RetrogeneDB ID: retro_mdom_670

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 2:59627117..59627681(+)
• Located in intron of: ENSMODG00000002597

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMD
• Ensembl ID: ENSMODG00000014847
• Aliases: None
• Description: monocyte to macrophage differentiation-associated [Source:HGNC Symbol;Acc:7153]

Sequence

>retro_mdom_670
AGACTATTGGATGACAGTTGGGAAAGGCTCACAGTACGGATTTATGGAATGGGTCTATGTGCCCTCTTCATAGTTTTCCA
CAGTATTTCACATTGTTTCATGGGGAAAGAGTCACTTAAGGACAATAGAGTATTGTTTTCATATGTGTGATGGAATGGTG
ATCTGTGTCTTCATTGCCCCCTCCTATGCGCCATGGTTAAATCTCCGAGAACTTGGACCCCTGACATCTCATATGCGTTG
GTTTATCTGGCTCACAGCAGCTGGAGGAACCATTTATGCATTTCTCTACCATGAAAAGTATGAAGTGGTTGAGCTATTTT
TTCTATCTAACAATGGGTTTTTCTCAAGCATTGGTAGTTACATCAATGAATAACACTGATGGGTTATAAGAACTCCCCTG
CAGAGGCTTCATTTACTTCTTGGGAGGCGTGTTCTCCAAAAAACGATGGCATCATTCCATTCTCCCATGCCATTTGGTAC
CTTTTTGTGGCCACAGTGGCAGCAGTATATTACTATGCCATTTGGAAATACCTATACCGAAGTCCTGAAGACTTTATCCA
ACAC

Alignment

ORF - retro_mdom_670 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.05 %
• Parental protein coverage: 78.57 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  RLSDDCWEKITAWIYGMGLCALFIV-STVFHIVSWKKSHLRTMEHCFHMCDRMVIYFFIAASYAPWLNLR
          RL.DD.WE..T..IYGMGLCALFIV.STVFHIVSW.KSHLRT.E.CFHMCD.MVI..FIA.SYAPWLNLR
Retrocopy RLLDDSWERLTVRIYGMGLCALFIV>STVFHIVSWGKSHLRTIEYCFHMCDGMVICVFIAPSYAPWLNLR

Parental  ELGPLASHMRWFIWLMAAGGTIYVFLYHEKYKVVEL-FFYLTMGFSPALVVTSMNNTDGLQELAYGGIIY
          ELGPL.SHMRWFIWL.AAGGTIY.FLYHEKY.VVEL.FFYLTMGFS.ALVVTSMNNTDGL.EL...G.IY
Retrocopy ELGPLTSHMRWFIWLTAAGGTIYAFLYHEKYEVVEL>FFYLTMGFSQALVVTSMNNTDGL*ELPCRGFIY

Parental  CLGVVFF-KSDGIIPFAHAIWHLFVATAAAVHYYAIWKYLYRSPTDFIRH
          .LG.VF..K.DGIIPF.HAIW.LFVAT.AAV.YYAIWKYLYRSP.DFI.H
Retrocopy FLGGVFS>KNDGIIPFSHAIWYLFVATVAAVYYYAIWKYLYRSPEDFIQH

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_670 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_670 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 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000000205	1 retrocopy	retro_btau_777,
Choloepus hoffmanni	ENSCHOG00000013437	1 retrocopy	retro_chof_1814,
Dasypus novemcinctus	ENSDNOG00000017248	1 retrocopy	retro_dnov_2313,
Macropus eugenii	ENSMEUG00000007054	1 retrocopy	retro_meug_714,
Myotis lucifugus	ENSMLUG00000012876	1 retrocopy	retro_mluc_289,
Monodelphis domestica	ENSMODG00000014847	5 retrocopies	retro_mdom_1029, retro_mdom_1569, retro_mdom_1591, retro_mdom_670 , retro_mdom_951,
Oryctolagus cuniculus	ENSOCUG00000010549	1 retrocopy	retro_ocun_222,
Otolemur garnettii	ENSOGAG00000005902	2 retrocopies	retro_ogar_3070, retro_ogar_3071,
Procavia capensis	ENSPCAG00000004969	1 retrocopy	retro_pcap_231,
Ictidomys tridecemlineatus	ENSSTOG00000016227	1 retrocopy	retro_itri_913,
Tursiops truncatus	ENSTTRG00000007915	1 retrocopy	retro_ttru_469,