RetrogeneDB ID: retro_mdom_308

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 1:73759537..73760197(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMODG00000004245
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000007316
• Aliases: None
• Description: None

Sequence

>retro_mdom_308
AATTATTCAATACATTTCTCCAAAACAAAACACAGCAAGTTTAATGAGTCTGGTCAACTTAGTGCATTCTACCTTTTTTC
TTGTATTTGGGGCACAAGCATTCTGGTGTCTGAGAACTTCATCTCAGATCCAGCTATACTGTGGAAGTCCTACCCCCTTA
CCCTGATGACATTTCAAATGAAGTTTTTCTACATATCACAGCTGGCTTACTGGTTTCATGCTTTTCCCGAGCTCTACTTC
CAGAAAACCAAAAAAGAAGATATTCCACGACAGCTTGTCTACATTGGACTTTACCTCTTTCACATTGGTGGAGCTTATCT
TTTGAACTTAAACCATCTGGGACTTGTTCTTTTGGTGCTGCATTACTTTGTTGAGTTTCTGTTCCATATTTCCAGACTGT
TTTATTTTAGTGATGAAAAATATCAGAAAGGATTTTCTTTGTGGGCAATTCTGTTTGTTTTGGGAAGACTTCTGACTTTG
ATTCTCTCTGTGTTAACTGTTGGCTTTGGCCTAGCAAGAGCAGAAAATCAGAAGCTGGATTTCAGTACTGGAAATTTCAA
TGTGTTACCTGTGAGAATTGCTGTTCTTGCATCTATTTGCATCACTCAGGCATTTATGATGTGGAAGTTCATTAATTTCC
AGCTTCGAAGGTGGAGGGAC

Alignment

ORF - retro_mdom_308 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.18 %
• Parental protein coverage: 58.82 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  NRRMHFSKTKHSKFNESGQLSAFYLFSCIWGTSILVSENFISDPAILWKSYPLTLMTFQMKFFYISQLAY
          N...HFSKTKHSKFNESGQLSAFYLFSCIWGTSILVSENFISDPAILWKSYPLTLMTFQMKFFYISQLAY
Retrocopy NYSIHFSKTKHSKFNESGQLSAFYLFSCIWGTSILVSENFISDPAILWKSYPLTLMTFQMKFFYISQLAY

Parental  WFHAFPELYFQKTKKEDIPRQLVYIGLYLFHIGGAYLLNLNHLGLVLLVLHYFVEFLFHISRLFYFSDEK
          WFHAFPELYFQKTKKEDIPRQLVYIGLYLFHIGGAYLLNLNHLGLVLLVLHYFVEFLFHISRLFYFSDEK
Retrocopy WFHAFPELYFQKTKKEDIPRQLVYIGLYLFHIGGAYLLNLNHLGLVLLVLHYFVEFLFHISRLFYFSDEK

Parental  YQKGFSLWAILFVLGRLLTLILSVLTVGFGLARAENQKLDFSTGNFNVLPVRIAVLASICITQAFMMWKF
          YQKGFSLWAILFVLGRLLTLILSVLTVGFGLARAENQKLDFSTGNFNVLPVRIAVLASICITQAFMMWKF
Retrocopy YQKGFSLWAILFVLGRLLTLILSVLTVGFGLARAENQKLDFSTGNFNVLPVRIAVLASICITQAFMMWKF

Parental  INFQLRRWRE
          INFQLRRWR.
Retrocopy INFQLRRWRD

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	0.24 RPM	0.00 RPM
SRP007412_cerebellum	0.33 RPM	0.00 RPM
SRP007412_heart	0.20 RPM	0.00 RPM
SRP007412_kidney	0.00 RPM	0.00 RPM
SRP007412_liver	1.51 RPM	0.00 RPM
SRP007412_testis	0.79 RPM	0.00 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_308 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_308 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 19 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006325	1 retrocopy	retro_amel_78,
Bos taurus	ENSBTAG00000007562	1 retrocopy	retro_btau_24,
Canis familiaris	ENSCAFG00000007866	1 retrocopy	retro_cfam_15,
Callithrix jacchus	ENSCJAG00000007893	1 retrocopy	retro_cjac_168,
Dasypus novemcinctus	ENSDNOG00000009296	2 retrocopies	retro_dnov_27, retro_dnov_906,
Dipodomys ordii	ENSDORG00000001901	1 retrocopy	retro_dord_27,
Felis catus	ENSFCAG00000028775	1 retrocopy	retro_fcat_136,
Homo sapiens	ENSG00000067167	1 retrocopy	retro_hsap_51,
Loxodonta africana	ENSLAFG00000011625	1 retrocopy	retro_lafr_9,
Macaca mulatta	ENSMMUG00000001516	1 retrocopy	retro_mmul_235,
Monodelphis domestica	ENSMODG00000007316	1 retrocopy	retro_mdom_308 ,
Mus musculus	ENSMUSG00000025935	1 retrocopy	retro_mmus_117,
Nomascus leucogenys	ENSNLEG00000011376	1 retrocopy	retro_nleu_73,
Oryctolagus cuniculus	ENSOCUG00000008734	1 retrocopy	retro_ocun_52,
Pongo abelii	ENSPPYG00000018660	1 retrocopy	retro_pabe_169,
Rattus norvegicus	ENSRNOG00000007892	1 retrocopy	retro_rnor_287,
Ictidomys tridecemlineatus	ENSSTOG00000005537	1 retrocopy	retro_itri_38,
Tarsius syrichta	ENSTSYG00000013887	1 retrocopy	retro_tsyr_24,
Tursiops truncatus	ENSTTRG00000000328	1 retrocopy	retro_ttru_24,