RetrogeneDB ID: retro_mdom_976

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 3:98291589..98291852(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000027578
• Aliases: None
• Description: None

Sequence

>retro_mdom_976
ATGCAAAGAGTAGCAGCAGGGATTTTACTAATTATGGCATCCCTGCCTGCTTTAGAAGACAGTGATCCAGGTGATAAGGG
CAGTCCTTTCTATTATGATTGGCACAATTTTCATGTGGGCAGTGTGGTTTAAAATGGCATCTGGTGTGCCATTGGCATCA
TTGTTCACATGAGTGGCAAATGTAAATGCAAATCAGCCAGAAGCACAACCCTAGGGCAAGAGAAATCACATCCCCCAATG
CACCAGGCTCTGCCAGTAACTGC

Alignment

ORF - retro_mdom_976 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.28 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MQRVAAGILLMMAALPALEANDPADKDSPFYYDWHSLRVGGMVCAGILCAVGIIVLVSSKCKCK-FSQKH
          MQRVAAGILL.MA.LPALE..DP.DK.SPFYYDWH...VG..V..GI.CA.GIIV..S.KCKCK..SQKH
Retrocopy MQRVAAGILLIMASLPALEDSDPGDKGSPFYYDWHNFHVGSVV*NGIWCAIGIIVHMSGKCKCK<ISQKH

Parental  NPRAGEITSLNAPGSASNC
          NPRA.EITS.NAPGSASNC
Retrocopy NPRAREITSPNAPGSASNC

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_976 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_976 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 9 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000024923	1 retrocopy	retro_cfam_1820,
Dasypus novemcinctus	ENSDNOG00000017385	1 retrocopy	retro_dnov_643,
Erinaceus europaeus	ENSEEUG00000010030	4 retrocopies	retro_eeur_148, retro_eeur_264, retro_eeur_524, retro_eeur_559,
Felis catus	ENSFCAG00000022417	2 retrocopies	retro_fcat_284, retro_fcat_990,
Monodelphis domestica	ENSMODG00000027578	1 retrocopy	retro_mdom_976 ,
Nomascus leucogenys	ENSNLEG00000011027	1 retrocopy	retro_nleu_107,
Oryctolagus cuniculus	ENSOCUG00000006722	1 retrocopy	retro_ocun_1050,
Tupaia belangeri	ENSTBEG00000016033	1 retrocopy	retro_tbel_1911,
Tarsius syrichta	ENSTSYG00000014460	3 retrocopies	retro_tsyr_1494, retro_tsyr_70, retro_tsyr_875,