RetrogeneDB ID: retro_mdom_1594

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 6:88562862..88563297(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMODG00000001940
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: C11orf74
• Ensembl ID: ENSMODG00000019838
• Aliases: None
• Description: chromosome 11 open reading frame 74 [Source:HGNC Symbol;Acc:25142]

Sequence

>retro_mdom_1594
GAAGAGCAGATCATGATTGATGAAGGCCAAAAAGTTGGTATTTCCATTAAAGACGACCTAAATCAGACAAAAAAGGTAAA
GATAGACAATTTCCTAGATCTGGAAGATTTTGACATGAATGAAGAAACTGACTACAAGTTGATCCCAGAGTTGCTATTGC
TTCCAGGAGAGGTAGAAGAAGCATTTTTCTCTGCCTCAGGCTATATGCCTTCTTTTAACCAGCGTTCTCACCCTGAACCA
AAAGCCTGGCCAACAGAACAACCCACATACAGGCATGTAAAGGAGGTACCTGAGAATGAAGTTCAGCCTTTCTCACTTGA
TGAAGAATTTGACTATGATAATGTGATGCTAACTCCCAAGTTCTCTAATGAAGAGATGAAAATTCTAGAAATGTACAGCC
AAAGTAGACTGAATCCTGACATGAAAGCCAAAGAA

Alignment

ORF - retro_mdom_1594 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.07 %
• Parental protein coverage: 58.33 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EPEIVIDEGQKVGISSQGDLHRAGKVKVDNFLDLEDFDRDEETGHKQSPELMLLPGEVEDEAHFSVSSYV
          E..I.IDEGQKVGIS...DL....KVK.DNFLDLEDFD..EET..K..PEL.LLPGEVE.EA.FS.S.Y.
Retrocopy EEQIMIDEGQKVGISIKDDLNQTKKVKIDNFLDLEDFDMNEETDYKLIPELLLLPGEVE-EAFFSASGYM

Parental  PSFDQHSCPEPKTQPAEQPAYRHLKEVSGDEVQPFSLDEEFDYDTVTLTPKFSNAEMKTILEMSSRSRLN
          PSF.Q.S.PEPK..P.EQP.YRH.KEV...EVQPFSLDEEFDYD.V.LTPKFSN.EMK.ILEM.S.SRLN
Retrocopy PSFNQRSHPEPKAWPTEQPTYRHVKEVPENEVQPFSLDEEFDYDNVMLTPKFSNEEMK-ILEMYSQSRLN

Parental  PGLEGKE
          P....KE
Retrocopy PDMKAKE

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_1594 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1594 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 9 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Dipodomys ordii	ENSDORG00000010963	2 retrocopies	retro_dord_388, retro_dord_615,
Homo sapiens	ENSG00000166352	1 retrocopy	retro_hsap_418,
Gorilla gorilla	ENSGGOG00000004773	1 retrocopy	retro_ggor_411,
Macropus eugenii	ENSMEUG00000003065	1 retrocopy	retro_meug_328,
Microcebus murinus	ENSMICG00000008620	1 retrocopy	retro_mmur_383,
Monodelphis domestica	ENSMODG00000019838	1 retrocopy	retro_mdom_1594 ,
Pongo abelii	ENSPPYG00000003347	1 retrocopy	retro_pabe_302,
Pan troglodytes	ENSPTRG00000003514	2 retrocopies	retro_ptro_2924, retro_ptro_320,
Tupaia belangeri	ENSTBEG00000004277	2 retrocopies	retro_tbel_2155, retro_tbel_2277,