RetrogeneDB ID: retro_mdom_177

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 4:383653759..383654404(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMODG00000023771
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000008731
• Aliases: None
• Description: None

Sequence

>retro_mdom_177
ATGGGCCGTCGTCCCGCCCACTGTTACGGGTACTGTAAAAACAAGCTGTATCCCAAGTCCCGTTTCTGCAGGGGAGTTCC
CGATGCCAAAATCCGAATCTTTGATCTTGGGAGGAAGAAAGCAAAAGTGGACAAGTTTCCACTGTGTGGCCACATGGTGT
CTGATGAGTACGAACAGCTGTCATCTGAAGTCTTGGAAGCAGCTTGCATCTGTGCCAACAAGTACATGGTGAAGAGCTGT
GGCAAGGATGGCTTCCATATTCGCATGTGCCTCCACCCTTTTCATGTCATTTGCATCAATAAGATGCTATCATGTGCTGG
GGCTGATAGACTCCAGACTGACATGTGGGGGGCTGTTGGGAAGCCCCAGGGCACCGTAGCCCGTGTCCACATTGGCCAGG
TTATCATGTCCATTCAGACCAAGGCCCAGAACAAAGAACATGTGATTGAAGCTTTGTGGAGGGCTAAGTTCAAGTTCCCT
GGCCGCCAAAAGATCCATATCTCCAAGAAATGGGGTTTCACCAAGTTCAATGCCGATCAGTTTGAGGATATGATCTCTGA
GAGGTGGCTCATTCCTGATGGCTGTGGGGTCAAATACATCCCTAACCGAGGCCCCTTGGACAAGTGGCGCGCGCTCCACT
CCTGA

Alignment

ORF - retro_mdom_177 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.06 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MGRRPARCYRYCKNKPYPKSRFCRGVPDAKIRIFDLGRKKAKVDEFPLCGHMVSDEYEQLSSEALEAARI
          MGRRPA.CY.YCKNK.YPKSRFCRGVPDAKIRIFDLGRKKAKVD.FPLCGHMVSDEYEQLSSE.LEAA.I
Retrocopy MGRRPAHCYGYCKNKLYPKSRFCRGVPDAKIRIFDLGRKKAKVDKFPLCGHMVSDEYEQLSSEVLEAACI

Parental  CANKYMVKSCGKDGFHIRVRLHPFHVIRINKMLSCAGADRLQTGMRGAFGKPQGTVARVHIGQVIMSIRT
          CANKYMVKSCGKDGFHIR..LHPFHVI.INKMLSCAGADRLQT.M.GA.GKPQGTVARVHIGQVIMSI.T
Retrocopy CANKYMVKSCGKDGFHIRMCLHPFHVICINKMLSCAGADRLQTDMWGAVGKPQGTVARVHIGQVIMSIQT

Parental  KVQNKEHVIEALRRAKFKFPGRQKIHISKKWGFTKFNADQFEDMISEKRLIPDGCGVKYIPNRGPLDKWR
          K.QNKEHVIEAL.RAKFKFPGRQKIHISKKWGFTKFNADQFEDMISE..LIPDGCGVKYIPNRGPLDKWR
Retrocopy KAQNKEHVIEALWRAKFKFPGRQKIHISKKWGFTKFNADQFEDMISERWLIPDGCGVKYIPNRGPLDKWR

Parental  ALHS
          ALHS
Retrocopy ALHS

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_177 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_177 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 26 parental genes, and 82 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000007454	2 retrocopies	retro_btau_140, retro_btau_99,
Callithrix jacchus	ENSCJAG00000011822	5 retrocopies	retro_cjac_156, retro_cjac_174, retro_cjac_260, retro_cjac_277, retro_cjac_61,
Cavia porcellus	ENSCPOG00000002355	1 retrocopy	retro_cpor_64,
Dipodomys ordii	ENSDORG00000004369	2 retrocopies	retro_dord_14, retro_dord_715,
Equus caballus	ENSECAG00000017154	1 retrocopy	retro_ecab_113,
Echinops telfairi	ENSETEG00000001712	10 retrocopies	retro_etel_1073, retro_etel_1284, retro_etel_1517, retro_etel_1654, retro_etel_249, retro_etel_338, retro_etel_403, retro_etel_47, retro_etel_538, retro_etel_631,
Felis catus	ENSFCAG00000011395	1 retrocopy	retro_fcat_81,
Homo sapiens	ENSG00000147403	3 retrocopies	retro_hsap_2030, retro_hsap_3265, retro_hsap_3437,
Gorilla gorilla	ENSGGOG00000000131	4 retrocopies	retro_ggor_1873, retro_ggor_2425, retro_ggor_253, retro_ggor_61,
Loxodonta africana	ENSLAFG00000031860	1 retrocopy	retro_lafr_616,
Macropus eugenii	ENSMEUG00000013163	3 retrocopies	retro_meug_1839, retro_meug_5, retro_meug_547,
Microcebus murinus	ENSMICG00000004658	2 retrocopies	retro_mmur_1077, retro_mmur_4,
Myotis lucifugus	ENSMLUG00000014337	3 retrocopies	retro_mluc_1592, retro_mluc_191, retro_mluc_275,
Macaca mulatta	ENSMMUG00000005494	5 retrocopies	retro_mmul_1506, retro_mmul_1654, retro_mmul_307, retro_mmul_335, retro_mmul_906,
Monodelphis domestica	ENSMODG00000008731	2 retrocopies	retro_mdom_177 , retro_mdom_829,
Mustela putorius furo	ENSMPUG00000009320	3 retrocopies	retro_mputfur_1405, retro_mputfur_54, retro_mputfur_84,
Mus musculus	ENSMUSG00000008682	1 retrocopy	retro_mmus_71,
Oryctolagus cuniculus	ENSOCUG00000015919	2 retrocopies	retro_ocun_107, retro_ocun_147,
Otolemur garnettii	ENSOGAG00000000099	3 retrocopies	retro_ogar_293, retro_ogar_2995, retro_ogar_3284,
Pongo abelii	ENSPPYG00000020874	5 retrocopies	retro_pabe_173, retro_pabe_1854, retro_pabe_2036, retro_pabe_2843, retro_pabe_2955,
Rattus norvegicus	ENSRNOG00000027149	5 retrocopies	retro_rnor_1007, retro_rnor_1090, retro_rnor_270, retro_rnor_2998, retro_rnor_482,
Sorex araneus	ENSSARG00000012256	1 retrocopy	retro_sara_2,
Ictidomys tridecemlineatus	ENSSTOG00000011857	2 retrocopies	retro_itri_174, retro_itri_506,
Tupaia belangeri	ENSTBEG00000003734	1 retrocopy	retro_tbel_61,
Tarsius syrichta	ENSTSYG00000004067	7 retrocopies	retro_tsyr_11, retro_tsyr_1644, retro_tsyr_1739, retro_tsyr_1986, retro_tsyr_559, retro_tsyr_640, retro_tsyr_960,
Tursiops truncatus	ENSTTRG00000011407	7 retrocopies	retro_ttru_1085, retro_ttru_122, retro_ttru_1226, retro_ttru_1437, retro_ttru_820, retro_ttru_858, retro_ttru_867,