RetrogeneDB ID: retro_mdom_1901

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 8:43481239..43481570(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000017312
• Aliases: None
• Description: None

Sequence

>retro_mdom_1901
ATATCTGGAAGCTTCTACTTTGTAATTTATAGGACATCATGATAATCCAAGCATTGGAATGGAATTTTTACCAGTTGGGA
AAGTGGAATCTAGGGAAAGTGGAATCTAGATAATCATCATCATCTCAACCATAGCTATTTCAGCTCTTGATGTAGTAGAT
GAAAATATGAAGTTGCTAACAATATGTACCTGAAAACTGTGGTCAAATCCAATGAGTGGATTGTTTTTGTCTTTTGTTAC
TGCAGACCCAATGAGATGTATTATGCTTCATGATGTAAGGCAAGATGATGGAATAAAGAACTTCTTTAGTGATGTTTAAT
TTGTATTTATA

Alignment

ORF - retro_mdom_1901 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.64 %
• Parental protein coverage: 76.43 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MSGSFYFVI-VGHHDNPVFEMEFLPAGKVESKDDHRHLNQFIAHAALDLVD---ENMWL-SNNMYLKTVD
          .SGSFYFVI..GHHDNP...MEFLP................I...A....D...ENM.L..NNMYLKTV.
Retrocopy ISGSFYFVI>IGHHDNPSIGMEFLPVXXXXXXXXXXXIIIIISTIAISALDVVDENMKL<ANNMYLKTVV

Parental  KFNEWFV-SAFVTAGHMRFIMLHDVRQEDGIKNFFSDVYDLYI
          K.NEW.V...FVTA..MR.IMLHDVRQ.DGIKNFFSDV....I
Retrocopy KSNEWIV>LSFVTADPMRCIMLHDVRQDDGIKNFFSDV*FVFI

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_1901 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1901 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
Anolis carolinensis	ENSACAG00000001719	1 retrocopy	retro_acar_53,
Canis familiaris	ENSCAFG00000011754	2 retrocopies	retro_cfam_1608, retro_cfam_368,
Homo sapiens	ENSG00000196459	1 retrocopy	retro_hsap_73,
Microcebus murinus	ENSMICG00000004690	1 retrocopy	retro_mmur_1022,
Macaca mulatta	ENSMMUG00000022619	1 retrocopy	retro_mmul_326,
Monodelphis domestica	ENSMODG00000017312	2 retrocopies	retro_mdom_1737, retro_mdom_1901 ,
Mus musculus	ENSMUSG00000079317	2 retrocopies	retro_mmus_198, retro_mmus_2522,
Otolemur garnettii	ENSOGAG00000002870	2 retrocopies	retro_ogar_369, retro_ogar_60,
Pan troglodytes	ENSPTRG00000021674	1 retrocopy	retro_ptro_72,
Sorex araneus	ENSSARG00000006353	1 retrocopy	retro_sara_244,
Ictidomys tridecemlineatus	ENSSTOG00000025097	1 retrocopy	retro_itri_1014,