RetrogeneDB ID: retro_mdom_1764

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 7:20102439..20103194(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000002633
• Aliases: None
• Description: None

Sequence

>retro_mdom_1764
AGCTTAAAAGACAAAATTGCCCAAATGGAAAAAGAGGCACAGAAATAAAATGAGGTAATAAGCAAATTGGAGACCGGAAC
TGACCTGCTAGAAGCCATGAAAAGCAGGATAGACCAAACCAAGAAGGGAAATCAATCTAGAATTGGGCAAGTAGAAGCTA
ATGATCTCAGAAGACAGCAAGAACTAAGAAAGCAAAATCAAAAGAATGAAAAAATAGAAGGAAACATGAAATATGTCATT
GAAAAGACAAGTGACCTTGAAAACAGATGTAGGACAGAAAATTTGAGAATTATTGGTCTACCAGAAAGTCTGGAACAAAA
TAAAAGCCTTGACATTATGTTACAAGAAATTATCCAAGAAAATTACCCTGATATTCTTGAATAATAGGCAAAATAAACAT
TGAAAGAATCCATAGATCACCCCCCACACATTAAATACCCAAAAGACACCTCCAGGTCAAGGAAAAAATAATGCAAGTGG
CCAGAAAAAGACAATTCAGATATCAAGGACCCCCAATCAGGATTACACAGGATCTGGCAGTCTCCACACTAAAGGACCAC
AAGGCTTGGAATATGATATTCAGGAAGGCAAGAGAATTGGGTCTACAACCAAAAATCACCTACCCATCAAAACTGACTCT
ATACTTTCAGGGGAAAGTATGGGCATTTAACAAAAGAAGTTTCTTAGCATTCTTAAAGAGAAGACCAGAACTAAATGGAA
ATTTTGATGTCCAAATATAAAATTCAAGAGAATCA

Alignment

ORF - retro_mdom_1764 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 52.9 %
• Parental protein coverage: 75.88 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SLKTRIKQLEDKQEKHEKVNTKHRETEKRISDQKEKDDEKARDEIQSFKTRIQQLEASDFTRHQHTIKQN
          SLK..I.Q.E....K...V..K...........K...D............RI.Q.EA.D..R.Q...KQN
Retrocopy SLKDKIAQMEKEAQK*NEVISKLETGTDLLEAMKSRIDQTKKGN----QSRIGQVEANDLRRQQELRKQN

Parental  QKNKIIEENMKHLIHKTEDLENRSRRDNLRIIGLLEDYDKRKSLDIILQEIIQENCPDITEQEGK-VEIE
          QKN..IE.NMK..I.KT.DLENR.R..NLRIIGL.E.....KSLDI.LQEIIQEN.PDI.E...K...IE
Retrocopy QKNEKIEGNMKYVIEKTSDLENRCRTENLRIIGLPESLEQNKSLDIMLQEIIQENYPDILE**AK<INIE

Parental  RIHRSTHRNVLAKFKKSQTKEKILQVDKKKSFRKHGTIVRITQDLTASTLKDLQAWNMIFWKARELGLQP
          RIHRS.......K....Q.KEKI.QV..K..FR..G...RITQDL..STLKD..AWNMIF.KARELGLQP
Retrocopy RIHRSPPTH*IPK-RHLQVKEKIMQVARKRQFRYQGPPIRITQDLAVSTLKDHKAWNMIFRKARELGLQP

Parental  RIIYTAKLTIFLQGKVWSFNKIEDFQAFVKKRPDMNRKFDAEAQNSRES
          .I.Y..KLT...QGKVW.FNK...F.AF.K.RP..N..FD....NSRES
Retrocopy KITYPSKLTLYFQGKVWAFNK-RSFLAFLKRRPELNGNFDVQI*NSRES

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_1764 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1764 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 1 parental gene, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Monodelphis domestica	ENSMODG00000002633	6 retrocopies	retro_mdom_1009, retro_mdom_1362, retro_mdom_1477, retro_mdom_1723, retro_mdom_1764 , retro_mdom_329,