RetrogeneDB ID: retro_mdom_758

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 2:366226567..366227223(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CAMLG
• Ensembl ID: ENSMODG00000014251
• Aliases: None
• Description: calcium modulating ligand [Source:HGNC Symbol;Acc:1471]

Sequence

>retro_mdom_758
AGGAAATTGCTGATGAACTTAGTATTGTGAACCAACCAAACCCTGGGCTTCCACTGTAGTAAGAGCACCTCAGGTGAGAA
GCTGGGGCCCTCTGAATTAGAAGTGAACAAAGAACAAAGCAGCATGACACTGATAAAATAAATTTCCTTGCTGTTCCCTC
AGTTTCAAATTGAGTTATGCTGGGTAATTCAATGAGAACAGAAACAGTGAACCAGCAGGGTGGCATTGCAAAGTTCAAGG
GAACCCAATTGGTAGATAAATAGGGCACTTTAATCAATCCACCTGAGAGCAGTAATGATGGTAAGTCTTGAACTCTGACA
CTGAAAAAGAAGGGTTCTCATAGCTGACACTGTCCAGAGTAACTCCTAGCATTGCTTAGCCAGTATCTTTCCAGGTTTGA
TGAAAACAATGAAATTAAGGCAATAATTGATTACTGAGAAACCTAGTCAAGAGAATGGGAATTAAAGAAGAATTTTGATA
CTTTTCAAATTTTCAGATTGGTAGGATATGCATTTCTTGCCCTTGTAGTTCTGGTTTTTGTGTATAAATATTTGTCCATA
TTGATTCCATTTGTTACAATTTGCATGGGATTCTTTAAGTACTTACTAAAGAATGAAAAGGTGAAGATGAAAGTGCTAAC
TGCTACAATTTTTATT

Alignment

ORF - retro_mdom_758 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.65 %
• Parental protein coverage: 73.11 %
• Number of stop codons detected: 7
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  RKLLMNSEQRINRIMGFHRSGTSAGEKLGPPEDEVNTE-TKQHDTDKLNSLAVPSVSKRVVLGDSTSTGT
          RKLLMN.....N...GFH.S....GEKLGP.E.EVN.E.TKQHDTDK.N.LAVPSVS..V.LG.S..T.T
Retrocopy RKLLMNLVL*TNQTLGFHCSKSTSGEKLGPSELEVNKE<TKQHDTDKINFLAVPSVSN*VMLGNSMRTET

Parental  LEHQDGTTEFKGTQLVDKKDPLINPPESNNDG-NLELRHRKRGDLTTDTIQRSSQHG-LDQYLSRFDE-A
          ...Q.G...FKGTQLVDK...LINPPES.NDG..LEL.H.KR..L..DT.Q..S.H..L.QYLSRFDE..
Retrocopy VNQQGGIAKFKGTQLVDK*GTLINPPESSNDG>SLEL*H*KRRVLIADTVQSNS*HC<LSQYLSRFDE>T

Parental  MKLRKQLISEKSSQENGS-TGEEFDTFRIFRLVGCALLALGVRAFVCKYLSIFAPFLTLQLAFMGLSKYF
          MKLR..LI.EK.SQENG......FDTF.IFRLVG.A.LAL.V..FV.KYLSI..PF.T.....MG..KY.
Retrocopy MKLRQ*LITEKPSQENGN<LKKNFDTFQIFRLVGYAFLALVVLVFVYKYLSILIPFVTI---CMGFFKYL

Parental  PKSEKKMKTTVLTAALLL
          .K.E.K.K..VLTA....
Retrocopy LKNE-KVKMKVLTATIFI

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	93.93 RPM
SRP007412_cerebellum	0.00 RPM	86.51 RPM
SRP007412_heart	0.00 RPM	43.26 RPM
SRP007412_kidney	0.00 RPM	57.94 RPM
SRP007412_liver	0.00 RPM	59.41 RPM
SRP007412_testis	0.00 RPM	153.81 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_758 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_758 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	ENSMEUG00000013676	1 retrocopy	retro_meug_1965,
Monodelphis domestica	ENSMODG00000014251	1 retrocopy	retro_mdom_758 ,
Otolemur garnettii	ENSOGAG00000003580	1 retrocopy	retro_ogar_2062,