RetrogeneDB ID: retro_mdom_696

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 2:150356675..150359330(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000013001
• Aliases: None
• Description: Ubiquitin carboxyl-terminal hydrolase [Source:UniProtKB/TrEMBL;Acc:F7C8N3]

Sequence

>retro_mdom_696
ATGGGGGAAGATGGAGACTGTGGGTAGTGGCCAGATGCCGAGACCCAGAAATCTGAGCTTGGGGCCCTGATGAAGATGGC
ACTTCAGCAAAGGGCACAGTGGTATCTGATTGACAGAAAATGGTTCAAGCAGTGGAAGGAATATGTGGGCTTTGATAGCT
GGGATACATACAATGTGGGTGAAAACAACTTGTTTCCTGGCCCAATAGATACCTTTGGACTTTTTTCATATCCTGAAAGT
CAAAGAATAAAGGAGCATTTAACTGATGAACTAGACTATGTATTGGTTCCTACTGAAGCCTGGAATAAATTAATGAGTTG
GTATGGCTGTGTAGAGAGGTAACAGCCCATAGTCAGAAAAGTTGTGGAACATAGTCTGTTTGTCAAATACTGCAAAGTAG
AAGTTTATTTGCTGGAACTGAAGCTCTGTGAAAACAGTGACCCCACCAATATGCTGAGTTGCCATTTCAGCAAAGCAGAT
AGCATAGCAACCATTGAGAAGGAAATGCAGAAACTATTTAACATTCCTGATGAGAGGAAGACCAGGTTATGAAACAAATT
ATGTGAGTAATACATATGAGCAGCTCAACAAGCCAGACAACACTGTGAAAGATGCTGGTTTATACCAAGGGCAGGTACTA
GTCATTGAGCCCCAAAATGAAGATGGCACATAGCCTAGGCAGACACTTCAGTTCAAATCAAGCACTAGCAGAGCATTTAC
TACCTCTCCAAAATCAACAGCAAGCTCCTATTCCTCCATGTCCACTTCTCCCATTACAAATGGTGATAGCCCTAACTCTT
CTGGCATGCACAGTTCTGGTCTCACCAGGGGAGGTTCTGGCTTCTCAACTCTTATAGTTGCGGAGAGTCTCAATCTCACA
CTCAACCTAGGCTTTGTGGACATGGAAACCTGGGGAACATCTACTTCATGAATTCTGCTTTGCAGTGCCTGAGTAACACT
GCACCATTGACAGAATACTTTCTAAAACATAAATATGAGGCTGAAATCAATTAAGACAATCCTTTGGGCATGAAAGGGGA
AATTGCTGAGGCTTATGCTGAACTCATTAAACAGATGGGATCTGGGAGGAATACTCAGGTTACCCCACGGATGTTCAAAA
CCCAAGTTAGTCGTTTTGCCCCTCAGTTTTCAGGTTACCAGCAACAGGATTCTTAAGAGTTATTAGCCTTTTTTTCTGGA
AGGATTGCATGAAGATCTAAACCATGTGAAGAAGAAACCATACTGGGAACTAAAAGATGCCAATGGACAGCCTGACTTGG
TGGTGGCAAAGGAAGCATAGGAGAATCACAGGATAAGAAATGATTCTGTGATAGTGGACACATTCCATGGCCTTTTCAAA
TCTACATTGGCTTGCCCAGAATGTTCTAAAATTTCTGTGACTTTTGATCCATTCTGTTATTTAGTTCTCCCTTTGCCCTT
GAAGATGATGGAGGTGTTCTTGGTCTCTGCAGATCCACAATGTAGCCCTACCCAGTATCGTGTGACTGTATCAATGTGGG
CACTGTGTCTGATCTGTGTGAGGCTCTCTCAAAGCTCTCTGGCATTGCTACTGAAAATAGGGTGGTCACAGATATGTATA
ATCATCTGTTCCACAAAATTTTCCAAATGGATGAAGGTTTAAATCATATTATGACCTGGGATTACATCTTTGTATACAAA
GTCTGCAACATAGCCAAGGATGGATCAAAATGTGTCACTTTTCCAGTTTACTTCAGAGAGAGGAAAATCAGGCAGACAAG
CTCATCTTCTGGGACCATTCTATATGGGCAAGTATTGTTAAACTCTGTCTCAAAGCACAAGTTAACCCTTGACTACTTGT
ACCAGGTTTTCTGTGGGCATATCAGCCACTACATAAAACATCCTTTACCAGATGACTCTGCAATACCACACTTGGACAAT
CCTACCTGTAATGGTCCCAATGGCATTTGTGAAGAAGAAGAAGAAGAAATGGAACACCAAGATGACAGCAAAGGACAAGC
TACAGAGACAGAGTCCTGTTCAGCTGAAGACTGTGCTGAACATGAATTGGGAAATGAGTCCTGTCAGAAAGTCCCAAAGA
GATTCAGAAGCCAGCACTGCAAAAAAAGGCTTTTCACCTTCAGCCTGGTGAATTCCTATGGCACCACTGACATCAATTCT
CTTGTAGCAGATGGGAAGTTCTTCAAACTGAATTCTCATTCCACAATTACTGTTAATTGGGATACCGAAACCCGGTGTCT
TCACTATGATGAACAAGAATCAAAGGCTTATGATAAATGTAGCAGCATGCTCCAGCCCCAGAAGAAGAAGAAAACAATGG
TGGCCCTTCAAGACTGCATTGAGCTCTTCAATACCATGGAAATCCTGGGGTAGCATGATCCCTGGTATTGTCTTAATTAT
AAGAAACATCAACAGACCACAAAGAAATTTGACTTGTGGTCCTTGCCAAAGGTTCACCTCAAACAATTTTCATACAAGAG
ATGCTGGAGAGATAAACTTAACCCTGTGGTTAAATTTCTAATAAGAGACCTACATATGTCTCAGTTTGTCTGTGACCCAG
CAGCTGGCCCTTATGTCTATAACCTCATTGCTGTATCCAATTATTATGGAGCCATGGGTGTGGTTCACTATATTGCATAT
GAAAAAAACAAATTG

