RetrogeneDB ID: retro_mdom_283

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 1:564862182..564863601(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMODG00000011278
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000019540
• Aliases: None
• Description: None

Sequence

>retro_mdom_283
ATGGCACAGTATGACTTTGCTCCAGCCTGGCTTACTTTTCCTACTCCACCATTGTCAACAAAGTCATCACTGAATTTTGA
AAAACATTCTGAAAAGTTCCACAGGGCAGAGAATCATTATGATATAAATCATAGACAATACAATTCTTCAGATGGCTTTG
ATTCTTGTGTTGGACATTCTGATGGAGGAAACTTTGGAAGGAAAGAAAAAAATGGATGGTGTTCACATGCAAGAAATGGT
ACTAAAAACATAAATCATCAAGGGAGATACCATGATGGAAATTCCCGTTCTCTTAGCACTGCTTTTCACTCTGGAAAAAG
CCAAGGACTGCATGAAAGCAATGTCCTGGACAATGAAACTGGGAAAAATGAAGACAAGGAAGAACTCAAACAATTTGAGG
TTGAAGATTTTCCACCTTTAAATCCTGAATATGAGAGAAAGACAAATCAGAATAAATCTTTAGCTGCAGGTGTATGGGAG
TATCCTCTGAATCCTAAATCTAGAGCTCCAGGAATGCTGGACATTAAAAAAGGCAGTACAAAAGATTTACAGATATCTGG
ATTCCCTGAAGTAGGAAATCTTCATTCTCAGCAAGTTAAAAATGAAACTGGTACTAGTGTTTATAAAGGATTAATTCCTA
AACTTGCTATTCCACATAGAAAGTCTACACAATGGAAACGCCGAACTAAAGAAAATAAAATTGGAACTCCCTTCCCTCGT
GAGCCTATATATGGCATTGGCAAATTTAATGCCTTCAAATCAACTGCCAAGAATTTTAGTGTATCAACAAATTCAGTTAA
GAAGTGTAATTGCTCAAAGTCCTCTTCTTTTCTGGACAAATTTAATCAGCCTCATCTAACCAAACTCACCCAGATGAGTA
CTGTTAAGAAGAAAGAATGCTTAAAAGCATTGAAAAGGGACAGAGTGAAGAAGGAGCAGAAAGATGGAAGTCACATGGGG
CCAGAGAAGGATGATGACTCATTTAATTTGCATAATAGCAACAACACTCACCATGAAAGTGACATAAACCCAAATTCTGA
TGACAATGAAATTTTGCAGGAGAATGGCAAATTGACCTCTATGATTTCCCAACCGATCATTCAGCCTTCTACCTTTCCAC
TAGCTGATGTCTTTTCAAGTTCAGTTGAGGAAGAGCATAGGCTATTAAAGGAGATGGGTTGGCAGGAAGACAGTGAAAAT
GATGAAACATGTGCTCCCTTAACAGAGGATGAGATGAGGGAATTCCAAGTTATTTGTGAACAGTTACAGAAGAATGGCCT
TAGAAAAAATGGTATTTTGAAAAATAGCCTAATCTCTGACTTCAAATTTGGACCCTGGAAAAACAGCACTTTCAAACCCA
CTTTTGAGAATGATGACACAGAGACAAGCAGCAGTGACACATCAGATGATGATGATTAT

Alignment

ORF - retro_mdom_283 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.57 %
• Parental protein coverage: 99.79 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAQHDFAPAWLNFPTPPSSTKSSLNFEKHSENFQWAENRYDVNRRRHNSSDGFDSGIGRSNGGNFGRKEK
          MAQ.DFAPAWL.FPTPP.STKSSLNFEKHSE.F..AEN.YD.N.R..NSSDGFDS..G.S.GGNFGRKEK
Retrocopy MAQYDFAPAWLTFPTPPLSTKSSLNFEKHSEKFHRAENHYDINHRQYNSSDGFDSCVGHSDGGNFGRKEK

