RetrogeneDB ID: retro_mdom_98

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 1:610710108..610710489(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMODG00000023134
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000016021
• Aliases: None
• Description: None

Sequence

>retro_mdom_98
ATGGCCGAGGCCACGGCTGGGCTGAGCGAGACCGTCACCGAGACATCGGTTACCGTGACAACCGAGCCCGAAAATCGTAG
TCTAACTATTAAACTTCGGAAACGGAAACCAGACAAGAAGGTGGAATGGTCAAGTGATACTGTGGACAATGAACACTTAG
GACGCCGTTCATCAAAATGTTGCTGTATTTATGAAAAGCCTAGGGCTTTTGGTGAGAGCTCCACAGAGAGCGAAGATGAA
GATGATGAAGGTTGTGGTCACACTCACTGGGTTCGGGGCCACCGAAAGGGACAGCGCCGTACTACCACTGGCCCACCCCC
AACTACTCTTTCCCACCTCCCTAACTCCTCCCAACCCTCACCTGGGCCCATGCAGCACTGA

Alignment

ORF - retro_mdom_98 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.5 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAEATAGLSETVTETSVTVTTEPVRKTGENRSLTIKLRKRKPDKKVEWSSDTVDNEHLGRRSSKCDCIYE
          MAEATAGLSETVTETSVTVTTEP..............RK..PDKKVEWSSDTVDNEHLGRRSSKC.CIYE
Retrocopy MAEATAGLSETVTETSVTVTTEPENR---SLTIKLRKRK--PDKKVEWSSDTVDNEHLGRRSSKCCCIYE

Parental  KPRAFGESSTESEDEDDEGCGHTHWVRGHRKGQRRTTTGPPPTT-PHLPNSSQPSPGPMQH
          KPRAFGESSTESEDEDDEGCGHTHWVRGHRKGQRRTTTGPPPTT..HLPNSSQPSPGPMQH
Retrocopy KPRAFGESSTESEDEDDEGCGHTHWVRGHRKGQRRTTTGPPPTTLSHLPNSSQPSPGPMQH

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	100.60 RPM	0.00 RPM
SRP007412_cerebellum	83.25 RPM	0.00 RPM
SRP007412_heart	59.21 RPM	0.00 RPM
SRP007412_kidney	0.00 RPM	0.00 RPM
SRP007412_liver	0.00 RPM	0.00 RPM
SRP007412_testis	160.88 RPM	0.00 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_98 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_98 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 12 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000020710	1 retrocopy	retro_cjac_2880,
Felis catus	ENSFCAG00000013592	1 retrocopy	retro_fcat_1794,
Gorilla gorilla	ENSGGOG00000026830	1 retrocopy	retro_ggor_80,
Macropus eugenii	ENSMEUG00000006493	2 retrocopies	retro_meug_715, retro_meug_933,
Macaca mulatta	ENSMMUG00000012122	1 retrocopy	retro_mmul_359,
Monodelphis domestica	ENSMODG00000016021	1 retrocopy	retro_mdom_98 ,
Nomascus leucogenys	ENSNLEG00000004933	1 retrocopy	retro_nleu_2257,
Otolemur garnettii	ENSOGAG00000001598	1 retrocopy	retro_ogar_1458,
Pongo abelii	ENSPPYG00000029642	1 retrocopy	retro_pabe_492,
Pan troglodytes	ENSPTRG00000017915	1 retrocopy	retro_ptro_2969,
Pteropus vampyrus	ENSPVAG00000008330	1 retrocopy	retro_pvam_894,
Ictidomys tridecemlineatus	ENSSTOG00000003632	1 retrocopy	retro_itri_159,