RetrogeneDB ID: retro_mdom_1767

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 7:35857535..35858253(-)
• 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_1767
CTCCATAGAAAATTGGACCAGAAAGAGAAGGATGACCAAAAAGCCAGGTATGAAATCCAGTTTTTGAGAACCAGAATACA
ACTAGAATTAAGTGACCTCACAAGGCATCAGGGCAGTATAAAACAAAACCAAAAGAATTAAAAAATTGCGGAAAATATGA
AGCATCTCATTCACAAAACAGAGGATTTAGAAAATCATTCGAGGAGAGACAATTTAAGAATCATTGGTCTACCAGAAGAC
CATGACAAAAGAAAAAGCCTGGACACAATACTACAGGAAATTATTCAAGAAAACTGCCCTGATATTCTAGAACAAGAGGA
AAAAGTGGAAATTGAAAGAATTCACAGATCACCTCCTGTACTTAATCCCAGGAATGTTATAGCCAAATTCAAGAACTATC
AGACCAAAGAAAAAATATTACAAGCTGCCAAGAAGAAGTCCTTCAGATACCATGGAACCACAGTGAGGATAATGCAGGAT
CTGGATGTATCCACACTGAATGACTGAAAAGCATGGAATATGATATTCTGGAAAGCAAGGGATCTAGGTCTACAACCAAG
AATAAATTACCCAGCAAAACTGACTATATTCTTACAGGGAGAAATTATGATCATTCAACAAAATAGAAGAATTCCAAGAA
TTTGCAAAGAAAAGACCAGACCTGAACATTACATTTGATGTCCAAACCCAGAACTCAAGAGAATCATTCCAAGGTAAT

Alignment

ORF - retro_mdom_1767 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.86 %
• Parental protein coverage: 76.19 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LQRKTDQKEKDDQKARDEIQSLRTRIQQLELSDLTRQKDTIKQNQKNEKIKENMKHLIHKTDDLENRSRR
          L.RK.DQKEKDDQKAR.EIQ.LRTRIQ.LELSDLTR....IKQNQKN.KI.ENMKHLIHKT.DLEN.SRR
Retrocopy LHRKLDQKEKDDQKARYEIQFLRTRIQ-LELSDLTRHQGSIKQNQKN*KIAENMKHLIHKTEDLENHSRR

Parental  DNLRIIGLPEDHDKRKSLDIMLQEIIKENFPNILEQEGINTRSHPVLNPQLTTARNVIAKFKNYQTKEKI
          DNLRIIGLPEDHDKRKSLD..LQEII.EN.P.ILEQE...........P.....RNVIAKFKNYQTKEKI
Retrocopy DNLRIIGLPEDHDKRKSLDTILQEIIQENCPDILEQEEKVEIERIHRSPPVLNPRNVIAKFKNYQTKEKI

Parental  LQAAKKKSFRYHGTTVRITQDLAASTLKHRKARKNIIHTQRKNCLQPRINYPAKLTIFLQGKVW-SFNKI
          LQAAKKKSFRYHGTTVRI.QDL..STL...KA...I....R...LQPRINYPAKLTIFLQG....SFNKI
Retrocopy LQAAKKKSFRYHGTTVRIMQDLDVSTLND*KAWNMIFWKARDLGLQPRINYPAKLTIFLQGEIM>SFNKI

Parental  EEFQEFVKKRPHLIRKFDVQAQNSRESSKDN
          EEFQEF.KKRP.L...FDVQ.QNSRES...N
Retrocopy EEFQEFAKKRPDLNITFDVQTQNSRESFQGN

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_1767 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1767 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,