Parental  NGWRSHGRNGTENINHRGGYHGGSSRSRSSAFHSGKSQGLHENNVPDNETGKKEDKEERKQFEAEDFPSL
          NGW.SH.RNGT.NINH.G.YH.G.SRS.S.AFHSGKSQGLHE.NV.DNETGK.EDKEE.KQFE.EDFP.L
Retrocopy NGWCSHARNGTKNINHQGRYHDGNSRSLSTAFHSGKSQGLHESNVLDNETGKNEDKEELKQFEVEDFPPL

Parental  NPEYEREPNQNKSLAAGVWEYPLNPKSRAPRMLVIKKGSTKDLQISGFPAVGNLHSQPVKNGTGPSVYKG
          NPEYER..NQNKSLAAGVWEYPLNPKSRAP.ML.IKKGSTKDLQISGFP.VGNLHSQ.VKN.TG.SVYKG
Retrocopy NPEYERKTNQNKSLAAGVWEYPLNPKSRAPGMLDIKKGSTKDLQISGFPEVGNLHSQQVKNETGTSVYKG

Parental  LVPKPAAPPTKPTQWKSQTKENKVGTPYPHESTYGIGNFNAFKSTAKNFSASTNSVKECNRSNSSSPVDK
          L.PK.A.P..K.TQWK..TKENK.GTP.P.E..YGIG.FNAFKSTAKNFS.STNSVK.CN.S.SSS..DK
Retrocopy LIPKLAIPHRKSTQWKRRTKENKIGTPFPREPIYGIGKFNAFKSTAKNFSVSTNSVKKCNCSKSSSFLDK

Parental  LNQPRLTKLTRMRTDKKSEFLKALKRDRVEEEHEDGSHMGPEKDDDSFNLHNSNNTHHERDINRNFDENE
          .NQP.LTKLT.M.T.KK.E.LKALKRDRV..E..DGSHMGPEKDDDSFNLHNSNNTHHE.DIN.N.D.NE
Retrocopy FNQPHLTKLTQMSTVKKKECLKALKRDRVKKEQKDGSHMGPEKDDDSFNLHNSNNTHHESDINPNSDDNE

Parental  ISQENGN-ASMISQQIIRSSTFPQADVLSSSLEAEHRLLKEMGWQEDSENDETCAPLTEDEMREFQVISE
          I.QENG...SMISQ.II..STFP.ADV.SSS.E.EHRLLKEMGWQEDSENDETCAPLTEDEMREFQVI.E
Retrocopy ILQENGKLTSMISQPIIQPSTFPLADVFSSSVEEEHRLLKEMGWQEDSENDETCAPLTEDEMREFQVICE

Parental  QLQKNGLRKNGILKNGLICDFKFGPWKNSTFKPTFENDDTETSSSDTSDDDD
          QLQKNGLRKNGILKN.LI.DFKFGPWKNSTFKPTFENDDTETSSSDTSDDDD
Retrocopy QLQKNGLRKNGILKNSLISDFKFGPWKNSTFKPTFENDDTETSSSDTSDDDD

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	0.12 RPM	0.00 RPM
SRP007412_cerebellum	0.00 RPM	0.00 RPM
SRP007412_heart	0.00 RPM	0.00 RPM
SRP007412_kidney	1.32 RPM	0.00 RPM
SRP007412_liver	0.00 RPM	0.00 RPM
SRP007412_testis	0.59 RPM	0.00 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_283 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_283 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
Callithrix jacchus	ENSCJAG00000015104	1 retrocopy	retro_cjac_3961,
Microcebus murinus	ENSMICG00000014678	1 retrocopy	retro_mmur_1198,
Myotis lucifugus	ENSMLUG00000007462	1 retrocopy	retro_mluc_155,
Monodelphis domestica	ENSMODG00000019540	1 retrocopy	retro_mdom_283 ,
Otolemur garnettii	ENSOGAG00000013991	1 retrocopy	retro_ogar_1077,
Ictidomys tridecemlineatus	ENSSTOG00000003057	1 retrocopy	retro_itri_1678,