTATGTGGTCCAAGAAGTGATTGTTGTCATCAGGGACATCTTCCACAAATACTCCAACAAGTATGAAGAT
ATCATTGCCACTCTATGTGAGAACTTAGACTCGCTGGATGAGCCAGATGCTCGAGCGGCTATGATTTGGATTGTGGGAGA
ATATGCTGAAAGAATTGACAATGCAGATGAGTTACTAGAAAGCTTCCTGGAGGGTTTTCATGATGAAAGCACCCAGGTGC
AGCTCACTCTGCTTACTGCCGTAATGAAGCTGTTTCTCAAGAAACCACCAGAAACACAGGAGCTAGTCCAGCAGATGTTG
ACTTTGCCAACACAGGATTCTGATAATCCTGACCTTCGAGAACTGGGCTATACTTACTGGATTCTTCTCTCAACTGACCC
TCTCACGGCTAAAGAAGTAGTCTTGTCTGAGAAGCCACTGATCTCTGAGGAGACGGAACCTATTGAGCCAACTGTGTTGG
AGGAGCTAATCTGCCACATTGGTTCTTTGGCCTCTGTGTATCATAAGCCTTCCAAGGCTTTTGTGGAAGGAAGTCATGGA
ATCCATCATAAACACTTGCCAATTCATCATGGGAGCACTGATGCAGGTGACAGCCCTGTTGGCACCACCACTGCAACAAA
CCTGGAACAGCCTCAGGTTATCCACTCTCAAGGTCTTCTGGGGAGTCTTTTAAACCTTGACCTCAGTCTCCCAGTCAATG
TGCCACAGGTGTCCTCCATGCAGATGGGAGCAGTGGATCTCCTAGGAGGAGGACTAGATAGTCTGGTGGGA

Alignment

ORF - retro_nleu_2554 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.64 %
• Parental protein coverage: 69.93 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MTDSKYFTTNKKGEIFELKAELNNEKKEKRKEAVKKVIAAMTVGKDVSSLFPDVVNCMQTDNLELKKLVY
          MTDSKYF.TNKK.EIFELKAELNNEKKEKRKEAVKKVIA.MTVGKDVS..FPD.VNC.QTDNL.L.KLVY
Retrocopy MTDSKYFATNKKAEIFELKAELNNEKKEKRKEAVKKVIAVMTVGKDVSAVFPDIVNCTQTDNLKLTKLVY

Parental  LYLMNYAKSQPDMAIMAVNSFVKDCEDPNPLIRALAVRTMGCIRVDKITEYLCEPLRKCLKDEDPYVRKT
          LYLMNYAKSQPDMAI.AVNSFVKDCED.N.LIRALAVRT.GCI.VDKITEYLCEPL.KCL.DEDPYVRKT
Retrocopy LYLMNYAKSQPDMAIIAVNSFVKDCEDANHLIRALAVRTTGCIWVDKITEYLCEPLLKCLEDEDPYVRKT

Parental  AAVCVAKLHDINAQMVEDQGFLDSLRDLIADSNPMVVANAVAALSEISESHPNSNLLDLNPQNINKLLTA
          AAVCVAKLHDINAQMV.DQGFLDSLR.LIADSNPMVVANAVAALSEI.ESHPNSNL..LN.QNINKLLTA
Retrocopy AAVCVAKLHDINAQMVDDQGFLDSLRGLIADSNPMVVANAVAALSEIRESHPNSNLHNLNTQNINKLLTA

Parental  LNECTEW-GQIFILDCLSNYNPKDDREAQSICERVTPRLSHANSAVVLSAVKVLMKFLELLPKDSDYYNM
          LN.CTE..GQIFILDCLSNYNPKDDR.AQ.ICE.VTP.LSHANSAVVLSAVKVLMKFLELLPKDSDYYNM
Retrocopy LNKCTEG<GQIFILDCLSNYNPKDDRKAQRICEQVTPQLSHANSAVVLSAVKVLMKFLELLPKDSDYYNM

