RetrogeneDB ID: retro_mdom_26

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 7:176326222..176326588(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMODG00000015533
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000017744
• Aliases: None
• Description: None

Sequence

>retro_mdom_26
ATGGCGACTGAAGGCGATGTGGAGCTAGAGCTGGAAACAGAATCGAGTGGCCCAGAGAGGCTGCCTGAGAAACCTCGGAA
ACATGACAGTGGCGCAGCTGACCTGGAACGAGTGACCGACTATGCAGAAGAGAAAGAGATCCAAAGCTCCAACTTGGAGA
CAGCGATGTTGGTGATTGGTGATCAACGGTCCCGGGAGCAGAAGGCCAAAGAGGAACGGGAAAAGGAACTGGCCAAAGTT
ACAATCAAGAAGGAAGATCTGGAACTGATTATGACAGAGATGGAAATCTCACGGGCAGCTGCAGAACGTAGTTTGCGGGA
ACACATGGGCAACATAGTAGACGCTCATATAACCCTTACCAACTAA

Alignment

ORF - retro_mdom_26 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.39 %
• Parental protein coverage: 94.49 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MATEGDVELELETEPSGPERPPEKPRKHDSGAADLERVTDYAEEKEIQSSNLETAMSVIGDRRSREQKAK
          MATEGDVELELETE.SGPER.PEKPRKHDSGAADLERVTDYAEEKEIQSSNLETAM.VIGD.RSREQKAK
Retrocopy MATEGDVELELETESSGPERLPEKPRKHDSGAADLERVTDYAEEKEIQSSNLETAMLVIGDQRSREQKAK

Parental  QEREKELAKVTIKKEDL-LIMTEMEISRAAAERSLREHMGNVVDALITLTN
          .EREKELAKVTIKKEDL.LIMTEMEISRAAAERSLREHMGN.VDA.ITLTN
Retrocopy EEREKELAKVTIKKEDLELIMTEMEISRAAAERSLREHMGNIVDAHITLTN

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	140.77 RPM
SRP007412_cerebellum	0.00 RPM	118.50 RPM
SRP007412_heart	0.00 RPM	157.69 RPM
SRP007412_kidney	0.00 RPM	34.24 RPM
SRP007412_liver	0.00 RPM	111.27 RPM
SRP007412_testis	0.00 RPM	93.90 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_26 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_26 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 13 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000002541	2 retrocopies	retro_cjac_1352, retro_cjac_748,
Echinops telfairi	ENSETEG00000007464	3 retrocopies	retro_etel_1504, retro_etel_1616, retro_etel_1830,
Gorilla gorilla	ENSGGOG00000014809	1 retrocopy	retro_ggor_2557,
Macropus eugenii	ENSMEUG00000013059	1 retrocopy	retro_meug_1583,
Monodelphis domestica	ENSMODG00000017744	2 retrocopies	retro_mdom_26 , retro_mdom_306,
Nomascus leucogenys	ENSNLEG00000005454	1 retrocopy	retro_nleu_2150,
Oryctolagus cuniculus	ENSOCUG00000001161	2 retrocopies	retro_ocun_1395, retro_ocun_967,
Otolemur garnettii	ENSOGAG00000010201	1 retrocopy	retro_ogar_1064,
Pongo abelii	ENSPPYG00000006424	1 retrocopy	retro_pabe_3108,
Pan troglodytes	ENSPTRG00000038721	1 retrocopy	retro_ptro_2582,
Rattus norvegicus	ENSRNOG00000015703	1 retrocopy	retro_rnor_2477,
Ictidomys tridecemlineatus	ENSSTOG00000006916	2 retrocopies	retro_itri_1861, retro_itri_1864,
Tursiops truncatus	ENSTTRG00000003726	1 retrocopy	retro_ttru_1499,