RetrogeneDB ID: retro_mdom_93

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 3:392299937..392301239(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMODG00000004037
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000003104
• Aliases: None
• Description: None

Sequence

>retro_mdom_93
ATGGCTTCTTCTGAGGTGGCACGGCATATGGTCTATCAGTCTCTTGTGGGAATCAAAGCAACTTGTGTCACCTCCCAACC
ATGTAAAGAAGAAAGGATAACAGACGAAGACCCTCGTTCTTTAACTATAACCGGCCATGTGGGTTTTGAAAGTTTGCCTG
ATCAGTTGGTCAACAGGACCCTTCAGCAAGGGTTCTGTTTCAACATTCTCTGTGTGGGGGAAACTGGAATCGGAAAGTCG
ACCCTGATAGACACGTTGTTTAACACTAATTTTGATCACTGCGGTTCCTCTCACTTTCACCCCAATGTAAGACTTAAAGC
CCAAACATATGAACTCCAGGAAAGCAATGTCCGCTTGAAACTGACCATCGTAAATACAGTGGGATTTGGAGACCAGATAA
ATAAAGAAGATAGCTATCGACCAATAGTGGATTACATAGATGCCCAATTTGAGGCATATCTTCAAGAAGAATTGAAGGTT
AAACGTTCACTCTTTAACTACCGAGATTCTCGAATCCATGTTTGCCTTTACTTTATTGCACCTACAGGGCATTCCCTTAA
GGCTCTTGACTTGTTAACCATGAAGCATCTGGATAGCAGGGTAAACATCATTCCGGTGATTGCCAAAGCTGATACACTTT
CTAAATGCGACTTGCAGAAGTTTAAGCTTAAACTCATGAATGAATTGGTCTCCAATGGGATCCAGTTTTACCAATTCCCA
ACAGACGATGAAACTGTTGCTCAGCTTAATTCTTCAATGAATGGACATTTACCATTTGCTGTTGTGGGGAGTACAGAGGA
GGTCAAACTTGGGAATAAGATGGTGAAAGCTCGTCGGTATCCCTGGGGCATTGTACAAGTAGAAAATGAAAATCACTGTG
ACTTTGTAAAGCTCCGGGAAATGCTTATTTGCACAAATATGGAAGACCTGAGAGAACAAACCCATATTCGACACTATGAA
AATTATAGGCGTTGCAAACTGGAGGAAACCGGCTTTAAAGAGGTATGTCCAGAGAAAAAGCCTCTAAGTGTTCTGGAGTC
ACAAGAAATCAAAAGGTATGATTCCTTTTGTGAACTTCAAAGGAAAGAAGAGGAGATGAAACAGTTGTTTGTCAAGCGAG
TGAAAGAAAAAGAAGCTATTTTGAAAGAAGCTGAGCGAGAGCTCCAGGCAAAATTTGAACATCTTAAAAGACTTCATCAA
GAAGAAAGAATCAAACTTGAAGAAAGGAGAAGAAATTTAGAAGAGGAAATAAGTGCTCTTGGAAAACGGAAAGCTGCATG
TGAACTAAAAGCCAGCCTTTAA

Alignment

ORF - retro_mdom_93 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.65 %
• Parental protein coverage: 93.03 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MTSSDVARHTVLQSLGGLKS-CPSPQPGKEDKV-DDSLRCLSINGRVGFENLPDQLVNRSIQQGFCFNIL
          M.SS.VARH.V.QSL.G.K..C...QP.KE....D...R.L.I.G.VGFE.LPDQLVNR..QQGFCFNIL
Retrocopy MASSEVARHMVYQSLVGIKATCVTSQPCKEERITDEDPRSLTITGHVGFESLPDQLVNRTLQQGFCFNIL

Parental  CVGETGIGKSTLIDTLFNTNFNDLESSHFHPNVRLKAQTYELQESSVRLKLTIVNTVGFGDQINKEESYQ
          CVGETGIGKSTLIDTLFNTNF....SSHFHPNVRLKAQTYELQES.VRLKLTIVNTVGFGDQINKE.SY.
Retrocopy CVGETGIGKSTLIDTLFNTNFDHCGSSHFHPNVRLKAQTYELQESNVRLKLTIVNTVGFGDQINKEDSYR

Parental  PIVDYIDAQFEAYLQEELKIKRSLFNYHDSRIHACLYFISPTGHSLKTLDLLTMKSLDSKVNIIPVIAKA
          PIVDYIDAQFEAYLQEELK.KRSLFNY.DSRIH.CLYFI.PTGHSLK.LDLLTMK.LDS.VNIIPVIAKA
Retrocopy PIVDYIDAQFEAYLQEELKVKRSLFNYRDSRIHVCLYFIAPTGHSLKALDLLTMKHLDSRVNIIPVIAKA

Parental  DTISKTELQKFKLKLMSELVSNGVQIYQFPTDDESISKINSSMNGQLPFAVVGSMEEVKLGNKMVKARQY
          DT.SK..LQKFKLKLM.ELVSNG.Q.YQFPTDDE.....NSSMNG.LPFAVVGS.EEVKLGNKMVKAR.Y
Retrocopy DTLSKCDLQKFKLKLMNELVSNGIQFYQFPTDDETVAQLNSSMNGHLPFAVVGSTEEVKLGNKMVKARRY

Parental  PWGIVQVENETHCDFVKLREMLICTNMEDLREQTHTRHYELYRRCKLEEMGFKDVGPENKPVSLQEAYEI
          PWGIVQVENE.HCDFVKLREMLICTNMEDLREQTH.RHYE.YRRCKLEE.GFK.V.PE.KP.S..E..EI
Retrocopy PWGIVQVENENHCDFVKLREMLICTNMEDLREQTHIRHYENYRRCKLEETGFKEVCPEKKPLSVLESQEI

Parental  KRHEFYGERQRKEEEMKQMFVQRVKEKESILKEAERELQAKFEHLKRLHQEERMKLEEKRRYLEEEINAF
          KR.....E.QRKEEEMKQ.FV.RVKEKE.ILKEAERELQAKFEHLKRLHQEER.KLEE.RR.LEEEI.A.
Retrocopy KRYDSFCELQRKEEEMKQLFVKRVKEKEAILKEAERELQAKFEHLKRLHQEERIKLEERRRNLEEEISAL

Parental  AKKKAASEL
          .K.KAA.EL
Retrocopy GKRKAACEL

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_93 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_93 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 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000009949	1 retrocopy	retro_chof_2159,
Monodelphis domestica	ENSMODG00000003104	1 retrocopy	retro_mdom_93 ,
Monodelphis domestica	ENSMODG00000011825	1 retrocopy	retro_mdom_224,
Monodelphis domestica	ENSMODG00000016041	1 retrocopy	retro_mdom_888,
Monodelphis domestica	ENSMODG00000021167	1 retrocopy	retro_mdom_1672,
Sarcophilus harrisii	ENSSHAG00000007189	1 retrocopy	retro_shar_59,