RetrogeneDB ID: retro_mmus_2503

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 4:115239997..115241528(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000081138
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Ap2b1
• Ensembl ID: ENSMUSG00000035152
• Aliases: Ap2b1, 1300012O03Rik, AI788979
• Description: adaptor-related protein complex 2, beta 1 subunit [Source:MGI Symbol;Acc:MGI:1919020]

Sequence

>retro_mmus_2503
AAACTGAACTCAACAATGAAAAGAAAGAAAAGAGGAAGGATGTCGGATGTCGTGAAGAAAGTGATTGCTGCTATGACTGT
GGGGAAGGATGTGAGCTCTTTCTTCCCAGATGTGGTGAACTGTATGCAGACTGACAACCTGGAACTAAAGAAGATCATGT
ACTTCTATCTGATGAATTATGCTAAGAGTCAGCCAGACATGGCCATCATGGCTGTCAACAGCTTTGTGGAGGGTTGTGAA
GATCCCAATCCTTTGATTCGAGCCTTGGCTGTTAGAACCATGGGATGCATCCAGGTGGACAAGATTACAAAGTATCTCTG
TGAACCCCTCCAGCAAGTGCTTGAAGGATGAAGACCCCTATGTTCAAAAAATGGCAGCAGTATGTGTAGCAAAACTCCAT
ATATCAATGCCCAGATGGTAGACAATCAAGGATTTCTGGATTCTCTGTCAGATCTCATAGCAGATTCAGACCCAATGGTG
GTGGCTAATGCTGTTATCAGCATTGTCTGAGATCAGTGGGTCTCACACAAACAGCAACATACTTGATTTGAACCCTCAGA
ATATCAATAAGTTGCTCACAGCCATGAATGAATGCACTGAATGGGGCCAGATTTTCATCCTGGACTGCCTGTCTAATTAC
AACCATAAAGATGACCAGGAATCTGAGAGCATCTGTGAGCATGTAACACCTCTGCTATCCCATGCCGGCTCTTCAGTGAT
GCTTTCAGCAGTAAAAGTCCTACTGAAGTTTCTAGAATTCTTGCCCAAGGACTCTGACTACTACAGTATGCTGCTAAAGA
AGTTAGCACCTCCACTTGACACATTGCTGTCTGAGGAGCCAGAAGTGCATTAGGTCACCCTGAGGAACTTCAACCTAATT
GTCTAGAAAAGGCCTGAAATCTTGAAGCAGGAAATCAAGGTCTTCTTTGTGAAGTACAATGATCCTATCTATGTTAAACT
AGAGAAGTTAGGCATCATGATTCGTCTTGCATCCCAAGCCAACATTGCTCAGGTTCTGGTGGAGCTGAAGGAATATGCCA
CTGAAGTTGATGTGGACTTTGTTCACAAAGCTGTGAGGGCCATTAGACGGTGTGCCATCGAAGTGGAGCAATCTGCAGAA
TGCTGTGTAAGAATATTGCTTGACCTAATCCAGACCAAAGTAAACTATGTGGCCCAAGAAGCAATAGTCATCATCAGGGA
CATCTTCCAAAAATAACTCAACAAGTATGAAAGTATTATAGCCACACTCTGTGAAAGCTTGGACTCCCTGGATGAACCAG
ATGCCCGAGCAGCTATGATTTGGATTGTAGGAGAATATGCTGAAAGAATCAATGATTCAGATGAATTACTAGAGAGCTTC
CTAGAGGGTCATCATGATGATAGCACCCAGGTGCAGCTCACACTGCTTACCGCCATAGTGAAGCTATTTCTCAAGAAGCC
ATCAGAAACACAGGAGCTGTTCCAACAGGTCTTGAGCTTAGCCACACAGGATTCCAATAATCCTGACCTTCGAAAATAGG
GTTATATATAT

Alignment

ORF - retro_mmus_2503 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.21 %
• Parental protein coverage: 53.63 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  ELKAELNNEKKEKRKEAVKKVIAAMTVGKDVSSLFPDVVNCMQTDNLELKKLVYLYLMNYAKSQPDMAIM
          .L.......K.......VKKVIAAMTVGKDVSS.FPDVVNCMQTDNLELKK..Y.YLMNYAKSQPDMAIM
Retrocopy KLNSTMKRKKRGRMSDVVKKVIAAMTVGKDVSSFFPDVVNCMQTDNLELKKIMYFYLMNYAKSQPDMAIM

