RetrogeneDB ID: retro_mdom_1597

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 6:99593816..99594256(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000021248
• Aliases: None
• Description: None

Sequence

>retro_mdom_1597
ATGTCTCTTCCAACACAATGGATAGCAGTACCACCACCAATGAATTGTCCACCTGGACTGGAACCCTTAATTCAGCTAGA
CCAGTTACTGATCCATCAGCAAACTGAACGTCTGGAAGTACTCAAAGGGTTTGAAACCAACAACAAATATGAAATTAAGA
ATAGCCTTAGGCAGAGAGTTTACTTTGTAGTGGAGGAACATGATTTCTGTACTCCAAACTGCTATGGATTCTCAAGACTT
TTGTTATAAAGATTCTGAGCTATTCAAACATGGAAGCAATACGCCTTGAGAGACCTCTGAGATGTACTTCCTGTTGTTTC
CCCTGCTGCCTGCAGAAGGGGGAAATAGAATCACCTCCTGGTGTACCAATAAGTTAAGTTGTCCAAACATGGCACCCTTT
TCTGCCAAAGTTTGCAGTTCTAAATGAGAGCCATGTTGAA

Alignment

ORF - retro_mdom_1597 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.68 %
• Parental protein coverage: 51.22 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MPPPTQWIPAPPPMNCPPGLEYLTQIDQLLIHQQIELLEVLTGFETNNKYEIKNSLGQRVYFAAEENDFC
          M..PTQWI..PPPMNCPPGLE.L.Q.DQLLIHQQ.E.LEVL.GFETNNKYEIKNSL.QRVYF..EE.DFC
Retrocopy MSLPTQWIAVPPPMNCPPGLEPLIQLDQLLIHQQTERLEVLKGFETNNKYEIKNSLRQRVYFVVEEHDFC

Parental  TLNCCG-SLRPFVIKILDYSNREVIQIERPLRCSSCYYPCCLQKMEIQSPPGVPIGYVVQKWHPFLPKFA
          T.NC.G..L..FVIKIL.YSN.E.I..ERPLRC.SC..PCCLQK.EI.SPPGVPI..VVQ.WHPFLPKFA
Retrocopy TPNCYG<ILKTFVIKILSYSNMEAIRLERPLRCTSCCFPCCLQKGEIESPPGVPIS*VVQTWHPFLPKFA

Parental  VLNEHQEE
          VLNE...E
Retrocopy VLNESHVE

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_1597 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1597 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 5 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Felis catus	ENSFCAG00000027005	1 retrocopy	retro_fcat_797,
Myotis lucifugus	ENSMLUG00000008749	1 retrocopy	retro_mluc_1779,
Monodelphis domestica	ENSMODG00000021248	2 retrocopies	retro_mdom_1443, retro_mdom_1597 ,
Mus musculus	ENSMUSG00000032369	1 retrocopy	retro_mmus_462,
Rattus norvegicus	ENSRNOG00000033412	1 retrocopy	retro_rnor_1962,