RetrogeneDB ID: retro_mdom_2008

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: X:14355428..14356238(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000025406
• Aliases: None
• Description: None

Sequence

>retro_mdom_2008
CTGGAAACAGAGGCACATGAACTAAAACAAGAAAATAGTATCTTGAAAGTCAGAATTGACCAGCTTGAAAATGAGGCAAA
GAAGATGAAAGATGACCTAAAATGAAAATCATACCAAAAGGAGGATGGCCAAAAAGCCAGAAATTAAAATCAGTCTTTAA
AAATTAGAATCCAACAACTAGAAGCAAATGACTTTGCAAGGCAACAAGAGTCTATAAAACAAAATCAAAAGAATGAAGAA
TTTGAGGAAAATATAAAACATCTCATTGAGAAAACCATGGACCTTGAAAGCAGATCCAGGAGAGACAGTTTAAGAATTCT
GGACTACCAGAAGATCATGACAAAAAAAAAGCCTGGACATCATTCTACAGAAAATTCACTAAGAAAACTGCCCCAACATT
CTCAAAAAAAGAGGGAAAAGTAGAGATTAAAAGAATCTACAGATCACAATGCCCAGGAATGTCATAGCAAAATTCAAGAA
CTACCAGACCAAGGAAAAAATATTATAAGCTGTTAAGAAGAAGTCATTTAGATACCATGGAACCACAGTGAGAATAACAC
AGGATTTGGATGCATATACACTGAAGGACCTGAAGGCATGGAATATGATATTCCAGAAAGCAAGAGAACTGGGTCTACAA
CCAAGAATCAACTACCCAGCAAACTGATTATATTCTTGCAGGGGAAAGTATGATCATTTAATAAAATAGAAGACTTCTAA
GTGTTCATAAAGAAAAGACCGGACTTAAACAGAAAATTTGATGCTCAAACATAGAACTCAAGAGAATCACCAAAAGGTAA
TTAAGAAAGA

Alignment

ORF - retro_mdom_2008 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.51 %
• Parental protein coverage: 87.3 %
• Number of stop codons detected: 9
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  LKVKINQLGNEAKKMKDEKKEMKDEVKRMKDDLQRKTDQKEKDDQKARDEIQSLRTRIQQLELSDLTRQK
          L......L..E....K........E.K.MKDDL..K..QKE.D.QKAR...QSL..RIQQLE..D..RQ.
Retrocopy LETEAHELKQENSILKVRIDQLENEAKKMKDDLK*KSYQKE-DGQKARN*NQSLKIRIQQLEANDFARQQ

Parental  DTIKQNQKNEKIKENMKHLIHKTDDLENRSRRDNLRII-GLPEDHDKRKS-LDIMLQEIIKENFPNILEQ
          ..IKQNQKNE...EN.KHLI.KT.DLE.RSRRD.LRI..GLPEDHD.....LDI.LQ.I..EN.PNIL..
Retrocopy ESIKQNQKNEEFEENIKHLIEKTMDLESRSRRDSLRIL<GLPEDHDXXXA<LDIILQKIH*ENCPNILKK

Parental  EGINTRSHPVLNPQLTTARNVIAKFKNYQTKEKILQAAKKKSFRYHGTTVRITQDLAASTLKHRKARKNI
          .G....S....N.Q.T..RNVIAKFKNYQTKEKIL.A.KKKSFRYHGTTVRITQDL.A.TLK..KA...I
Retrocopy RG---KSRD*KNLQITMPRNVIAKFKNYQTKEKIL*AVKKKSFRYHGTTVRITQDLDAYTLKDLKAWNMI

Parental  IHTQRKNCLQPRINYPA-KLTIFLQGKVWSFNKIEEFQEFVKKRPHLIRKFDVQAQNSRESSKDNLKR
          ....R...LQPRINYPA.KL.IFLQGKV.SFNKIE.F..F.KKRP.L.RKFD.Q..NSRES.K.N..R
Retrocopy FQKARELGLQPRINYPA<KLIIFLQGKV*SFNKIEDF*VFIKKRPDLNRKFDAQT*NSRESPKGN*ER

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_2008 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_2008 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 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Monodelphis domestica	ENSMODG00000025406	12 retrocopies	retro_mdom_1000, retro_mdom_1578, retro_mdom_1642, retro_mdom_1712, retro_mdom_1767, retro_mdom_1795, retro_mdom_2008 , retro_mdom_502, retro_mdom_770, retro_mdom_842, retro_mdom_900, retro_mdom_972,