RetrogeneDB ID: retro_mdom_1

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: X:46041739..46043893(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMODG00000025205
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000009745
• Aliases: None
• Description: None

Sequence

>retro_mdom_1
ATGTTTGTTAACGGAGCTTCTGAGCACATTGCTGAATATATCCCAGAAAAAGTGAAGAAAGCAGAAAAGAAACTAGAAAA
TAATTCATATGACCTTACTGCTTGGAGCATTCTGATTAGAGAGGCACAGAGTCAATCTGTAGAAAAAGCACGGAAGACAC
TTGAACGTCTTGTTGCTCAATTCCCCAGTTCTGGCAGATTCTGGAAACTGTACATTGAAGCAGAGATTAAAACTAAAAAT
TTTGACAAGGCTGAAAAGTTATTTCAGAGATGCCTCATAAAAGTTTTACATATTGACTTGTGGAAGTGTTATCTGACTTA
TATCAGAGAAACCAAGGCAAGACTTCCCAGTTTCAAAGAAAAAATGGCACAAGCATATGACTTTACTTTGGATAAAATTG
GAATGGAGATTATGTCTCATCAAATTTGGATGGATTACATCAATTTCTTGAAAGGGGTAGAAGCTATTGGATCTTATGCA
GAAAATCAAAGAATAACAGCTGTCCGAAGAGTTTATCAACGTGGTTGTGTTAATCCAATGATCAATATTGAGCAACTTTG
GAAGGACTATAATAAATATGAAGAGGGCATCAACATACATATAGCTAAAAAAATGATTGATGATAGAAGCAGAGATTACA
TGAATGCAAGACGTGTGGCAAAGGAGTATGAAACAGTCGTGAAAGGTTTAGACCGCAATGCTCCTTCAGTACCTCCACAG
AATACTCCCCAAGAAGCTCAGCAAGTAGACATGTGGAAGAAATACATCCAGTGGGAAAAGAACAATCCTCTCCGAACAGA
AGATCACACGCTCATAACAAAAAGAGTGATATTTGCATATGAGCAGTGCCTGCTTGTGCTGGGTCATCACCCAGATATTT
GGCACGAAGCTGCGCAGTACCTGGAGCAATCCAGTAAGCTGTTGGCTGAGAAAGGGGACATGAACAATTCCAAATTATTT
AGCAATGAAGCCGCTAATATATATGAAAGAGCTATCAGCTCTTTACTGAAGAAAAATATGCTGCTTTATTTTGCATATGC
AGATTATGAAGAAAGTCGAATGAAATACGAGAAGGTACATAGCATATATAATAGATTTCTAGTTATTGAAGATATTGATC
CTACTCTGGTTTATATCCAATATATGAAATTTGCAAGGCGAGCAGAAGGCATCAAAGCTGGAAGGATGGTATTTAAAAGA
GCGAGAGGAGACACTAGAGCACGCTACCATATCTATGTTGCAGCAGCATTAACGGAGTACTACTGTAGTAAAGATAAAAT
AGTGGCCTTTAAGATTTTTGAGCTGGGGTTAAAAAAATATGGGAACATTCCAGAATATGTATTAGCCTATATTGACTACC
TCTCTCACCTTAATGAGGACAATAATACACGAGTTTTGTTTGAACGAGTATTAACATCTGGAGTCCTTCCACCTGACAAA
TCTGGAGAAATCTGGGCCAGATATCTAGCTTTTGAAAGTAGCTTTGGTGATCTAGTCAGTATCCTGAAAGTGGAGAAGAG
ACTGTTCACAGCGTTCAAGGAAGAATATGAATTCAAGGAAACAGCGTTACGGGTTGATAGATATAAGTTCCTGGATTTGT
ATCCCTGCCGTGCAAGTGAATTAAAGGCTTTTGGCTATAAAGATGTTTCTCGGACCAAGCTAGGAATCATCATTCCTGAC
CCCATGGTAACTCCTTCTGTAGTGTCTGTTCTTAAAAATGAAGAGGATAGAAAACCGAAATACCCCAGACCAGACGTCCG
GCAGATGATACCCTTTCAGCCAAGGCATTTTGCATCCCCAGGCTTACACCCTGTGTCTGGTGGAGTGTTTCCGGTGCCAC
CTGCTGCTGTACTTTTAATGAAACTCCTCCCTCCTCCAGTCTGTTTCCAGGGTCCTTTTGTGCAAGTAGATGAATTGATG
GAAATTTTCCGAAGATGTGAGATCCCGAGCACTCTTGATGAAGCTGTGAAAATCATCACTGGAAGAGTACCATACCGGGC
CAGGGACCGAAACAGTTTTCTGGAAAGCAGTAGCACAGTGAAAAGAGTAGCCAAACGACCCAATGAAGATATGAATGAGG
AAGGAGGAAAACACAAAGCAAGGCCACCTGTCCACGACATTTACAGAGCCCGACAACAGAAGAGAATCCGATGA

Alignment

ORF - retro_mdom_1 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.87 %
• Parental protein coverage: 99.58 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  DGAAEQAAEYVPEKVKKAEKKLEENPYDLDAWSILIREAQNQPIDKARKTYERLVAQFPSSGRFWKLYIE
          .GA.E..AEY.PEKVKKAEKKLE.N.YDL.AWSILIREAQ.Q...KARKT.ERLVAQFPSSGRFWKLYIE
Retrocopy NGASEHIAEYIPEKVKKAEKKLENNSYDLTAWSILIREAQSQSVEKARKTLERLVAQFPSSGRFWKLYIE

