RetrogeneDB ID: retro_mdom_848

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 2:190738440..190738833(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000001863
• Aliases: None
• Description: None

Sequence

>retro_mdom_848
GAACACTTCTCAAAGTTCTTCCGTGAGTAGTCCAAAAATAAGAAGTAACAATGGAGACAATTCTTCAGTATCTAATCAAA
GGGGGAGGACATCTTGTTCTGGAAACTATCCTAAAATCAGAGGTAGAAGCCTGGTCAGATGGCCTGCAGGCTCTGGATGA
AGCTCTTACTGTTGAGAAGGCTGTTAATGAGGAATTGTTGGCTCTGTACATAAGGCAAAGGATCACAAATATCCACATCT
CTGTGGCTTCTTTGATTCTGAATTACTTGATAAACAAGTGAAGGTGATCAAACTGTTTGGAGATTATATCACTAACTTGA
AGAGATTGGGATTGTCTGAAAATAGTCTGGGGAATACATATTTGGCAAGCATACATTAGGAGAAAATTGTCAG

Alignment

ORF - retro_mdom_848 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.37 %
• Parental protein coverage: 72.13 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  KHFSMFFREQS-KKKMKHAEKILQYLTKRGGHPVLENILKSEVQYWSDGLQALEEALVIEKAVNEELLIL
          .HFS.FFRE.S..K.....E.ILQYL.K.GGH.VLE.ILKSEV..WSDGLQAL.EAL..EKAVNEELL.L
Retrocopy EHFSKFFRE*S<QK*EVTMETILQYLIKGGGHLVLETILKSEVEAWSDGLQALDEALTVEKAVNEELLAL

Parental  -CNKAKEHEDPHLCGFLESELLDEQVKIIKLLGDYITNLKRLGMPENR-SGEYIFDKYTLGKTCQ
          ...KAK.H..PHLCGF..SELLD.QVK.IKL.GDYITNLKRLG..EN..SGEYIF.K.TLG..CQ
Retrocopy <VHKAKDHKYPHLCGFFDSELLDKQVKVIKLFGDYITNLKRLGLSENS<SGEYIFGKHTLGENCQ

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_848 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_848 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 4 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000004685	1 retrocopy	retro_acar_188,
Monodelphis domestica	ENSMODG00000001863	5 retrocopies	retro_mdom_1250, retro_mdom_302, retro_mdom_551, retro_mdom_789, retro_mdom_848 ,
Monodelphis domestica	ENSMODG00000007582	9 retrocopies	retro_mdom_1134, retro_mdom_122, retro_mdom_1294, retro_mdom_1407, retro_mdom_1742, retro_mdom_300, retro_mdom_564, retro_mdom_643, retro_mdom_809,
Monodelphis domestica	ENSMODG00000013730	3 retrocopies	retro_mdom_1989, retro_mdom_6, retro_mdom_745,