RetrogeneDB ID: retro_mdom_1448

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 5:92932501..92933083(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: AIDA
• Ensembl ID: ENSMODG00000004774
• Aliases: None
• Description: axin interactor, dorsalization associated [Source:HGNC Symbol;Acc:25761]

Sequence

>retro_mdom_1448
ATTCCCCTATGAAGAATTTTAGCACCTAGTAAAGAAGAGAATTTGGAATTTGAGGATGATGATGAAGAGGGTGGTGTTGG
AGCGGGTCTCCAGACTCCTTCCCTCCTAGAGTTCAAGGTACTTGAACTTCAAGGTACCCAAGTTGTCATCTGAACCAGGA
ATGACCGTTGCTCGCTATCAAAATTGAGAAAATTGGTCTGAAAGATGCTTGGCAGTGCATTGCCACCTATATTACAGTTA
GTGTATAGGATCTGAGTGGCATAGATTTAACCACTGTGCAAGATACTCCTGTGGCTTCAAGGAAGGAGGATACATATGTT
CACTTTAATGTGGACATTGAACTTCAGAAACACATTGAAAAATTAACCAAAGGTGCAGCTATTTTCTTTGAATTCAAACA
CTATAAGCCTAAAAAAGGTTTACCAGCACCAAGTGTTTTGCTTTCATGGAGATGGATGAAATTAAACCTGGGCCAATTAT
AATAGAACTATACAAGAAACCCACTGAATTTAAAAGAAAGAAACTGTAGTTGTTGACCAAGAAACCACTTTATCTTCACC
TCCATCAACTTTGCACAAGGAA

Alignment

ORF - retro_mdom_1448 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.83 %
• Parental protein coverage: 52.32 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  VPLRRILAPGEEENLEFEDDDEEGG--AGAGSPD-SFPARVPGTLLPRLPSEPGMT-LLTIKIEKIGLKD
          .PL.RILAP..EENLEFEDDDEEGG..AG...P..S...R......P.L.SEPGMT.LL.IKIEKIGLKD
Retrocopy IPL*RILAPSKEENLEFEDDDEEGGVGAGLQTPS>S*SSRYLNFKVPKLSSEPGMT>LLAIKIEKIGLKD

Parental  AGQCIDPYITVSVKDLNGIDLTPVQDTPVASRKEDTYVHFNVDIELQKHIEKLTKGAAIFFEFKHYKPKK
          A.QCI..YITVSV.DL.GIDLT.VQDTPVASRKEDTYVHFNVDIELQKHIEKLTKGAAIFFEFKHYKPKK
Retrocopy AWQCIATYITVSV*DLSGIDLTTVQDTPVASRKEDTYVHFNVDIELQKHIEKLTKGAAIFFEFKHYKPKK

Parental  -RFTSTKCFAFMEMDEIKPGPIIIELYKKPTDFKRKKLQLLTKKPLYLHLHQ-TLHKE
          .RFTSTKCFAFMEMDEIKPGPIIIELYKKPT.FKRKKL.LLTKKPLYLHLHQ.TLHKE
Retrocopy <RFTSTKCFAFMEMDEIKPGPIIIELYKKPTEFKRKKL*LLTKKPLYLHLHQ<TLHKE

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_1448 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1448 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 35 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000007593	2 retrocopies	retro_btau_1163, retro_btau_573,
Choloepus hoffmanni	ENSCHOG00000010095	2 retrocopies	retro_chof_1919, retro_chof_97,
Dasypus novemcinctus	ENSDNOG00000008380	5 retrocopies	retro_dnov_1765, retro_dnov_1909, retro_dnov_1961, retro_dnov_2172, retro_dnov_2280,
Homo sapiens	ENSG00000186063	4 retrocopies	retro_hsap_1901, retro_hsap_2076, retro_hsap_2998, retro_hsap_410,
Gorilla gorilla	ENSGGOG00000015289	3 retrocopies	retro_ggor_1394, retro_ggor_1627, retro_ggor_2077,
Macaca mulatta	ENSMMUG00000015025	1 retrocopy	retro_mmul_1918,
Monodelphis domestica	ENSMODG00000004774	3 retrocopies	retro_mdom_1417, retro_mdom_1418, retro_mdom_1448 ,
Mus musculus	ENSMUSG00000042901	3 retrocopies	retro_mmus_1939, retro_mmus_3098, retro_mmus_763,
Nomascus leucogenys	ENSNLEG00000013583	1 retrocopy	retro_nleu_748,
Oryctolagus cuniculus	ENSOCUG00000017030	1 retrocopy	retro_ocun_688,
Pongo abelii	ENSPPYG00000000196	2 retrocopies	retro_pabe_2015, retro_pabe_2485,
Pan troglodytes	ENSPTRG00000002010	3 retrocopies	retro_ptro_1254, retro_ptro_1528, retro_ptro_2027,
Pteropus vampyrus	ENSPVAG00000010662	1 retrocopy	retro_pvam_940,
Tarsius syrichta	ENSTSYG00000005745	3 retrocopies	retro_tsyr_101, retro_tsyr_1795, retro_tsyr_514,
Tursiops truncatus	ENSTTRG00000016594	1 retrocopy	retro_ttru_1084,