Parental  AVNSFVKDCEDPNPLIRALAVRTMGCIRVDKITEYLCEPLR-KCLKDEDPYVRKTAAVCVAKLHD-INAQ
          AVNSFV..CEDPNPLIRALAVRTMGCI.VDKIT.YLCEPL..KCLKDEDPYV.K.AAVCVAKLH..INAQ
Retrocopy AVNSFVEGCEDPNPLIRALAVRTMGCIQVDKITKYLCEPLQ>KCLKDEDPYVQKMAAVCVAKLHI<INAQ

Parental  MVEDQGFLDSLRDLIADSNPMVVANAV-AALSEISESHPNSNLLDLNPQNINKLLTALNECTEWGQIFIL
          MV..QGFLDSL.DLIADS.PMVVANAV..ALSEIS.SH.NSN.LDLNPQNINKLLTA.NECTEWGQIFIL
Retrocopy MVDNQGFLDSLSDLIADSDPMVVANAV>SALSEISGSHTNSNILDLNPQNINKLLTAMNECTEWGQIFIL

Parental  DCLSNYNPKDDREAQSICERVTPRLSHANSAVVLSAVKVLMKFLELLPKDSDYYNMLLKKLAPPLVTLLS
          DCLSNYN.KDD.E..SICE.VTP.LSHA.S.V.LSAVKVL.KFLE.LPKDSDYY.MLLKKLAPPL.TLLS
Retrocopy DCLSNYNHKDDQESESICEHVTPLLSHAGSSVMLSAVKVLLKFLEFLPKDSDYYSMLLKKLAPPLDTLLS

Parental  GEPEVQYVALRNINLIVQKRPEILKQEIKVFFVKYNDPIYVKLEKLDIMIRLASQANIAQVLAELKEYAT
          .EPEV..V.LRN.NLIV.KRPEILKQEIKVFFVKYNDPIYVKLEKL.IMIRLASQANIAQVL.ELKEYAT
Retrocopy EEPEVH*VTLRNFNLIV*KRPEILKQEIKVFFVKYNDPIYVKLEKLGIMIRLASQANIAQVLVELKEYAT

Parental  EVDVDFVRKAVRAIGRCAIKVEQSAERCVSTLLDLIQTKVNYVVQEAIVVIRDIFRKYPNKYESIIATLC
          EVDVDFV.KAVRAI.RCAI.VEQSAE.CV..LLDLIQTKVNYV.QEAIV.IRDIF.K..NKYESIIATLC
Retrocopy EVDVDFVHKAVRAIRRCAIEVEQSAECCVRILLDLIQTKVNYVAQEAIVIIRDIFQK*LNKYESIIATLC

Parental  ENLDSLDEPDARAAMIWIVGEYAERIDNADELLESFLEGFHDESTQVQLTLLTAIVKLFLKKPSETQELV
          E.LDSLDEPDARAAMIWIVGEYAERI...DELLESFLEG.HD.STQVQLTLLTAIVKLFLKKPSETQEL.
Retrocopy ESLDSLDEPDARAAMIWIVGEYAERINDSDELLESFLEGHHDDSTQVQLTLLTAIVKLFLKKPSETQELF

Parental  QQVLSLATQDSDNPDLRDRGYIY
          QQVLSLATQDS.NPDLR..GYIY
Retrocopy QQVLSLATQDSNNPDLRK*GYIY

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	0.09 RPM	408.48 RPM
SRP007412_cerebellum	0.09 RPM	302.65 RPM
SRP007412_heart	0.00 RPM	66.06 RPM
SRP007412_kidney	0.08 RPM	127.03 RPM
SRP007412_liver	0.03 RPM	70.40 RPM
SRP007412_testis	0.14 RPM	626.12 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_2503 was not detected

EST

No EST(s) were mapped for retro_mmus_2503 retrocopy.

TSS

No TSS is located nearby retro_mmus_2503 retrocopy 5' end.

Lab

retro_mmus_2503 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2503 has 0 orthologous retrocopies within eutheria group .

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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,