RetrogeneDB ID: retro_mmul_2615

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: X:91887319..91888970(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: AP1B1
• Ensembl ID: ENSMMUG00000021380
• Aliases: None
• Description: None

Sequence

>retro_mmul_2615
ATGACTGACTCCAAGTATTTCACAACCAATAAAAAAGGAGAAATATTTGAACTAAAAGCTGAACTCAACAATGAAAAGAA
AGAAAAGAGAAAGGAGGCTGCGAAGAAAGTGATTGCTGTTGCGACCGTGGGGAAGGATGCTAGTTCTGTCTTTCCAGACA
TAATGAACTGTATGCAGACTGGCAATCTGGAACTAAAGAAGCTTGTGTATCTCTATTTGATGAACTATGCCAAGAGTCAG
CCAGGCATGGCCATCATGGCTGTAAACAGTTTCATAAAGGACTGTGAAGATCCTAATCCTTTGATTAGAGCCTTGGCAGT
CAAAACCATGGGGTGCATCCGGGCAGACAAAATTACAGAATATCTCTGTGAGCCCCTCCTCAAGTGGTTGGAGGATGAGG
ATTCCTATGTTCGGAAAACAGCAGCAGTATGCGTGGCAAATCTCCATGATATCGACGCCCAAATGGTGGAAGATCAGGGG
TTTTTGGATTCTCTATGAGGTCTTATAGCAGATTCAAATCTAATGGTGGTGGCTAATGCTGTAGCAGCATTATCTGAAAT
CAGTGAGTCTCAACCAAACAGCAACTTACTCAATCTGAACACACAGAACATTAATAAGCTGCTGACAGCCCTGAATGAGT
ACACTGAAGGGGCCAGATTTCATCCTGGACTGCCTGTCTAATTACAACCCTAAAGATGATCGGGAGGCTCAGCGCATCTG
TGAGCGGGTAACTCCCCAGCTATCCCATGCCAACTCAGCAGTGGTGCTTTCAGCAGTAAAAGTCCTAATGAAGTTTCCAG
AATTGTTACCTAAGGATTCTGACTACTACAATATGCTGCTGAAGAAGTTAGCCCCTCCACTTGTCATTTTGCTGTCCGGG
GAGTCAGAAGTGCAGTATGTCTCCCTGAGGAACATCAACTTAATTGTCCAGAAAAGGCCTGAAATCTTGAAGCAGGAAAT
CAAAGTCTTCTTTGTGAAGTACAATGATCCCATCTATGTTAAACTAGAGAAGCTGGACATCAGGATTCATTTGGCATCAC
AAGCCAACATCACTCAAATTCTGGCAGAACTGAAGGAACATGCCACAGTGGTGAATGTTGACTTTGTTCAAAAAGCTGTG
AGGGCCATTGGACGGTGTGCCATCAAGATGGAGCAATCTGCAGTGTGCTGTGTAAGCACATTGCTTGATCTAATCCAGAC
CAAAGTGAATTATGTGGTCCAAGAAATGATTGTTGTCATCAGGGACATCTTCCGCAAATACTCTAACAAGTGTGAAAGTA
TCATTGCCACTGTATGTGAGAACTTAGACTCACTGGATGAGCCAGATGCTCGAGAGGCTATGATTTGGATTGTGGGAGAA
TATGCTGAAAGAATTAACAATGCAGATGAGTTACTAGAAAGCTTCCTGGAGGGTTTTCATGATGAAAGCACCCAGGTGCA
GCTCACTCTGCTTACTGCCATAGTGAAGCTGTTTCTCAAGAAACCACCAGAAACACAGAAGCTAGTCCAGCAGGTGTTGA
CTTTGGCAACACAGGATTCTGATAATCCTGACCTTCAAGACCAGGGCTATATTTATTGGGATCTTTTCTCAACTGACCCT
GTCACAGCTAAATAAGTAGTCTTGTCTGAGAAGCCACGGATCTCTGAAGAC

Alignment

ORF - retro_mmul_2615 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.36 %
• Parental protein coverage: 59.96 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MTDSKYFTTTKKGEIFELKAELNSDKKEKKKEAVKKVIASMTVGKDVSALFPDVVNCMQTDNLELKKLVY
          MTDSKYFTT.KKGEIFELKAELN..KKEK.KEA.KKVIA..TVGKD.S..FPD..NCMQT.NLELKKLVY
Retrocopy MTDSKYFTTNKKGEIFELKAELNNEKKEKRKEAAKKVIAVATVGKDASSVFPDIMNCMQTGNLELKKLVY

