RetrogeneDB ID: retro_mdom_233

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 3:117331371..117331890(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMODG00000003590
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000003226
• Aliases: None
• Description: None

Sequence

>retro_mdom_233
ATGGCGGGATCGGTGGCCCAGAGAGAGGCACTTGAGAAACTAGAAGATAGGCATTTAAACAACTTCTTGGGATCTACTTT
CCATGCGGAAGTGTACTTGCCAAGACTGATAATACCATTCTGTGGGCCTATTAAAGGTGGAATGAGGCCAGGCAAGAAGA
TCTTAGTGATGGGTATTGTAGACCTCAACCCTGAGAGTTTCAAGATCAGTTTGACTTGTGGGGACTCCGAAGACCCTCCT
GCCGATGTGGCCATTGAACTGAAAGCTGTATTTACAGATAAGCAACTGATCAGAAATTCTTGTATATCTGGAGAAAGAGG
TGAAGAACAATCAGCAATTCCTTATTTTCCTTTCATCCCAGATCAGCCATTTAGGGTGGAAATTCTTTGTGAACACCCAG
GATTTAGAGTAATTGTAGATGGACGCCAGCTTTTTGATTTTTACCATCGAATTGAATCATTGTCTACAATTGACACAATA
AAGATCAATGGAGACCTCCAGATCACTAAACTTGGCTGA

Alignment

ORF - retro_mdom_233 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.86 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAGSVAEREALEKLEDGHLNNSLGSPVQAEVYFPRLIVPFCGHIKGGMRPGKKILVMGIVDLNPESFKIS
          MAGSVA.REALEKLED.HLNN.LGS...AEVY.PRLI.PFCG.IKGGMRPGKKILVMGIVDLNPESFKIS
Retrocopy MAGSVAQREALEKLEDRHLNNFLGSTFHAEVYLPRLIIPFCGPIKGGMRPGKKILVMGIVDLNPESFKIS

Parental  LTCGDSEDPPADVAIELKAVFTDKQLIRNSCISGERGEEQSAIPYFPFIPDQPFRVEILCEHPRFRVFVD
          LTCGDSEDPPADVAIELKAVFTDKQLIRNSCISGERGEEQSAIPYFPFIPDQPFRVEILCEHP.FRV.VD
Retrocopy LTCGDSEDPPADVAIELKAVFTDKQLIRNSCISGERGEEQSAIPYFPFIPDQPFRVEILCEHPGFRVIVD

Parental  GHQLFDFYHRIETLSAIDTIKINGDLQITKLG
          G.QLFDFYHRIE.LS.IDTIKINGDLQITKLG
Retrocopy GRQLFDFYHRIESLSTIDTIKINGDLQITKLG

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	35.76 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	31.63 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_233 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_233 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 7 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000001067	1 retrocopy	retro_amel_429,
Bos taurus	ENSBTAG00000000156	1 retrocopy	retro_btau_1263,
Dasypus novemcinctus	ENSDNOG00000015222	1 retrocopy	retro_dnov_493,
Felis catus	ENSFCAG00000001209	1 retrocopy	retro_fcat_1280,
Monodelphis domestica	ENSMODG00000003226	2 retrocopies	retro_mdom_1350, retro_mdom_233 ,
Mus musculus	ENSMUSG00000042363	3 retrocopies	retro_mmus_1637, retro_mmus_272, retro_mmus_2942,
Sarcophilus harrisii	ENSSHAG00000011885	2 retrocopies	retro_shar_315, retro_shar_732,