RetrogeneDB ID: retro_meug_1205

Retrocopy location

• Organism: Wallaby (Macropus eugenii)
• Coordinates: Scaffold32504:5207..6812(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: AP1B1
• Ensembl ID: ENSMEUG00000008438
• Aliases: None
• Description: adaptor-related protein complex 1, beta 1 subunit [Source:HGNC Symbol;Acc:554]

Sequence

>retro_meug_1205
GAGATCTTTGAACTGAAGGCGGAGCTCAGCAACGAAAAGAAGGAGAAAAGGAAAGAAGCTATCAAGAAAGTGATTGCAGT
CATGACAGTGGGGAAGGATGCCAGCTCTCTCTTTCCAGATGTGGTGAATTGTGTGCAAATGGATAACCTGGAGCTAAAGA
AGCTTGTCTATCTATATCTGATGAACTATGCCAAGAGCCAGCCAGATATGGCCATCATGACTGTCAACAACTTTGTGAAG
GACTGTGAAGACCCTAACCCATTAATCTGTGCCCTGGCATTCAGGACTATGGGGTGTATTTGGGTGGACAAGATCACAAA
GTATCTCTGTGAGCCACTTCTCAAATGTCTGAACGATGAAGATCCTTATGTCCAAAAGACGGCAGCAGTCTGTGTGGCCA
AGCTGCACAACATCAATGCCCAGATGGTGGAGGACCAAGGCTCCTTGGATTCTCCTCGGGATCTCATTGCAGACTCAAAT
CCCATGGTGGTTGCTAATGCTGTGGCAGCCTTGTCAGAAATCAGTGAGTCTCACCCAAATAGCAACCTGCTTGACCTGAA
CCCTCAGAATATTAATAAGCTGTTAACAGCCCTAAACAAATGCGCCGAATGGGGTCAGATCTTCATCTTGGACTGCCTGT
CCAATTACAACCCCAAGGATGATCGGGAGGCTCAGAGTATCTGTGAGCAGGTGACTCCCAGGCTCTCACATGCCAGCTCA
GCAGTGGTCCTATCAGCTGTGAAAGTCCTGATGAAGTTCTTAGAGCTGCTGCCCAAGGACTCTGACTACTACAACATGCT
ACTAAGAAGCTGGCTCCTCCCCTGGTAACTCTGCTCCCTGGGGAACCTGAAGTGCAGTACGTCACCCTGAGGAACATCAA
CCTCATTGTACAGAAAAGGCCTGAAATCTTAAAGCAAGAGATCAAAGTCTTCTTTGTGAAGTACAATGACCCCATCTATA
TCAAGTTGGAAAAGCTTGACATCATGATCCATTTGGCATCCCAAGCCAACATTGCCCAGGTCCTGGCAGAACTAAAGGAA
TATGCCACTGAACTGGACGTTGATTTTGTCCATAAAGCTGTGCAAGCTATTGGCCAATGTGCCATCAAGGTTGAGCAATC
TGCCGAGCACTGCGTGAGCACATTGCTGGACCTTATCCAGACCAAAGTCAACTACGTGGTTCAGGAGGCGATTGCTGTCA
TCAAGGACATCCTCCGCAAATATCCCAACAAGTATGAAAGTATCATTGCTACTCTGTATGAGAACCTTGATTCCCTTGAT
GAGCCAGATGCTCAAGCTGCCATGATCTGGATGGTAGGAGAATATGCTGAGAGAATCGATAATGCAGATGAGCTTCTGGA
AAGTTTCCTGGAGGGCTTCCATGATGAGAGCACCCAGGTGCAGCTAACCCTGCTTACAGCAATAGTGAATCTGTTTCTCA
AGAAACCTTCAGAAACTCAGGAACTGGTCCAGCAGGTCTTGAGTTTGGCAACTCAGGATTCTGATATCCTGATCTTCAAG
ACCAGGGTTATATCTACTGGTGCCTTCTTCCACAGATCCTGTGACAGCCAAGGATGTAGTCTTATCCAAACAGCCTTTGA
TCTCT

Alignment

ORF - retro_meug_1205 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.9 %
• Parental protein coverage: 57.33 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  EIFELKAELNSDKKEKKKEAVKKVIASMTVGKDVSALFPDVVNCMQTDNLELKKLVYLYLMNYAKSQPDM
          EIFELKAEL...KKEK.KEA.KKVIA.MTVGKD.S.LFPDVVNC.Q.DNLELKKLVYLYLMNYAKSQPDM
Retrocopy EIFELKAELSNEKKEKRKEAIKKVIAVMTVGKDASSLFPDVVNCVQMDNLELKKLVYLYLMNYAKSQPDM

