RetrogeneDB ID: retro_mdom_183

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: Un:58258842..58260123(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMODG00000022672
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000010034
• Aliases: None
• Description: None

Sequence

>retro_mdom_183
CTCTCCGAACCCATCTTCGGCCGCTGGACCCAAGGCTTTGTGTTCAGCGAGTCCGAGGGCTCGGCCCTGGAGCAGTTCGA
AGGGGGCCCCTGCGCCGTCATCGCGCCGGTGCAGGCCTTCCTCCTGAAGCAGCTGCTCTTCACCTCGGAGAAGCCCTCCT
GGAGGGAGTGCCGAGAGGACGAGCGGAAGGACCTGCTCTGCCACACCCTGAGTGACATCCTGGAGGCGGCCGGCTTCGAC
TCCTCGGGCCCCTACTGCCTGGTAGCCTGGCTCCGAGGCAAGGAGGCCCTGGCCCTGGCCAACCGGCCCACAGCTGCTGG
TGAGTGCAGCTGCCCCGAGGGCTTCTCCCCGGGCCTGGCGGGCCAGGAGCAGCTGGGCTTCGAGCGCTTCCACTCGCTCA
TCCACAAGATGTCGTTCAAAAGCTTCCCGGAGCTCAAAGACGCCATCTGGGAGCAGTACTCCATGTGGGCCAACAAGTTC
GGGGTGCTGCTCTTCCTCTACTCCGTCATCCTGACCAAAGGCATCGAGAACATCAAGAACGAGATCGAGGACTCGGCCGA
GCCCCTGATCGATCCCGTCTACGGGCATGGGAGCCAGAGCCTGATTAACCTGCTGCTGACCGGCCACGCCGTTTCCAACG
TGTGGGACGGAGACAAGGAGTGCTCCGGAATGAAGCTCCTGGGAATCCACAAGCAAGCCACCGTGGGCTTCCTGACCCTC
ATGGAGTCGCTCAGTTACTGCAAGGTGGGCTCTTACCTGAAGTCCCCCAAGTTCCCCATTTGGATTGTGGGGAGTGAAAC
CCACCTTACTGTCTTCTTTGCCAAAGACATGGCCTTGGTGGCTCCCGAGACGCCTTCTGAGCAAGCCCGCAGGATTTTCC
AGAACTATGACCCTGAGGATAACGGATTCATTCCCGACTCGCTGCTGGAGGATGTGATGAAAGCCCTGGACCTGGTTTCA
GATCCTGAGTATGTCAACCTCATGAAAAACAAACTGGACCCTGAAAGGCTGGGAATCATCTTGCTGGGGCCCTTCCTTCA
AGAGTTCTTTCCAGAACAAGACTCCAGCATCCCGGAGTCCTTCACCGTGTATCACTACAATGGCCTCAAGCAGTCCAACT
TCAACGAGAAAGTCATGTATGTAGAAGGCACTGCAGTCGTGATGGGTTTTGAAGACCCGCTGCTCCAGACAGACGACACT
CCCGTTAAACGCTGTCTCCAAACCAAGTGGCCATCCATAGAATTGCTCTGGACCACCGATCGGTCTCCTTCACTCAACTA
A

Alignment

ORF - retro_mdom_183 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.62 %
• Parental protein coverage: 95.51 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LSDTIFCRWTQGFVFSESEGSALEQLEGGPCAVIAPVQAFLLKKLLFTSEKSSWRDCQEEERKDLLCHTL
          LS..IF.RWTQGFVFSESEGSALEQ.EGGPCAVIAPVQAFLLK.LLFTSEK.SWR.C.E.ERKDLLCHTL
Retrocopy LSEPIFGRWTQGFVFSESEGSALEQFEGGPCAVIAPVQAFLLKQLLFTSEKPSWRECREDERKDLLCHTL

Parental  CDILETALSDNSGSYCLAAWIRGKTTEDTASISEGPAESSCQEEHTSALA-VEELGFERFHSLLHKRSFK
          .DILE.A..D.SG.YCL.AW.RGK.....A.......E.SC.E.....LA..E.LGFERFHSL.HK.SFK
Retrocopy SDILEAAGFDSSGPYCLVAWLRGKEALALANRPTAAGECSCPEGFSPGLAGQEQLGFERFHSLIHKMSFK

Parental  SFPELKEAIWDQYSMWANKFGVLLFLYSVILTKGIENIKNEIEDSTEPLIDPVYGHGSQSLINLLLTGHA
          SFPELK.AIW.QYSMWANKFGVLLFLYSVILTKGIENIKNEIEDS.EPLIDPVYGHGSQSLINLLLTGHA
Retrocopy SFPELKDAIWEQYSMWANKFGVLLFLYSVILTKGIENIKNEIEDSAEPLIDPVYGHGSQSLINLLLTGHA

Parental  VSNVWDGDRECSGMKLLGIHKQAAIGFLTLMESLRYCKVGSYLKSPKFPIWIVGSETHLTVFFAKDMALV
          VSNVWDGD.ECSGMKLLGIHKQA..GFLTLMESL.YCKVGSYLKSPKFPIWIVGSETHLTVFFAKDMALV
Retrocopy VSNVWDGDKECSGMKLLGIHKQATVGFLTLMESLSYCKVGSYLKSPKFPIWIVGSETHLTVFFAKDMALV

Parental  APEAPSEQARRVFQTYDPEDNGFIPDTLLEDVMKALDLVSDPEYVNLMKNKLDPEGLGIILLGPFLQEFF
          APE.PSEQARR.FQ.YDPEDNGFIPD.LLEDVMKALDLVSDPEYVNLMKNKLDPE.LGIILLGPFLQEFF
Retrocopy APETPSEQARRIFQNYDPEDNGFIPDSLLEDVMKALDLVSDPEYVNLMKNKLDPERLGIILLGPFLQEFF

Parental  PEQDSSVPESFTVYHYNGLKQSNYNEKVMYVEGTAVVMGFEDPMLQTDDTPVKRCLQTKWPYIELLWTTD
          PEQDSS.PESFTVYHYNGLKQSN.NEKVMYVEGTAVVMGFEDP.LQTDDTPVKRCLQTKWP.IELLWTTD
Retrocopy PEQDSSIPESFTVYHYNGLKQSNFNEKVMYVEGTAVVMGFEDPLLQTDDTPVKRCLQTKWPSIELLWTTD

Parental  RSPSLN
          RSPSLN
Retrocopy RSPSLN

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_183 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_183 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 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Monodelphis domestica	ENSMODG00000010034	1 retrocopy	retro_mdom_183 ,
Sarcophilus harrisii	ENSSHAG00000012259	1 retrocopy	retro_shar_92,