Alignment

ORF - retro_mdom_696 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.14 %
• Parental protein coverage: 92.33 %
• Number of stop codons detected: 8
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MAEGGGCGQRPDAETQKSELGALMRTALQRGAQWYLIDSRWFKQWKKYVGFDSWDMYNVGENNLFPGPID
          M.E.G.CG..PDAETQKSELGALM..ALQ..AQWYLID..WFKQWK.YVGFDSWD.YNVGENNLFPGPID
Retrocopy MGEDGDCG*WPDAETQKSELGALMKMALQQRAQWYLIDRKWFKQWKEYVGFDSWDTYNVGENNLFPGPID

Parental  NSGLFSDPESQTLKEHLIDELDYVLVPTEAWNKLVNWYGCVEGQQPIVRKVVEHGLFVKHCKVEVYLLEL
          ..GLFS.PESQ..KEHL.DELDYVLVPTEAWNKL..WYGCVE..QPIVRKVVEH.LFVK.CKVEVYLLEL
Retrocopy TFGLFSYPESQRIKEHLTDELDYVLVPTEAWNKLMSWYGCVER*QPIVRKVVEHSLFVKYCKVEVYLLEL

Parental  KLCENSDPTNMLSCHFSKADTIATIEKEMRKLFNIPDERETRLWNK-YMSNTYEQLSKPDNTVQDAGLYQ
          KLCENSDPTNMLSCHFSKAD.IATIEKEM.KLFNIPDER.TRL.NK.Y.SNTYEQL.KPDNTV.DAGLYQ
Retrocopy KLCENSDPTNMLSCHFSKADSIATIEKEMQKLFNIPDERKTRL*NK>YVSNTYEQLNKPDNTVKDAGLYQ

Parental  GQVLVIEPQNEDGTWPRQTLQSKSSTSRAFTTSPKSAASSYSSMSASPITNGDSANSSGVHSSGLSRGGS
          GQVLVIEPQNEDGT.PRQTLQ.KSSTSRAFTTSPKS.ASSYSSMS.SPITNGDS.NSSG.HSSGL.RGGS
Retrocopy GQVLVIEPQNEDGT*PRQTLQFKSSTSRAFTTSPKSTASSYSSMSTSPITNGDSPNSSGMHSSGLTRGGS

Parental  GFS-NSYSCRESQSHTQPGLCGLGNLGNTCFMNSALQCLSNTAPLTEYFLKDKYEAEINRDNPLGMKGEI
          GFS.NSYSC.ESQSHTQP.LCG.GNLGN..FMNSALQCLSNTAPLTEYFLK.KYEAEIN.DNPLGMKGEI
Retrocopy GFS<NSYSCGESQSHTQPRLCGHGNLGNIYFMNSALQCLSNTAPLTEYFLKHKYEAEIN*DNPLGMKGEI