Parental  LYLMNYAKSQPDMAIMAVNTFVKDCEDPNPLIRALAVRTMGCIRVDKITEYLCEPLRKCLKDEDPYVRKT
          LYLMNYAKSQP.MAIMAVN.F.KDCEDPNPLIRALAV.TMGCIR.DKITEYLCEPL.K.L.DED.YVRKT
Retrocopy LYLMNYAKSQPGMAIMAVNSFIKDCEDPNPLIRALAVKTMGCIRADKITEYLCEPLLKWLEDEDSYVRKT

Parental  AAVCVAKLHDINAQLVEDQGFLDTLKDLISDSNPMVVANAVAALSEIAESHPSSNLLDLNPQSINKLLTA
          AAVCVA.LHDI.AQ.VEDQGFLD.L..LI.DSN.MVVANAVAALSEI.ES.P.SNLL.LN.Q.INKLLTA
Retrocopy AAVCVANLHDIDAQMVEDQGFLDSL*GLIADSNLMVVANAVAALSEISESQPNSNLLNLNTQNINKLLTA

Parental  LNECTEW-GQI-FILDCLANYTPKDDREAQSICERVTPRLSHANSAVVLSAVKVLMKFMEMLSKDLDYYG
          LNE.TE..GQI.FILDCL.NY.PKDDREAQ.ICERVTP.LSHANSAVVLSAVKVLMKF.E.L.KD.DYY.
Retrocopy LNEYTEG<GQI<FILDCLSNYNPKDDREAQRICERVTPQLSHANSAVVLSAVKVLMKFPELLPKDSDYYN

Parental  TLLKKLAPPLVTLLSAEPELQYVALRNINLIVQKRPEILKHEMKVFFVKYNDPIYVKLEKLDIMIRLASQ
          .LLKKLAPPLV.LLS.E.E.QYV.LRNINLIVQKRPEILK.E.KVFFVKYNDPIYVKLEKLDI.I.LASQ
Retrocopy MLLKKLAPPLVILLSGESEVQYVSLRNINLIVQKRPEILKQEIKVFFVKYNDPIYVKLEKLDIRIHLASQ

Parental  ANIAQVLAELKEYATEVDVDFVRKAVRAIGRCAIKVEQSAERCVSTLLDLIQTKVNYVVQEAIVVIKDIF
          ANI.Q.LAELKE.AT.V.VDFV.KAVRAIGRCAIK.EQSA..CVSTLLDLIQTKVNYVVQE.IVVI.DIF
Retrocopy ANITQILAELKEHATVVNVDFVQKAVRAIGRCAIKMEQSAVCCVSTLLDLIQTKVNYVVQEMIVVIRDIF

Parental  RKYPNKYESVIATLCENLDSLDEPEARAAMIWIVGEYAERIDNADELLESFLEGFHDESTQVQLQLLTGI
          RKY.NK.ES.IAT.CENLDSLDEP.AR.AMIWIVGEYAERI.NADELLESFLEGFHDESTQVQL.LLT.I
Retrocopy RKYSNKCESIIATVCENLDSLDEPDAREAMIWIVGEYAERINNADELLESFLEGFHDESTQVQLTLLTAI

Parental  VKLFMKKPTETQELVQQVLSLATQDSDNPDLRDRGYIYWRLLSTDPVAAKEVVLAEKPLISEE
          VKLF.KKP.ETQ.LVQQVL.LATQDSDNPDL.D.GYIYW.L.STDPV.AK.VVL.EKP.ISE.
Retrocopy VKLFLKKPPETQKLVQQVLTLATQDSDNPDLQDQGYIYWDLFSTDPVTAK*VVLSEKPRISED

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	3.25 RPM	72.27 RPM
SRP007412_brain_prefrontal_cortex	0.16 RPM	140.73 RPM
SRP007412_cerebellum	1.87 RPM	86.92 RPM
SRP007412_heart	0.18 RPM	44.87 RPM
SRP007412_kidney	0.82 RPM	71.83 RPM
SRP007412_liver	0.16 RPM	131.46 RPM
SRP007412_testis	10.93 RPM	71.01 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_2615 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_2615 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_2615 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4875
Pan troglodytes	retro_ptro_3248

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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 ,