RetrogeneDB ID: retro_mdom_553

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 1:279876505..279877161(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SCCPDH
• Ensembl ID: ENSMODG00000006356
• Aliases: None
• Description: saccharopine dehydrogenase (putative) [Source:HGNC Symbol;Acc:24275]

Sequence

>retro_mdom_553
TACTAGAAGTATCATGAAAAAGCTGTAGGAAAAGGAGTAAATATCAGTGGAAGCATTGGCCTTGATTCCATTTCAGCGGA
TCTGAGAGTATTATAAGTTGAAAGTACTCTTACTGCTGTTGAAAATTTCCAGTCAGGAAATTCAGGACCTGAGGGAATGT
GTATTTATGGTGGCACTTGGAAGTAAGGGGTTTTGGTGTTTTGGTGACCAAAAGAAAACTATAAAAAAGAGTCAAATATG
AAATCTTTCCTGTTATTAATGCAAAGTGGAAAAGATGGACTGTTTTGTCACTGTAGTGAATTGAGTGAATATTCTATTCA
ATTAATGGGAATTGATATCTCCTTTGTGAAAAAGATACAGCACTTCTTGTATGAAAATTTGCAGGGAAACACCAGTGTAG
TATACTGCTTATATAATTGTTGGAGACCTCACTTCTGTTACTAAGCTGATGATTGCAGTACTTTCCTCTTTACTTTTTGT
GAAGTTTAGTATTGGAAAACAATTTCTGTTAAATCTCCTTGGTTTTTCTCCTTTGGGCATTTCTCACACAAAACACAACA
CAAAAACAGATGTTTGATACTTCATTTACATTTATACTTTTTGGTCAAGGGTATAGTCAGGAATTTACTACAAAATATGG
CAGTCCTAATATTAAA

Alignment

ORF - retro_mdom_553 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.8 %
• Parental protein coverage: 51.25 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 7

Retrocopy - Parental Gene Alignment:

Parental  YWKYHEKAAEKGLYIIGSSGFDSIPADLGVLFTRNKLKGTLTAVESFLKVNSGPEGMCIHDGTWKSAV-H
          Y.KYHEKA..KG..I.GS.G.DSI.ADL.VL.....L....TAVE.F...NSGPEGMCI..GTWK..V..
Retrocopy Y*KYHEKAVGKGVNISGSIGLDSISADLRVL*VESTL----TAVENFQSGNSGPEGMCIYGGTWK*GV>W

Parental  GFGDQKRLKSLRK-QSNMKP-LPVVGAKLKRRWPV-SYCSELHEYSIPFMGADASVVKRTQRFLYENLQ-
          .FGDQK..K...K..SNMK...PV..AK.K.RW.V...CSEL.EYSI..MG.D.S.VK..Q.FLYENLQ.
Retrocopy CFGDQK--KTIKK<ESNMKS<FPVINAKWK-RWTV>CHCSELSEYSIQLMGIDISFVKKIQHFLYENLQ>

Parental  ETPVQYAAYVNVGGLTSIIKLMFAGLFFLFFVKFNFGRQLL-VKFPWFFSFGYFSE-QGPTQKQMDDSSF
          ETPV.Y.AY..VG.LTS..KLM.A.L..L.FVKF..G.Q.L.VK.PWFFSFG.FS..Q..TQKQM.D.SF
Retrocopy ETPV*YTAYIIVGDLTSVTKLMIAVLSSLLFVKFSIGKQFL<VKSPWFFSFGHFSH<QNTTQKQMFDTSF

Parental  TFTFFGQGYSQDHTTKHGKPNIK
          TF..FGQGYSQ..TTK.G.PNIK
Retrocopy TFILFGQGYSQEFTTKYGSPNIK

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	0.39 RPM	0.00 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_553 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_553 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
Canis familiaris	ENSCAFG00000015884	1 retrocopy	retro_cfam_842,
Dasypus novemcinctus	ENSDNOG00000016354	1 retrocopy	retro_dnov_1482,
Monodelphis domestica	ENSMODG00000006356	1 retrocopy	retro_mdom_553 ,