Parental  AIMAVNTFVKDCEDPNPLIRALAVRTMGCIRVDKITEYLCEPLRKCLKDEDPYVRKTAAVCVAKLHDINA
          AIM.VN.FVKDCEDPNPLI.ALA.RTMGCI.VDKIT.YLCEPL.KCL.DEDPYV.KTAAVCVAKLH.INA
Retrocopy AIMTVNNFVKDCEDPNPLICALAFRTMGCIWVDKITKYLCEPLLKCLNDEDPYVQKTAAVCVAKLHNINA

Parental  QLVEDQGFLDTLKDLISDSNPMVVANAVAALSEIAESHPSSNLLDLNPQSINKLLTALNECTEWGQIFIL
          Q.VEDQG.LD...DLI.DSNPMVVANAVAALSEI.ESHP.SNLLDLNPQ.INKLLTALN.C.EWGQIFIL
Retrocopy QMVEDQGSLDSPRDLIADSNPMVVANAVAALSEISESHPNSNLLDLNPQNINKLLTALNKCAEWGQIFIL

Parental  DCLANYMPKDDREAQSICERVTPRLSHANSAVVLSAVKVLMKFMEMLSKDLDYYGTLL-KKLAPPLVTLL
          DCL.NY.PKDDREAQSICE.VTPRLSHA.SAVVLSAVKVLMKF.E.L.KD.DYY..LL.KKLAPPLVTLL
Retrocopy DCLSNYNPKDDREAQSICEQVTPRLSHASSAVVLSAVKVLMKFLELLPKDSDYYNMLL<KKLAPPLVTLL

Parental  SAEPELQYVALRNINLIVQKRPEILKHEMKVFFVKYNDPIYVKLEKLDIMIRLASQANIAQVLAELKEYA
          ..EPE.QYV.LRNINLIVQKRPEILK.E.KVFFVKYNDPIY.KLEKLDIMI.LASQANIAQVLAELKEYA
Retrocopy PGEPEVQYVTLRNINLIVQKRPEILKQEIKVFFVKYNDPIYIKLEKLDIMIHLASQANIAQVLAELKEYA

Parental  TEVDVDFVRKAVRAIGRCAIKVEQSAERCVSTLLDLIQTKVNYVVQEAIVVIKDIFRKYPNKYESVIATL
          TE.DVDFV.KAV.AIG.CAIKVEQSAE.CVSTLLDLIQTKVNYVVQEAI.VIKDI.RKYPNKYES.IATL
Retrocopy TELDVDFVHKAVQAIGQCAIKVEQSAEHCVSTLLDLIQTKVNYVVQEAIAVIKDILRKYPNKYESIIATL

Parental  CENLDSLDEPEARAAMIWIVGEYAERIDNADELLESFLEGFHDESTQVQLQLLTAIVKLFLKKPTETQEL
          .ENLDSLDEP.A.AAMIW.VGEYAERIDNADELLESFLEGFHDESTQVQL.LLTAIV.LFLKKP.ETQEL
Retrocopy YENLDSLDEPDAQAAMIWMVGEYAERIDNADELLESFLEGFHDESTQVQLTLLTAIVNLFLKKPSETQEL

Parental  VQQVLSLATQDSD-NPDLRDRGYIYWRLL-STDPVAAKEVVLAEKPLIS
          VQQVLSLATQDSD..PDL.D.GYIYW.LL.STDPV.AK.VVL...PLIS
Retrocopy VQQVLSLATQDSD<YPDLQDQGYIYWCLL<STDPVTAKDVVLSKQPLIS

Legend:

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

Expression

RNA-Seq

Macropus eugenii was not studied using RNA-Seq expression data.

ChIP-Seq

Macropus eugenii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_meug_1205 retrocopy.

TSS

Macropus eugenii was not studied using FANTOM5 data.

Lab

retro_meug_1205 was not experimentally validated.

Homology

Retrocopy orthology:

Macropus eugenii 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000005293	1 retrocopy	retro_cpor_477,
Macropus eugenii	ENSMEUG00000008438	1 retrocopy	retro_meug_1205 ,
Macaca mulatta	ENSMMUG00000021380	1 retrocopy	retro_mmul_2615,