RetrogeneDB ID: retro_mdom_993

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 3:150468558..150469069(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000020680
• Aliases: None
• Description: None

Sequence

>retro_mdom_993
CAGCAAAAGCATTTACAAGAATGGAAAGCTCTTCAGAAAACACAAAAATTTGGGGAACTAAGAGAAATTTCTGGTGACCA
ATATGTGAAAGAAGTTACAAATGCAGAAAAAGATGTCTAGGTTATAATTCACTTATATAGACCAAGCATCCAAATGTGTT
TACTGCTTAATCAGCATCTGAGTGCAAGAAAATTTCCAGAAACTAAATTTGTTAAGGCTGTTGTAAATAGCTGTATTCAA
CACTACCATGACAGGTGTTTACCCACAATTTTCGTGTATAAAAATGGTCAGATAGAAGGAAAATTCATCGGAATTATTAA
ATGTGGAGGAATAAATCTGAAGTTAGAAGAACTTGAATGGAAACAAGCAGAAGTTGGAGCTATATAAACTGACTTGGAAG
AAAATCCTAAAAAAACAGGTTGTAGACATGATGGCATCTTCCATTAAAAACACTTCTATTTATGATGACAGTAATAGTTC
AAGCAGTGACAGCAATGAGACCAAATGTCCT

Alignment

ORF - retro_mdom_993 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.64 %
• Parental protein coverage: 70.49 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  RQKRLQEWKALQKTQKFGELREISGDQYVKEVTNAEKDVWVIIHLYRPSIQMCLLLNQHLSVLARKFPET
          .QK.LQEWKALQKTQKFGELREISGDQYVKEVTNAEKDV.VIIHLYRPSIQMCLLLNQHLS..ARKFPET
Retrocopy QQKHLQEWKALQKTQKFGELREISGDQYVKEVTNAEKDV*VIIHLYRPSIQMCLLLNQHLS--ARKFPET

Parental  KFVKAVVNSCIQHYHDRCLPTIFVYKNGQIEGKFIGIIECGGINLKLEELEWKLAEVGAIRTDLEENP-K
          KFVKAVVNSCIQHYHDRCLPTIFVYKNGQIEGKFIGII.CGGINLKLEELEWK.AEVGAI.TDLEENP.K
Retrocopy KFVKAVVNSCIQHYHDRCLPTIFVYKNGQIEGKFIGIIKCGGINLKLEELEWKQAEVGAI*TDLEENP>K

Parental  KQVVDMMASSIRNTSIYDDSNSSSSDSDETKCP
          KQVVDMMASSI.NTSIYDDSNSSSSDS.ETKCP
Retrocopy KQVVDMMASSIKNTSIYDDSNSSSSDSNETKCP

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_993 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_993 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 6 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000012692	3 retrocopies	retro_chof_1554, retro_chof_562, retro_chof_737,
Echinops telfairi	ENSETEG00000000666	1 retrocopy	retro_etel_1568,
Gorilla gorilla	ENSGGOG00000007908	1 retrocopy	retro_ggor_2890,
Monodelphis domestica	ENSMODG00000001489	1 retrocopy	retro_mdom_734,
Monodelphis domestica	ENSMODG00000020680	2 retrocopies	retro_mdom_1048, retro_mdom_993 ,
Pan troglodytes	ENSPTRG00000016073	7 retrocopies	retro_ptro_148, retro_ptro_1810, retro_ptro_1865, retro_ptro_2402, retro_ptro_2690, retro_ptro_2784, retro_ptro_675,