RetrogeneDB ID: retro_mdom_518

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 1:133942470..133943019(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMODG00000012810
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: C9orf78
• Ensembl ID: ENSMODG00000006832
• Aliases: None
• Description: chromosome 9 open reading frame 78 [Source:HGNC Symbol;Acc:24932]

Sequence

>retro_mdom_518
CTGGAGACCATGCAGGCGGGTAAGACTTTCCGCAAGCGGCGCGACGACTCGGAGTCGGAGTCCGATGAGCAGGACAGCGA
GGAGGTCCGGTTGAAACTGGAAGAAACCAAAGAAGTTCAGAGTTTGAGAAGACGTCCTAATGGGGTGAGTGCTGTAGCCC
TCCTGGTTGGGGAGAAAGTACAGGAAGAGACAACTCTAGTGGATGATCCCTTTAAGATCAAGGCTGGTGGGATGGTGGAC
ATGAAGAAACTTAAGGAAAGAAATAAAGACAGGATTAATGAAGAGGAGGACCTCAATTTAGGAACATCATTTTCAGCAGA
AACCAATCGAAGGGATGAAGATGCAGACATGATGAAGTACTTTGAGACTGAGCTAAAGAAGAGGAAAGGAATTGTGGAAA
ATGAGGAGCAGAAGGTGAAGTTGAAGAATGCTGAAGACTGTCTCTACGAGCTCCCTGAGAACATCCGAGTCTCCTCAGCT
AAGAAAACAGAAGAGATGCTGTCCAACCAGATGCTGAGTGGCATCCCTGAGGTGGATTTGGGCATTGAT

Alignment

ORF - retro_mdom_518 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.36 %
• Parental protein coverage: 60.8 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LETMRAGKTFRKRRDDSESESDEQDSEEVRLKLEETKEVQSLRRRPNGVSAVALLVGEKVQEETTLVDDP
          LETM.AGKTFRKRRDDSESESDEQDSEEVRLKLEETKEVQSLRRRPNGVSAVALLVGEKVQEETTLVDDP
Retrocopy LETMQAGKTFRKRRDDSESESDEQDSEEVRLKLEETKEVQSLRRRPNGVSAVALLVGEKVQEETTLVDDP

Parental  FKIKAGGMVDMKKLKERNKDRINEEEDLNLGTSFSAETNRRDEDADMMKYIETELKKRKGIVENEEQKVK
          FKIKAGGMVDMKKLKERNKDRINEEEDLNLGTSFSAETNRRDEDADMMKY.ETELKKRKGIVENEEQKVK
Retrocopy FKIKAGGMVDMKKLKERNKDRINEEEDLNLGTSFSAETNRRDEDADMMKYFETELKKRKGIVENEEQKVK

Parental  LKNAEDCLYELPENIRVSSAKKTEEMLSNQMLSGIPEVDLGIE
          LKNAEDCLYELPENIRVSSAKKTEEMLSNQMLSGIPEVDLGI.
Retrocopy LKNAEDCLYELPENIRVSSAKKTEEMLSNQMLSGIPEVDLGID

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	5.96 RPM	36.95 RPM
SRP007412_cerebellum	1.96 RPM	27.10 RPM
SRP007412_heart	3.39 RPM	39.07 RPM
SRP007412_kidney	0.00 RPM	52.67 RPM
SRP007412_liver	6.55 RPM	56.89 RPM
SRP007412_testis	15.91 RPM	152.83 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_518 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_518 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 21 parental genes, and 34 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000020307	1 retrocopy	retro_btau_1138,
Canis familiaris	ENSCAFG00000019979	1 retrocopy	retro_cfam_116,
Choloepus hoffmanni	ENSCHOG00000013895	3 retrocopies	retro_chof_1103, retro_chof_1747, retro_chof_978,
Callithrix jacchus	ENSCJAG00000020318	3 retrocopies	retro_cjac_1757, retro_cjac_2299, retro_cjac_2778,
Cavia porcellus	ENSCPOG00000009285	1 retrocopy	retro_cpor_712,
Dasypus novemcinctus	ENSDNOG00000019214	1 retrocopy	retro_dnov_1540,
Equus caballus	ENSECAG00000018958	1 retrocopy	retro_ecab_174,
Homo sapiens	ENSG00000136819	3 retrocopies	retro_hsap_2872, retro_hsap_2913, retro_hsap_320,
Gorilla gorilla	ENSGGOG00000013358	1 retrocopy	retro_ggor_1990,
Macropus eugenii	ENSMEUG00000010524	3 retrocopies	retro_meug_1046, retro_meug_1241, retro_meug_508,
Microcebus murinus	ENSMICG00000009596	1 retrocopy	retro_mmur_1466,
Macaca mulatta	ENSMMUG00000003795	2 retrocopies	retro_mmul_1460, retro_mmul_1870,
Monodelphis domestica	ENSMODG00000006832	1 retrocopy	retro_mdom_518 ,
Mus musculus	ENSMUSG00000026851	1 retrocopy	retro_mmus_2978,
Nomascus leucogenys	ENSNLEG00000017658	3 retrocopies	retro_nleu_1763, retro_nleu_614, retro_nleu_823,
Otolemur garnettii	ENSOGAG00000009770	1 retrocopy	retro_ogar_1015,
Pongo abelii	ENSPPYG00000019685	1 retrocopy	retro_pabe_2426,
Pan troglodytes	ENSPTRG00000021465	3 retrocopies	retro_ptro_1943, retro_ptro_1969, retro_ptro_258,
Sarcophilus harrisii	ENSSHAG00000012313	1 retrocopy	retro_shar_746,
Ictidomys tridecemlineatus	ENSSTOG00000020630	1 retrocopy	retro_itri_1783,
Tupaia belangeri	ENSTBEG00000013115	1 retrocopy	retro_tbel_514,