RetrogeneDB ID: retro_mdom_633

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 1:599752204..599752739(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MAD2L1
• Ensembl ID: ENSMODG00000018944
• Aliases: None
• Description: MAD2 mitotic arrest deficient-like 1 (yeast) [Source:HGNC Symbol;Acc:6763]

Sequence

>retro_mdom_633
ATGGAGCTGCAGCTCACCCAGGACCAGGGCATCACTTTGCGCGGTAGCACCACTATCATAGCCGAGTTCTTCTCATTTAG
TGTCAACAGTATCTTATATCAGCATGGTATATACCCATCTGAAACCTTTACTCAGGTACAAAAATATGGACTTACTTTGC
TTGTAACAACAGATCCTGATCTCATTAAATACTTAAATAATATGGTGGACCATCTAAAAGACTGGTTATACAAATGTTAG
GTTCAAGTTGGTGGTAGTGATTTCAAACACTGAAAGTGGTGAAGTCCTTGAATGATGGCAGTTTGATATTGAGTACAACA
AGACAGCAAAAGAAGATGGTGCACCAAGACAGAAATTCGTGAAATCTATCCAAGATAAAATCCAGTTGGTGATCCAACAA
ATTACAGCCACCATGACATTTCAGCCATTGTTAGAAGCAACTTGTTCATTTGATCAACTTATTTATATAGACAAAAAACT
GGTAGTCCCTGATAAATGGGAAGAGTCTGGACCACAGTTTATTGCCAATTCTGAA

Alignment

ORF - retro_mdom_633 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.67 %
• Parental protein coverage: 87.32 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MELQLTRDQGITLRGSADIVAEFFSFGVNSILYQRGIYPSETFTRVQKYGLTLLVTTDPDLIKYLNNVVD
          MELQLT.DQGITLRGS..I.AEFFSF.VNSILYQ.GIYPSETFT.VQKYGLTLLVTTDPDLIKYLNN.VD
Retrocopy MELQLTQDQGITLRGSTTIIAEFFSFSVNSILYQHGIYPSETFTQVQKYGLTLLVTTDPDLIKYLNNMVD

Parental  QLKDWLYKCSVQ-KLVVVISNIESGEVLERWQFDIECDKTAKEDSAPREKSAKSIQDEIRSVIRQITATV
          .LKDWLYKC.VQ...VV..SN.ESGEVLE.WQFDIE..KTAKED.APR.K..KSIQD.I..VI.QITAT.
Retrocopy HLKDWLYKC*VQ>LVVVI-SNTESGEVLE*WQFDIEYNKTAKEDGAPRQKFVKSIQDKIQLVIQQITATM

Parental  TFLPLLEAACSFDLLIYTDKELVVPDKWEESGPQFIANSE
          TF.PLLEA.CSFD.LIY.DK.LVVPDKWEESGPQFIANSE
Retrocopy TFQPLLEATCSFDQLIYIDKKLVVPDKWEESGPQFIANSE

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_633 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_633 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 26 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000012813	2 retrocopies	retro_chof_1340, retro_chof_2524,
Dasypus novemcinctus	ENSDNOG00000013456	1 retrocopy	retro_dnov_1348,
Erinaceus europaeus	ENSEEUG00000009629	1 retrocopy	retro_eeur_446,
Echinops telfairi	ENSETEG00000015756	1 retrocopy	retro_etel_724,
Gorilla gorilla	ENSGGOG00000002516	1 retrocopy	retro_ggor_1281,
Loxodonta africana	ENSLAFG00000029619	1 retrocopy	retro_lafr_1138,
Myotis lucifugus	ENSMLUG00000011092	8 retrocopies	retro_mluc_1242, retro_mluc_165, retro_mluc_1802, retro_mluc_1904, retro_mluc_1986, retro_mluc_2434, retro_mluc_609, retro_mluc_696,
Macaca mulatta	ENSMMUG00000004875	2 retrocopies	retro_mmul_1292, retro_mmul_1701,
Monodelphis domestica	ENSMODG00000018944	1 retrocopy	retro_mdom_633 ,
Mus musculus	ENSMUSG00000029910	2 retrocopies	retro_mmus_1684, retro_mmus_2573,
Otolemur garnettii	ENSOGAG00000004054	1 retrocopy	retro_ogar_199,
Ictidomys tridecemlineatus	ENSSTOG00000025410	2 retrocopies	retro_itri_1592, retro_itri_327,
Tupaia belangeri	ENSTBEG00000011065	3 retrocopies	retro_tbel_4460, retro_tbel_4666, retro_tbel_664,