RetrogeneDB ID: retro_mdom_141

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 4:402290215..402290599(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMODG00000023573
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000017696
• Aliases: None
• Description: None

Sequence

>retro_mdom_141
GCAAAAGAAACCTTTGGTGTTAATAACACAGTCTGTGGTATAGATGCTATGAACCCCTCTTCAAGAGATGACTTCACAGA
GTTTGGCAAGTTACTAAAAGATAAAATTACACAGTATGAAAAATCTCTATATTATGCCAGTTTCTTGGAAGCATTAGTTC
GAGATGTGTGCATTTCATTGGAAATTGATGACTTGAAAAAGATTACCAATTCACTGACAGTGCTATGCAGTGAAAAGCAG
AAACAAGAAAAGCAAAGCAAAGCCAAAAAGAAGAAGAAAGGTGTGGTTCCTGGAGGGGGATTAAAGGCTACAATGAAAGA
TGATCTTGCAGACTATGGTGGATATGATGGAGGATATGTGCAAGACTTTGAAGACTTCATGTGA

Alignment

ORF - retro_mdom_141 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 100. %
• Parental protein coverage: 97.6 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GVNNTVCGIDAMNPSSRDDFTEFGKLLKDKITQYEKSLYYASFLEALVRDVCISLEIDDLKKITNSLTVL
          GVNNTVCGIDAMNPSSRDDFTEFGKLLKDKITQYEKSLYYASFLEALVRDVCISLEIDDLKKITNSLTVL
Retrocopy GVNNTVCGIDAMNPSSRDDFTEFGKLLKDKITQYEKSLYYASFLEALVRDVCISLEIDDLKKITNSLTVL

Parental  CSEKQKQEKQSKAKKKKKGVVPGGGLKATMKDDLADYGGYDGGYVQDFEDFM
          CSEKQKQEKQSKAKKKKKGVVPGGGLKATMKDDLADYGGYDGGYVQDFEDFM
Retrocopy CSEKQKQEKQSKAKKKKKGVVPGGGLKATMKDDLADYGGYDGGYVQDFEDFM

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_141 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_141 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 15 parental genes, and 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000002412	1 retrocopy	retro_cjac_589,
Cavia porcellus	ENSCPOG00000012396	3 retrocopies	retro_cpor_1357, retro_cpor_1358, retro_cpor_500,
Dipodomys ordii	ENSDORG00000008339	7 retrocopies	retro_dord_208, retro_dord_364, retro_dord_451, retro_dord_470, retro_dord_633, retro_dord_738, retro_dord_746,
Equus caballus	ENSECAG00000008716	1 retrocopy	retro_ecab_635,
Echinops telfairi	ENSETEG00000005052	1 retrocopy	retro_etel_1376,
Homo sapiens	ENSG00000104131	1 retrocopy	retro_hsap_4189,
Gorilla gorilla	ENSGGOG00000000548	2 retrocopies	retro_ggor_1687, retro_ggor_41,
Macropus eugenii	ENSMEUG00000010372	1 retrocopy	retro_meug_256,
Microcebus murinus	ENSMICG00000005006	1 retrocopy	retro_mmur_100,
Monodelphis domestica	ENSMODG00000017696	1 retrocopy	retro_mdom_141 ,
Mus musculus	ENSMUSG00000027236	1 retrocopy	retro_mmus_18,
Nomascus leucogenys	ENSNLEG00000005568	1 retrocopy	retro_nleu_2848,
Oryctolagus cuniculus	ENSOCUG00000005376	1 retrocopy	retro_ocun_1350,
Otolemur garnettii	ENSOGAG00000004694	1 retrocopy	retro_ogar_1227,
Pongo abelii	ENSPPYG00000006431	1 retrocopy	retro_pabe_3429,