RetrogeneDB ID: retro_mdom_1779

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 7:70690475..70691049(-)
• Located in intron of: ENSMODG00000002588

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_1779
GAGTCTTCAAGAGGCAGGAAATTTCCTCTTGGGGGAAGGACTGGACAGCATCCATTGGAGAACTTACATTTCTTATGGGC
CTTATGTTTTGGCAAGAATGATGGGAACGGATTTGGCAGGATAACTTTCACTTTGTCACTAAATTTGATACCATGAAGGA
CTTCAGGTGATCTTCAGCCATATCCAACTGGCCATTGAGCTGTCCTTAGACAGTGACTATGACCTTTTCAAGCGTGGCAT
TGAGCTTTTGTAGAAAGATAGCAGGAGCAAGCATGGTTGCCACTGGCTACTCAGCCCAGTCATGCAACCACCTCAAAACA
ATCTCAACCAGCTTAGGATAGAGATGCTTCTTTGTCCAATTGGGGATAATTTTGAGGAGTACAGTAAGGAAGTGTGTGGG
GCTGCACTCAGTGCTCACACCAAGGGGAACAAGATAGGAATCCAGACCAGTGAGGCTGAGAACAAGCCAGCTGTCATCTT
TATTGGACATGTCTAGAAGGAGAGACTGGGGCTCTCATCAAAAGTTATAGTTCCTTGGCCTATGCAGACACACTCACCAA
GAGCAACTCTTTCA

Alignment

ORF - retro_mdom_1779 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.76 %
• Parental protein coverage: 86.18 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  ESPKERKLPLGEGLEKHPLENR---WALWFFKNDRN-RVWQDNLHLVTKFETVEDF-WAIHSHIKLASKL
          ES...RK.PLG.....HPLEN....WAL.F.KND.N.R.WQDN.H.VTKF.T..DF...I.SHI.LA..L
Retrocopy ESSRGRKFPLGGRTGQHPLENLHFLWALCFGKNDGN<RIWQDNFHFVTKFDTMKDF<QVIFSHIQLAIEL

Parental  SSGCDYALFKDGIEPMWEDSRNKHGGRWLVSLAKQQRQSNLDRLWLETLLCLIGEAFEEYSEEVCGAVLN
          S...DY.LFK.GIE....DSR.KHG..WL.S...Q..Q.NL..L..E.LLC.IG..FEEYS.EVCGA.L.
Retrocopy SLDSDYDLFKRGIELL*KDSRSKHGCHWLLSPVMQPPQNNLNQLRIEMLLCPIGDNFEEYSKEVCGAALS

Parental  VRTKGDKIAIWTSEAENQPAVTFIGRVYKERLGLSPKVIIGY--QAHADTATKS
          ..TKG.KI.I.TSEAEN.PAV.FIG.V.KERLGLS.KVI.....Q.H...AT.S
Retrocopy AHTKGNKIGIQTSEAENKPAVIFIGHV*KERLGLSSKVIVPWPMQTHSPRATLS

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_1779 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1779 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,