Parental  AEIKAKNYDKVEKLFQRCLMKVLHIDLWKCYLSYVRETKGKLPSYKEKMAQAYDFALDKIGMEIMSYQIW
          AEIK.KN.DK.EKLFQRCL.KVLHIDLWKCYL.Y.RETK..LPS.KEKMAQAYDF.LDKIGMEIMS.QIW
Retrocopy AEIKTKNFDKAEKLFQRCLIKVLHIDLWKCYLTYIRETKARLPSFKEKMAQAYDFTLDKIGMEIMSHQIW

Parental  VDYINFLKGVEAVGSYAENQRITAVRRVYQRGCVNPMINIEQLWRDYNKYEEGINIHLAKKMIEDRSRDY
          .DYINFLKGVEA.GSYAENQRITAVRRVYQRGCVNPMINIEQLW.DYNKYEEGINIH.AKKMI.DRSRDY
Retrocopy MDYINFLKGVEAIGSYAENQRITAVRRVYQRGCVNPMINIEQLWKDYNKYEEGINIHIAKKMIDDRSRDY

Parental  MNARRVAKEYETVMKGLDRNAPSVPPQNTPQEAQQVDMWKKYIQWEKSNPLRTEDQTLITKRVMFAYEQC
          MNARRVAKEYETV.KGLDRNAPSVPPQNTPQEAQQVDMWKKYIQWEK.NPLRTED.TLITKRV.FAYEQC
Retrocopy MNARRVAKEYETVVKGLDRNAPSVPPQNTPQEAQQVDMWKKYIQWEKNNPLRTEDHTLITKRVIFAYEQC

Parental  LLVLGHHPDIWYEAAQYLEQSSKLLAEKGDMNNAKLFSDEAANIYERAISTLLKKNMLLYFAYADYEESR
          LLVLGHHPDIW.EAAQYLEQSSKLLAEKGDMNN.KLFS.EAANIYERAIS.LLKKNMLLYFAYADYEESR
Retrocopy LLVLGHHPDIWHEAAQYLEQSSKLLAEKGDMNNSKLFSNEAANIYERAISSLLKKNMLLYFAYADYEESR

Parental  MKYEKVHSIYNRLLAIEDIDPTLVYIQYMKFARRAEGIKSGRMIFKKAREDTRTRHHVYVTAALMEYYCS
          MKYEKVHSIYNR.L.IEDIDPTLVYIQYMKFARRAEGIK.GRM.FK.AR.DTR.R.H.YV.AAL.EYYCS
Retrocopy MKYEKVHSIYNRFLVIEDIDPTLVYIQYMKFARRAEGIKAGRMVFKRARGDTRARYHIYVAAALTEYYCS

Parental  KDKSVAFKIFELGLKKYGDIPEYVLAYIDYLSHLNEDNNTRVLFERVLTSGSLPPEKSGEIWARFLAFES
          KDK.VAFKIFELGLKKYG.IPEYVLAYIDYLSHLNEDNNTRVLFERVLTSG.LPP.KSGEIWAR.LAFES
Retrocopy KDKIVAFKIFELGLKKYGNIPEYVLAYIDYLSHLNEDNNTRVLFERVLTSGVLPPDKSGEIWARYLAFES

Parental  NIGDLASILKVEKRRFTAFKEEYEGKETALLVDRYKFMDLYPCSASELKALGYKDVSRAKLATIIPDPVV
          ..GDL.SILKVEKR.FTAFKEEYE.KETAL.VDRYKF.DLYPC.ASELKA.GYKDVSR.KL..IIPDP.V
Retrocopy SFGDLVSILKVEKRLFTAFKEEYEFKETALRVDRYKFLDLYPCRASELKAFGYKDVSRTKLGIIIPDPMV

Parental  APSIVPVLKDEVDRKPEYPKPDTQQMIPFQPRHLAPPGLHPVPGGVFPVPPAAVVLMKLLPPPVCFQGPF
          .PS.V.VLK.E.DRKP.YP.PD..QMIPFQPRH.A.PGLHPV.GGVFPVPPAAV.LMKLLPPPVCFQGPF
Retrocopy TPSVVSVLKNEEDRKPKYPRPDVRQMIPFQPRHFASPGLHPVSGGVFPVPPAAVLLMKLLPPPVCFQGPF

Parental  VQVDELMEIFRRCKIPSTVDEAVRIITGGVPDLAVEGNGPVESSAVLTKAVKRPNEDSDEDEEKGAVVPP
          VQVDELMEIFRRC.IPST.DEAV.IITG.VP..A...N...ESS.......KRPNED..E...K....PP
Retrocopy VQVDELMEIFRRCEIPSTLDEAVKIITGRVPYRARDRNSFLESSSTVKRVAKRPNEDMNEEGGKHKARPP

Parental  IHDIYRARQQKRIR
          .HDIYRARQQKRIR
Retrocopy VHDIYRARQQKRIR

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_1 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Macropus eugenii	ENSMEUG00000005640	1 retrocopy	retro_meug_1862,
Myotis lucifugus	ENSMLUG00000003073	1 retrocopy	retro_mluc_240,
Monodelphis domestica	ENSMODG00000009745	1 retrocopy	retro_mdom_1 ,