RetrogeneDB ID: retro_mdom_710

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 2:176863014..176863615(+)
• Located in intron of: ENSMODG00000014826

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000005097
• Aliases: None
• Description: None

Sequence

>retro_mdom_710
GTGCTGGAGGAGTCCCCAAAAGAGAGGAAGTTGCTTCTTGGGGAAGGGCTGGAGAAGCATCCTTTGGAGAACAGGTGGGC
CTTATGGTTCTTCAAGAATGACAGGAACAGAGCTTGGCAAGATAATCTTCACCTAGTTACCAAGTTTGAGACTGTGGAGG
ACTTCTGGGCAATCCACAGCCACATCAAACTGGCCAGCAAACTGTCCTCAGGCTGTGACTATGCCCTTTTCAAGGATGGC
ATTGAGCCTATGTGGGAAGATAGCAGGAACAAACATGGTGGCCGATGGCTGGTCAGCTTGGCCAAACAACAGCATCAAAG
CAACCTGGATCGGCTCTGGCTAGAGATGCTTCTTTGTCTGATTGGGGGGGGCCTTTGAGGAATACAGTGAGGAAGTGTGT
GGGGCTGTGCTCAATGTTCGCACCAAGGGGGACAAGATAGCCATTTGGACCAGTGAGGCTGAGAACTAGCCAGCTGTCAC
CTTTATTGGACGTGTCTACAAGGAGAGTCTGGGACTCTCTCCGAAGGTCATTATTGGCTACCAGGCTCATGCAGACACAG
CCACCAAGAGCAACTCTTTCACCAAGAACAAATTTGTGGTG

Alignment

ORF - retro_mdom_710 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.02 %
• Parental protein coverage: 92.17 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VLEESPKERKLPLGEGLEKHPLENRWALWFFKNDRNRVWQDNLHLVTKFETVEDFWAIHSHIKLASKLSS
          VLEESPKERKL.LGEGLEKHPLENRWALWFFKNDRNR.WQDNLHLVTKFETVEDFWAIHSHIKLASKLSS
Retrocopy VLEESPKERKLLLGEGLEKHPLENRWALWFFKNDRNRAWQDNLHLVTKFETVEDFWAIHSHIKLASKLSS

Parental  GCDYALFKDGIEPMWEDSRNKHGGRWLVSLAKQQRQSNLDRLWLETLLCLI-GEAFEEYSEEVCGAVLNV
          GCDYALFKDGIEPMWEDSRNKHGGRWLVSLAKQQ.QSNLDRLWLE.LLCLI....FEEYSEEVCGAVLNV
Retrocopy GCDYALFKDGIEPMWEDSRNKHGGRWLVSLAKQQHQSNLDRLWLEMLLCLI>XXXFEEYSEEVCGAVLNV

Parental  RTKGDKIAIWTSEAENQPAVTFIGRVYKERLGLSPKVIIGYQAHADTATKSNSFTKNKFVV
          RTKGDKIAIWTSEAEN.PAVTFIGRVYKE.LGLSPKVIIGYQAHADTATKSNSFTKNKFVV
Retrocopy RTKGDKIAIWTSEAEN*PAVTFIGRVYKESLGLSPKVIIGYQAHADTATKSNSFTKNKFVV

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	0.12 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_710 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_710 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 11 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000003103	1 retrocopy	retro_btau_1679,
Erinaceus europaeus	ENSEEUG00000005920	1 retrocopy	retro_eeur_414,
Loxodonta africana	ENSLAFG00000027919	1 retrocopy	retro_lafr_866,
Monodelphis domestica	ENSMODG00000002680	1 retrocopy	retro_mdom_1717,
Monodelphis domestica	ENSMODG00000005097	3 retrocopies	retro_mdom_1779, retro_mdom_47, retro_mdom_710 ,
Monodelphis domestica	ENSMODG00000020716	1 retrocopy	retro_mdom_701,
Mus musculus	ENSMUSG00000074895	1 retrocopy	retro_mmus_510,
Nomascus leucogenys	ENSNLEG00000012532	1 retrocopy	retro_nleu_84,
Ochotona princeps	ENSOPRG00000008875	2 retrocopies	retro_opri_1088, retro_opri_21,
Tupaia belangeri	ENSTBEG00000001631	2 retrocopies	retro_tbel_3164, retro_tbel_3690,
Drosophila melanogaster	FBgn0035709	1 retrocopy	retro_dmel_68,