RetrogeneDB ID: retro_mdom_646

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 1:669301730..669302414(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TXNDC15
• Ensembl ID: ENSMODG00000014348
• Aliases: None
• Description: thioredoxin domain containing 15 [Source:HGNC Symbol;Acc:20652]

Sequence

>retro_mdom_646
CTAACTTCTTCTGGAACCAATATTCCTAATAATGGAGAAGAATATAATTTGGTTCTTGAAGCTGTGCCCACAAACCCATC
ATCTAAAGAAGACTCTAATAGTACAGCCAATGTAAAGACTCCACAGGTGAATTGTGAGGAGAGAAATGTTATGGGCTTAG
AAAGTTTCACTTTATAAATTCTAAATGTTTCACAGGACCTGATGGAATTTTTAAACCCAAACAGTAGTGATTGTACATTA
GACTTATTTTATACTCCTTGGTGTCGTTTCGCTGCCAGTCTGGCCCCACATTTTAATTCTTTACTATGAACATTTCCATC
TCTTCATTTTTTGGCATTGAATGCTTCTCAGCACAGCAGTCTGTCTACCCGGTTTGGTACTGTGGCTGTTCCCAACATCT
TGCTATTTCAACGAGCTAAACCAATGGCAAGATTTAATCATACAGATCGGACTCTGGAAACTCTAAAAGCCTTCACTTTT
AATCAGACAGGGATAGAAGCCAGAAATTATGTGGTAGTGACTGAAGATGACCAAAGAGGCCCTCTTTCCAGCACCTTGGT
GAAAAGTGTGGATTGGTTGCTTGTATTTTCTTTATTCTTTTTAATTAGTTTTATTATGTATGCTACTGTTTGGACTGAAA
GTATTCGATGGCTCATTCCAGGACAAGAACATGGACATACTGAA

Alignment

ORF - retro_mdom_646 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.35 %
• Parental protein coverage: 67.26 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LTTSGTNIPDKGEEYNLVLEAVPTSPSSKEDSNSTDNVKTPKVNCEERNVTGLESFTLQILNVSQDLMEF
          LT.SGTNIP..GEEYNLVLEAVPT.PSSKEDSNST.NVKTP.VNCEERNV.GLESFTL.ILNVSQDLMEF
Retrocopy LTSSGTNIPNNGEEYNLVLEAVPTNPSSKEDSNSTANVKTPQVNCEERNVMGLESFTL*ILNVSQDLMEF

Parental  LNPNSSDCTLVLFYTPWCRFSASLAPHFNSLPRAFPSLHFLALDASQHSSLSTRFGTVAVPNILLFQGAK
          LNPNSSDCTL.LFYTPWCRF.ASLAPHFNSL...FPSLHFLAL.ASQHSSLSTRFGTVAVPNILLFQ.AK
Retrocopy LNPNSSDCTLDLFYTPWCRFAASLAPHFNSLL*TFPSLHFLALNASQHSSLSTRFGTVAVPNILLFQRAK

Parental  PMARFNHTDRTLETLKAFIFNQTGIEARNDVVVTEDDQIGPLPSTLVKSVDWLLVFSLFFLISFIMYATV
          PMARFNHTDRTLETLKAF.FNQTGIEARN.VVVTEDDQ.GPL.STLVKSVDWLLVFSLFFLISFIMYATV
Retrocopy PMARFNHTDRTLETLKAFTFNQTGIEARNYVVVTEDDQRGPLSSTLVKSVDWLLVFSLFFLISFIMYATV

Parental  RTESIRWLIPGQEHEHPE
          .TESIRWLIPGQEH.H.E
Retrocopy WTESIRWLIPGQEHGHTE

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	193.46 RPM
SRP007412_cerebellum	0.00 RPM	119.16 RPM
SRP007412_heart	0.00 RPM	153.70 RPM
SRP007412_kidney	0.00 RPM	161.97 RPM
SRP007412_liver	0.00 RPM	194.85 RPM
SRP007412_testis	0.00 RPM	83.29 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_646 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_646 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 2 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Monodelphis domestica	ENSMODG00000014348	3 retrocopies	retro_mdom_1644, retro_mdom_646 , retro_mdom_759,
Tupaia belangeri	ENSTBEG00000015609	1 retrocopy	retro_tbel_2180,