RetrogeneDB ID: retro_meug_1894

Retrocopy location

• Organism: Wallaby (Macropus eugenii)
• Coordinates: Scaffold69766:7061..8336(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: AP1M2
• Ensembl ID: ENSMEUG00000003643
• Aliases: None
• Description: adaptor-related protein complex 1, mu 2 subunit [Source:HGNC Symbol;Acc:558]

Sequence

>retro_meug_1894
ATGCCTGCCTCTGCTGCTTTCATTGTGGACATGAAGGGGAAGCCCTTGATCTGCTGGAACTACAAGGGAGATGTTAACAT
GGCAGAGATTGACCACTTCATGCCCCTGCTGATGCAGAAGGAAGAAGAGGGAGCCCTGACCCCACTGCTGACCCATAGCA
GGGTACACTTCCTGTGGATCAAACATAGCAACCTTTATTTGGTGGCTACCATGCTCAAGAATGCCAGTACTTCCCTGGTG
TACTCATTCCTCTACAAAGCTTTGGAGGCATTCTCTGAATACTTCAAGGAGCTAGAGGAGGAGAGCATCCAGGACAATTT
CATCATTGTCTGTGAGCTGTTGGATGAACTCATGGATTTTGCCTTTCCACAGACCACAGACAGCAAAATTCTGCAGGAGT
ACATCACCCAGCAGGGCAACAAATTAGAGACAAACAAATCCTGGGTGCCCCCAACAGTCACCAGTGCTCTGTCCTGGCAC
TCAGAGGGCATCAGATATAAGAAGAATGAGGTTTTCTTTGATGTGATTGAGTCTGTCAACCTACTGGTCAATGCCAATAG
GAGTGTGCTGTTGAGTGAGATTGTAGGCACCATTAAGCTGAAGGCGTTTTTGTCTGGCATGCCAGAGCTAAGATTGGGCC
TCAATGACAAAGTGCTTTTTGAAGTCACTGGACTTTCAGGCAACAAAAACAAGTCTGTTCAATTAGAAGATGTTAAGTTC
CATCATTGTGTACAGCTCTGGAGATTTGACAACAATCGAACCATCTCCTTCATCCTACCTGATGGTGACTTTGAGCTCTT
GTCTTATTGGCTCAACACCCAGGTAAAACCACTAATCTGGATTGAGTCTATCATTGAGAAGTTTTCACACAGCTGAGTAG
AAATTATGGTTAAGGCTAAAGGCCAGTTTAAGAAGCAATCAGTGGCCAACAGTGTGGAGATCGCAGTTCCAATGCCCAGT
GATGCAGATTCCCCTCGATTCAAAACCAGTGTGGGCAGTGCCAAGTAGCTGCCTAAGAAAAATATGGTTCTCTGGAACAT
CAAGTCCTTTCCTGGAGGAAGTCCTTTCCCCATGAAAGCTCATTTTGGTTTACCCTGCATGGAGAAAGAAGAGGTGGAGG
GTCGACCTCCCATCTCTGTGAAATTTGAGATTCCTTATTTCACTGTCTCTGGGATTCAGGTCTGGTACATGAAGATCATT
GAGAAGCGTGGATATCAGGCCCTTCCCTGGGTTCGATACATCACCCAGAGTGGTGATTATCAGCTTCGGACCAGC

Alignment

ORF - retro_meug_1894 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.76 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSASAVFILDMKGKPLICRNYKGDVNMAEIDHFMPLLMQKEEEGALTPLLTHGRVHFLWIKHSNLYLVAT
          M.ASA.FI.DMKGKPLIC.NYKGDVNMAEIDHFMPLLMQKEEEGALTPLLTH.RVHFLWIKHSNLYLVAT
Retrocopy MPASAAFIVDMKGKPLICWNYKGDVNMAEIDHFMPLLMQKEEEGALTPLLTHSRVHFLWIKHSNLYLVAT

Parental  TLKNANASLVYSFLYKAVEVFSEYFKELEEESIRDNFVIVYELLDELMDFGFPQTTDSKILQEYITQQGN
          .LKNA..SLVYSFLYKA.E.FSEYFKELEEESI.DNF.IV.ELLDELMDF.FPQTTDSKILQEYITQQGN
Retrocopy MLKNASTSLVYSFLYKALEAFSEYFKELEEESIQDNFIIVCELLDELMDFAFPQTTDSKILQEYITQQGN

Parental  KLETGKSRVPPTVTNAVSWRSEGIKYKKNEVFIDVIESVNLLVNANGSVLLSEIVGTIKLKVFLSGMPEL
          KLET.KS.VPPTVT.A.SW.SEGI.YKKNEVF.DVIESVNLLVNAN.SVLLSEIVGTIKLK.FLSGMPEL
Retrocopy KLETNKSWVPPTVTSALSWHSEGIRYKKNEVFFDVIESVNLLVNANRSVLLSEIVGTIKLKAFLSGMPEL

Parental  RLGLNDRVLFELTG--RNKNKSVELEDVKFHQCVRLSRFDNDRTISFIPPDGDFELMSYRLNTQVKPLIW
          RLGLND.VLFE.TG...NKNKSV.LEDVKFH.CV.L.RFDN.RTISFI.PDGDFEL.SY.LNTQVKPLIW
Retrocopy RLGLNDKVLFEVTGLSGNKNKSVQLEDVKFHHCVQLWRFDNNRTISFILPDGDFELLSYWLNTQVKPLIW

Parental  IESVIEKFSHSRVEIMVKAKGQFKKQSVANSVEIAVPVPSDADSPRFKTSVGSAKYLPEKNVVIWNIKSF
          IES.IEKFSHS.VEIMVKAKGQFKKQSVANSVEIAVP.PSDADSPRFKTSVGSAK.LP.KN.V.WNIKSF
Retrocopy IESIIEKFSHS*VEIMVKAKGQFKKQSVANSVEIAVPMPSDADSPRFKTSVGSAK*LPKKNMVLWNIKSF

Parental  PGGKEYLMRAHFGLPSVEKEEVEGRPPISVKFEIPYFTVSGIQVRYMKIIEKSGYQALPWVRYITQSGDY
          PGG....M.AHFGLP..EKEEVEGRPPISVKFEIPYFTVSGIQV.YMKIIEK.GYQALPWVRYITQSGDY
Retrocopy PGGSPFPMKAHFGLPCMEKEEVEGRPPISVKFEIPYFTVSGIQVWYMKIIEKRGYQALPWVRYITQSGDY

Parental  QLRTS
          QLRTS
Retrocopy QLRTS

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_1894 retrocopy.

TSS

Macropus eugenii was not studied using FANTOM5 data.

Lab

retro_meug_1894 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 6 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Macropus eugenii	ENSMEUG00000002558	1 retrocopy	retro_meug_43,
Macropus eugenii	ENSMEUG00000003643	1 retrocopy	retro_meug_1894 ,
Macropus eugenii	ENSMEUG00000013497	1 retrocopy	retro_meug_2142,
Monodelphis domestica	ENSMODG00000005838	2 retrocopies	retro_mdom_1571, retro_mdom_451,
Ornithorhynchus anatinus	ENSOANG00000010455	1 retrocopy	retro_oana_88,
Oryctolagus cuniculus	ENSOCUG00000024334	1 retrocopy	retro_ocun_1089,