Parental  LLKKLAPPLVTLLSGEPEVQYVALRNINLIVQKRPEILKQEIKVFFVKYNDPIYVKLEKLDIMIRLASQA
          LLKKLAPPLVTL.SGE.E.QYV.LRNINLIVQ.RPEILKQEI.VFFVKYNDPIYVKLEKLDI.I.LASQA
Retrocopy LLKKLAPPLVTLMSGESEAQYVSLRNINLIVQ*RPEILKQEIEVFFVKYNDPIYVKLEKLDIRILLASQA

Parental  NIAQVLAELKEYATEVDVDFVRKAVRAIGRCAIKVEQSAERCVSTLLDLIQTKVNYVVQEAIVVIRDIFR
          NIAQVLAELKEYATEV.VDFVRKAVRAIGRCAIKVEQSAE.CVST.LDLI.TKVNYVVQE.IVVIRDIF.
Retrocopy NIAQVLAELKEYATEVSVDFVRKAVRAIGRCAIKVEQSAEHCVSTMLDLIKTKVNYVVQEVIVVIRDIFH

Parental  KYPNKYESIIATLCENLDSLDEPDARAAMIWIVGEYAERIDNADELLESFLEGFHDESTQVQLTLLTAIV
          KY.NKYE.IIATLCENLDSLDEPDARAAMIWIVGEYAERIDNADELLESFLEGFHDESTQVQLTLLTA..
Retrocopy KYSNKYEDIIATLCENLDSLDEPDARAAMIWIVGEYAERIDNADELLESFLEGFHDESTQVQLTLLTAVM

Parental  KLFLKKPSETQELVQQVLSLATQDSDNPDLRDRGYIYWRLLSTDPVTAKEVVLSEKPLISEETDLIEPTL
          KLFLKKP.ETQELVQQ.L.L.TQDSDNPDLR..GY.YW.LLSTDP.TAKEVVLSEKPLISEET..IEPT.
Retrocopy KLFLKKPPETQELVQQMLTLPTQDSDNPDLRELGYTYWILLSTDPLTAKEVVLSEKPLISEETEPIEPTV

Parental  LDELICHIGSLASVYHKPPNAFVEGSHGIHRKHLPIHHGSTDAGDSPVGTTTATNLEQPQVIPSQGDLLG
          L.ELICHIGSLASVYHKP..AFVEGSHGIH.KHLPIHHGSTDAGDSPVGTTTATNLEQPQVI.SQG.LLG
Retrocopy LEELICHIGSLASVYHKPSKAFVEGSHGIHHKHLPIHHGSTDAGDSPVGTTTATNLEQPQVIHSQG-LLG

Parental  DLLNLDLGPPVNVPQVSSMQMGAVDLLGGGLDSLLG
          .LLNLDL..PVNVPQVSSMQMGAVDLLGGGLDSL.G
Retrocopy SLLNLDLSLPVNVPQVSSMQMGAVDLLGGGLDSLVG

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Nomascus leucogenys was not studied using RNA-Seq expression data.

ChIP-Seq

Nomascus leucogenys was not studied using ChIP-Seq data.

EST

Nomascus leucogenys was not studied using EST data.

TSS

Nomascus leucogenys was not studied using FANTOM5 data.

Lab

retro_nleu_2554 was not experimentally validated.

Homology

Retrocopy orthology:

Nomascus leucogenys does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000020316	1 retrocopy	retro_btau_1675,
Choloepus hoffmanni	ENSCHOG00000010864	1 retrocopy	retro_chof_2310,
Callithrix jacchus	ENSCJAG00000014853	1 retrocopy	retro_cjac_1850,
Gorilla gorilla	ENSGGOG00000015593	1 retrocopy	retro_ggor_3044,
Loxodonta africana	ENSLAFG00000015777	1 retrocopy	retro_lafr_446,
Myotis lucifugus	ENSMLUG00000002837	1 retrocopy	retro_mluc_2443,
Mustela putorius furo	ENSMPUG00000014910	1 retrocopy	retro_mputfur_704,
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,