RetrogeneDB ID: retro_mdom_1684

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 6:192063854..192064268(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000020110
• Aliases: None
• Description: None

Sequence

>retro_mdom_1684
GCGGCTGGGTGCAGGCCATCCTACCTGATGCAGGAGCTCCCTAGGAGCACAGAGCTGACTGATAGCACCAATCTGATCCC
ACACAATTTGGAGAATGTCTATAATAAATTCTGTAGGAAAAAGGTGAAGGAGAATTTGAGTAATTTCCTGTCTGACCTGC
CAGGGGTGATTGAGCAACCTGGCTCCTACAACGGCAGCCTCTGCTCTTTCATTGAGAAGCCCCCCATTCTTGGGGCTCTT
TCAACTCTATCACTGACACCATGCTGGCAGGTTTACATCTCTACATTCATCCAGTGCCAGACTAGTGTTGCCTGATGGCA
CACCCAGTCCCCAAAGAAGAAAAACATGCACAAGTACAAACAGAGCTGTCACCAGGACCCTGTCCCCACAGAACCTCCAC
CTGATTTGGATCAC

Alignment

ORF - retro_mdom_1684 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.01 %
• Parental protein coverage: 57.14 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  AAGCGPFYLMRELPGSTELTGSTNLITHYNLEHAYNKFCGKKVKEKLSNFLPDLPGMIDLPGSHDNSGLR
          AAGC.P.YLM.ELP.STELT.STNLI.H.NLE..YNKFC.KKVKE.LSNFL.DLPG.I..PGS..N..L.
Retrocopy AAGCRPSYLMQELPRSTELTDSTNLIPH-NLENVYNKFCRKKVKENLSNFLSDLPGVIEQPGSY-NGSLC

Parental  SLIEKPPILG-GSFNPITGTMLAGFRLHAGPLPEQCRLM-HIQPPKKKNKHKHKQSRTQDPVPPETPSDS
          S.IEKPPILG.GSFN.IT.TMLAG..L...P.P..C.LM.H.Q.PKKKN.HK.KQS..QDPVP.E.P.D.
Retrocopy SFIEKPPILG<GSFNSITDTMLAGLHLYIHPVPD*CCLM>HTQSPKKKNMHKYKQSCHQDPVPTEPPPDL

Parental  DH
          DH
Retrocopy DH

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_1684 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1684 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 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Microcebus murinus	ENSMICG00000004907	1 retrocopy	retro_mmur_1367,
Monodelphis domestica	ENSMODG00000020110	2 retrocopies	retro_mdom_1684 , retro_mdom_27,