Parental  AEAYAELIKQMWSGRNTQVAPRMFKTQVGRFAPQFSGYQQQDSQELLAFL-LDGLHEDLNRVKKKPYLEL
          AEAYAELIKQM.SGRNTQV.PRMFKTQV.RFAPQFSGYQQQDS.ELLAF..L.GLHEDLN.VKKKPY.EL
Retrocopy AEAYAELIKQMGSGRNTQVTPRMFKTQVSRFAPQFSGYQQQDS*ELLAFF>LEGLHEDLNHVKKKPYWEL

Parental  KDANGRPDLVVAKEAWENHRLRNDSVIVDTFHGLFKSTLVCPECSKISVTFDPFCYLTLPLPLKKDRTME
          KDANG.PDLVVAKEA.ENHR.RNDSVIVDTFHGLFKSTL.CPECSKISVTFDPFCYL.LPLPLK....ME
Retrocopy KDANGQPDLVVAKEA*ENHRIRNDSVIVDTFHGLFKSTLACPECSKISVTFDPFCYLVLPLPLKM---ME

Parental  VFLVSADPQCRPTQYRVTVPM-MGAVSDLCEALSKLSGIAAENMVVTDVYNHRFHKIFQMDEGLNHIMTR
          VFLVSADPQC.PTQYRVTV.M..G.VSDLCEALSKLSGIA.EN.VVTD.YNH.FHKIFQMDEGLNHIMT.
Retrocopy VFLVSADPQCSPTQYRVTVSM<VGTVSDLCEALSKLSGIATENRVVTDMYNHLFHKIFQMDEGLNHIMTW

Parental  DDIFVYEVCNTAEDGSECVTFPVYFRERKIRQTSSSSGTVLYGQPLLISVPKHKLTLDYLYQVICERISR
          D.IFVY.VCN.A.DGS.CVTFPVYFRERKIRQTSSSSGT.LYGQ.LL.SV.KHKLTLDYLYQV.C..IS.
Retrocopy DYIFVYKVCNIAKDGSKCVTFPVYFRERKIRQTSSSSGTILYGQVLLNSVSKHKLTLDYLYQVFCGHISH

Parental  YIKHPLPDDSPRPHLDSATYNGSNGICEGEEEEMEHQDDSKGQATETESCSTEDCSEHELGNESCQNVPK
          YIKHPLPDDS..PHLD..T.NG.NGICE.EEEEMEHQDDSKGQATETESCS.EDC.EHELGNESCQ.VPK
Retrocopy YIKHPLPDDSAIPHLDNPTCNGPNGICEEEEEEMEHQDDSKGQATETESCSAEDCAEHELGNESCQKVPK

Parental  RVRSQHCKKRLFTFSLVNSYGTTDINSLAADGKLLKLNSRSTVAVDWDTETRCLHYDEQESEAYDKHSSM
          R.RSQHCKKRLFTFSLVNSYGTTDINSL.ADGK..KLNS.ST..V.WDTETRCLHYDEQES.AYDK.SSM
Retrocopy RFRSQHCKKRLFTFSLVNSYGTTDINSLVADGKFFKLNSHSTITVNWDTETRCLHYDEQESKAYDKCSSM

Parental  LQPQKKKKTTVALRDCIELFTTMETLGEHDPWYCPNCKKHQQATKKFDLWSLPKVLVVHLKRFSYNRYWR
          LQPQKKKKT.VAL.DCIELF.TME.LG.HDPWYC.N.KKHQQ.TKKFDLWSLPKV...HLK.FSY.R.WR
Retrocopy LQPQKKKKTMVALQDCIELFNTMEILG*HDPWYCLNYKKHQQTTKKFDLWSLPKV---HLKQFSYKRCWR

Parental  DKLDTVVEFPIRDLHMSEFVCDPAAGPYVYDLIAVSNHYGAMGVGHYTAYAKNKL
          DKL..VV.F.IRDLHMS.FVCDPAAGPYVY.LIAVSN.YGAMGV.HY.AY.KNKL
Retrocopy DKLNPVVKFLIRDLHMSQFVCDPAAGPYVYNLIAVSNYYGAMGVVHYIAYEKNKL

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	0.00 RPM	0.00 RPM
SRP007412_cerebellum	0.00 RPM	0.00 RPM
SRP007412_heart	0.00 RPM	0.00 RPM
SRP007412_kidney	0.00 RPM	0.00 RPM
SRP007412_liver	0.00 RPM	0.00 RPM
SRP007412_testis	0.00 RPM	0.00 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_696 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_696 was not experimentally validated.

Homology

Retrocopy orthology:

Monodelphis domestica 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Monodelphis domestica	ENSMODG00000013001	1 retrocopy	retro_mdom_696 ,
Sorex araneus	ENSSARG00000007703	1 retrocopy	retro_sara_550,