RetrogeneDB ID: retro_mdom_269

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 8:266670036..266671542(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMODG00000024045
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000017729
• Aliases: None
• Description: None

Sequence

>retro_mdom_269
ATGGAGACAATTTTGGAGCAGCAGAGGCACTACCATGATGAAAAGGAGCGACTCGTGGATGTTATGGCCAAGGAAATGCT
CATTAAGAAGTCCACACTCCAGGACCAGATCAATTCTGATCATCTCATGAGGGCTATGCAGGTCAGGTATATGGAAGCCA
GTGGGAAACTGAGAGATTTGTATAATGACAAGGATGGATTAAGAAAGGAGGAGCTCAGTGCTATTTCAGGGCCAAATGAA
TTTGCAGAATTCTATAATAGACTCAAAAAGATAAAAGATTTCCACCAGAAGCACCCAAAGCAGATTTGTGTGCCAATGTC
AGTGGAATTTGAGGAGCTCCTGAAAGCCAGAGAAAATCTTAGTGAAGAAGCACAAAACTTGGTGGAGTTCACTGATGAAG
AAGGCTATGGCCATTACCTGGATCTTCATGACTGTTACCTTAAGTACATCAACCTAAAAGCATCTGAGAAACTGGATTAT
ATCACATATCTGTCCATCTTTGATCAGTTATTTGATATTCCAAAGGAAAGGAAGAATGCAGAGTACAAGAGGTACCTGGA
GATGCTGCTTGAGTACCTCCAAGACTACACAGATAGAGTGAAGCCCCTGCAAGACCAAAATGAGCTGTTTGGGAAGATTC
AGAAAGAATTTGAGAAGAAGTGGGACAATGGTACCTTTCCAGGCTGGCCCAAAGAGACAAGTAGTGCACTGACCCATGCT
GGAGCCCACCTTGACCTCTCTACATTTTCTTCCTGGGAGGAGTTGGCCTCCTTGGGTCTGGACAGACTGAAATCTGCACT
CTTGGCTTTAGGACTGAAATGTGGTGGGACACTAGAAGAGCGAGCCCAGAGACTGTTCAGCACTAAAGGCAAGTCCCTGG
AATCACTTGACTCCTCTCTGTTTGCTAAGAATTCTAAATCAAAGGGAACCAAAAGGGGCACTGAGAGGAATAAAGACATT
GCTTTCTTTGAAGCCCAGATTTATGAATATGTAGAGATTCTTGGGGAACAGCGCCATCTCACTAGAGAAAATGTGCAGCG
CAAACAGGCCCAGACAGGAGAGGAAAGAATGGGAGAAGAGGAAGAAGAGATCAGTGAGAGTGAAAGTGACAATGAAGAGA
ATGAGATTATCTACAACCCCAAAAACCTGCCCCTGGGTTGGGATGGCAAACCCATTCCCTACTGGTTGTATAAGCTGCAT
GGCCTCAATATAAACTATAACTGTGAGATATGTGGGAACTACACCTACCAAGGACCCAAGGCCTTTCAGCGGCACTTTGC
GGAATGGCGCCATGCTCATGGCATGAGGTGCTTGGGCATTCCAAATACAGCTCATTTTGTTCATGTGACCCAGATTGAAG
ATGCTATCTCTTTATGGGGCAAATTGAAATTGCAGAAGGTTTCAGAACAGTGGCAGCCTGACATGGAGGAGGAATATGAG
GATTCCAGGGGAAATGTTGTGAATAAGAAGACATATGAGGACTTGCAACGCCAGGGACTTCTTTAG

Alignment

ORF - retro_mdom_269 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.9 %
• Parental protein coverage: 66.67 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  METILEQQRRYHEEKERLMDVMAKEMLIKKSTLRDQINSDHRTRAMQDRYMEVSGNLRDLYDDKDGLRKE
          METILEQQR.YH.EKERL.DVMAKEMLIKKSTL.DQINSDH..RAMQ.RYME.SG.LRDLY.DKDGLRKE
Retrocopy METILEQQRHYHDEKERLVDVMAKEMLIKKSTLQDQINSDHLMRAMQVRYMEASGKLRDLYNDKDGLRKE

Parental  ELSAISGPNEFAEFYNRLKQIKEFHRKHPNEICVPMSVEFEELLKARENPSEEAQNLVEFTDEEGYGRYL
          ELSAISGPNEFAEFYNRLK.IK.FH.KHP..ICVPMSVEFEELLKAREN.SEEAQNLVEFTDEEGYG.YL
Retrocopy ELSAISGPNEFAEFYNRLKKIKDFHQKHPKQICVPMSVEFEELLKARENLSEEAQNLVEFTDEEGYGHYL

Parental  DLHDCYLKYINLKASEKLDYITYLSIFDQLFDIPKERKNAEYKRYLEMLLEYLQDYTDRVKPLQDQNELF
          DLHDCYLKYINLKASEKLDYITYLSIFDQLFDIPKERKNAEYKRYLEMLLEYLQDYTDRVKPLQDQNELF
Retrocopy DLHDCYLKYINLKASEKLDYITYLSIFDQLFDIPKERKNAEYKRYLEMLLEYLQDYTDRVKPLQDQNELF

Parental  GKIQNEFEKKWDNGTFPGWPKETSSALTHAGAHLDLSAFSSWEELASLGLDRLKSALLALGLKCGGTLEE
          GKIQ.EFEKKWDNGTFPGWPKETSSALTHAGAHLDLS.FSSWEELASLGLDRLKSALLALGLKCGGTLEE
Retrocopy GKIQKEFEKKWDNGTFPGWPKETSSALTHAGAHLDLSTFSSWEELASLGLDRLKSALLALGLKCGGTLEE

Parental  RAQRLFSTKGKSLESLDSSLFAKNPKSKGTKRDTERNKDIAFLEAQIYEYVEILGVKR
          RAQRLFSTKGKSLESLDSSLFAKN.KSKGTKR.TERNKDIAF.EAQIYEYVEILG..R
Retrocopy RAQRLFSTKGKSLESLDSSLFAKNSKSKGTKRGTERNKDIAFFEAQIYEYVEILGEQR

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_269 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_269 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 12 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000001262	1 retrocopy	retro_amel_485,
Canis familiaris	ENSCAFG00000003222	1 retrocopy	retro_cfam_176,
Callithrix jacchus	ENSCJAG00000002176	1 retrocopy	retro_cjac_4109,
Cavia porcellus	ENSCPOG00000008660	1 retrocopy	retro_cpor_658,
Homo sapiens	ENSG00000183431	2 retrocopies	retro_hsap_2441, retro_hsap_937,
Macropus eugenii	ENSMEUG00000002534	3 retrocopies	retro_meug_1135, retro_meug_1346, retro_meug_642,
Macaca mulatta	ENSMMUG00000023199	1 retrocopy	retro_mmul_631,
Monodelphis domestica	ENSMODG00000005979	1 retrocopy	retro_mdom_1045,
Monodelphis domestica	ENSMODG00000017729	1 retrocopy	retro_mdom_269 ,
Nomascus leucogenys	ENSNLEG00000011720	1 retrocopy	retro_nleu_2775,
Pan troglodytes	ENSPTRG00000000559	2 retrocopies	retro_ptro_1411, retro_ptro_649,
Sorex araneus	ENSSARG00000014204	1 retrocopy	retro_sara_407,