RetrogeneDB ID: retro_mdom_1424

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 4:411050234..411050681(-)
• Located in intron of: ENSMODG00000023449

Retrocopy information

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

Parental gene information

• Parental gene symbol: MRPL20
• Ensembl ID: ENSMODG00000006562
• Aliases: None
• Description: mitochondrial ribosomal protein L20 [Source:HGNC Symbol;Acc:14478]

Sequence

>retro_mdom_1424
ATGGTGCTGCTCACGGCGCCACTAAAGGTACGCACCCACCTCACTGACCGCTTCTGGCAGACCCAGGACTTGCTGCAGTA
TGCCCAGCACTTTCGGGGAAGGAAGAATTGCTGCTACAGGTTGGCCATCAGGGCTGTGACTAGAGCGTTCGTGAAATGTA
CCAATGCCTGGAGGCTGAAGAAGAAGAACATGAGAACACTTTCGATTAATCGAATTACAGCCGCTTCCCAAGAACATGGT
TTGAAGTATCCATCATTTATTAGCAATTTAGTCAAGTGTCAAGTGGAATTCAACAGGAAAGTCCTTGCTGACCTGGCTAT
TTATGAACCCAAGATGTTTAAATCTTTGGCTGCTTTGGCAAAGAGGAGGAGAGAAGAAGGTTTCGCAGCTGCTCTGGGGG
ATGAGAAGGAGCCAGCGGGGATCTTTTCCCAGGTGGTGCACTATCAG

Alignment

ORF - retro_mdom_1424 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.92 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MVLLTAPLRVRARLTDRFWRTQDLLQYARHFRGRKNRCHRLAVRTETSAFVKCSKARRLKKKNMRTLWIN
          MVLLTAPL.VR..LTDRFW.TQDLLQYA.HFRGRKN.C.RLA.R..T.AFVKC..A.RLKKKNMRTL.IN
Retrocopy MVLLTAPLKVRTHLTDRFWQTQDLLQYAQHFRGRKNCCYRLAIRAVTRAFVKCTNAWRLKKKNMRTLSIN

Parental  RITAASQEHGLKYPSFISNLVKCQVELNRKVLADLAIYEPKTFKSLAALAKRRREEGFAAALGDEKEPAG
          RITAASQEHGLKYPSFISNLVKCQVE.NRKVLADLAIYEPK.FKSLAALAKRRREEGFAAALGDEKEPAG
Retrocopy RITAASQEHGLKYPSFISNLVKCQVEFNRKVLADLAIYEPKMFKSLAALAKRRREEGFAAALGDEKEPAG

Parental  IFSRVVHYQ
          IFS.VVHYQ
Retrocopy IFSQVVHYQ

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_1424 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1424 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
Ailuropoda melanoleuca	ENSAMEG00000013932	2 retrocopies	retro_amel_143, retro_amel_545,
Canis familiaris	ENSCAFG00000019259	2 retrocopies	retro_cfam_2112, retro_cfam_826,
Dasypus novemcinctus	ENSDNOG00000010105	1 retrocopy	retro_dnov_1620,
Homo sapiens	ENSG00000242485	1 retrocopy	retro_hsap_2508,
Gorilla gorilla	ENSGGOG00000027251	1 retrocopy	retro_ggor_1565,
Myotis lucifugus	ENSMLUG00000011857	1 retrocopy	retro_mluc_1423,
Monodelphis domestica	ENSMODG00000006562	2 retrocopies	retro_mdom_1424 , retro_mdom_719,
Mus musculus	ENSMUSG00000029066	1 retrocopy	retro_mmus_1624,
Otolemur garnettii	ENSOGAG00000005968	1 retrocopy	retro_ogar_2263,
Procavia capensis	ENSPCAG00000001425	1 retrocopy	retro_pcap_238,
Tupaia belangeri	ENSTBEG00000008735	2 retrocopies	retro_tbel_2193, retro_tbel_892,