RetrogeneDB ID: retro_mdom_2020

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: X:51780096..51780457(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: UBE2C
• Ensembl ID: ENSMODG00000013661
• Aliases: None
• Description: ubiquitin-conjugating enzyme E2C [Source:HGNC Symbol;Acc:15937]

Sequence

>retro_mdom_2020
CTCTTCAAATGAGTTGAGATCATTCATGGGGCAACTAAGACAGTATATCAAGACCTGAAGTATAAGCTCTTCTTGGAGTT
CCCCAGCAACTACCCATATAATGCTTCCATTGTGCAATTTGTCACACCCTGTTACCATCACAGTGTGAGCATCCAAGGCA
ATATCTACTTGGAAATCCTTAAGGACAAGTGGTCAATTTTCTATAATGTTGGGACCATCTTATTATCTACCCAGAGTCTT
CTAGAAGTGCACAACATTGACAACCCAATGAAAACATATACTACTGAGATCTGGATAAATCTCACAGCCTTCAAAAAAGT
GCCTACTAGAAACCTACCTGAAGCATGCCACTAGTCAAGAA

Alignment

ORF - retro_mdom_2020 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.94 %
• Parental protein coverage: 66.67 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LFKWVGTIHGAAGTVYEDLRYKLSLEFPSGYPYNAPTVKFVTPCYHPNVDTQGNICLDILKDKWSALYDV
          LFK.V..IHGA..TVY.DL.YKL.LEFPS.YPYNA..V.FVTPCYH..V..QGNI.L.ILKDKWS..Y.V
Retrocopy LFK*VEIIHGATKTVYQDLKYKLFLEFPSNYPYNASIVQFVTPCYHHSVSIQGNIYLEILKDKWSIFYNV

Parental  RTILLSIQSLLGEPNIDSPLNTHAAELWTNPTAFKKY-LLETYMKQVTSQE
          .TILLS.QSLL...NID.P..T...E.W.N.TAFKK..LLETY.K..TSQE
Retrocopy GTILLSTQSLLEVHNIDNPMKTYTTEIWINLTAFKKV>LLETYLKHATSQE

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	9.30 RPM
SRP007412_cerebellum	0.00 RPM	5.88 RPM
SRP007412_heart	0.00 RPM	16.35 RPM
SRP007412_kidney	0.00 RPM	2.63 RPM
SRP007412_liver	0.00 RPM	2.52 RPM
SRP007412_testis	0.00 RPM	74.64 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_2020 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_2020 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 28 parental genes, and 123 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000012547	5 retrocopies	retro_amel_1122, retro_amel_1353, retro_amel_157, retro_amel_1621, retro_amel_635,
Bos taurus	ENSBTAG00000016746	1 retrocopy	retro_btau_249,
Canis familiaris	ENSCAFG00000009745	6 retrocopies	retro_cfam_1031, retro_cfam_1805, retro_cfam_1878, retro_cfam_2078, retro_cfam_290, retro_cfam_356,
Cavia porcellus	ENSCPOG00000014102	2 retrocopies	retro_cpor_1007, retro_cpor_211,
Dipodomys ordii	ENSDORG00000011774	4 retrocopies	retro_dord_157, retro_dord_386, retro_dord_421, retro_dord_84,
Equus caballus	ENSECAG00000014619	2 retrocopies	retro_ecab_297, retro_ecab_316,
Erinaceus europaeus	ENSEEUG00000010643	14 retrocopies	retro_eeur_113, retro_eeur_177, retro_eeur_249, retro_eeur_253, retro_eeur_266, retro_eeur_272, retro_eeur_294, retro_eeur_346, retro_eeur_375, retro_eeur_518, retro_eeur_592, retro_eeur_604, retro_eeur_641, retro_eeur_80,
Echinops telfairi	ENSETEG00000012346	18 retrocopies	retro_etel_1212, retro_etel_1500, retro_etel_1560, retro_etel_157, retro_etel_1634, retro_etel_1729, retro_etel_1853, retro_etel_1856, retro_etel_2013, retro_etel_221, retro_etel_321, retro_etel_324, retro_etel_400, retro_etel_628, retro_etel_689, retro_etel_764, retro_etel_824, retro_etel_909,
Felis catus	ENSFCAG00000001885	4 retrocopies	retro_fcat_1440, retro_fcat_1530, retro_fcat_1667, retro_fcat_1734,
Homo sapiens	ENSG00000175063	3 retrocopies	retro_hsap_1474, retro_hsap_1922, retro_hsap_2935,
Gorilla gorilla	ENSGGOG00000026061	3 retrocopies	retro_ggor_1130, retro_ggor_1402, retro_ggor_2035,
Loxodonta africana	ENSLAFG00000003164	1 retrocopy	retro_lafr_73,
Macropus eugenii	ENSMEUG00000007177	14 retrocopies	retro_meug_1021, retro_meug_1128, retro_meug_1203, retro_meug_1398, retro_meug_1435, retro_meug_145, retro_meug_1476, retro_meug_1504, retro_meug_1575, retro_meug_1773, retro_meug_1808, retro_meug_2034, retro_meug_334, retro_meug_645,
Microcebus murinus	ENSMICG00000011218	2 retrocopies	retro_mmur_332, retro_mmur_988,
Myotis lucifugus	ENSMLUG00000006715	4 retrocopies	retro_mluc_2164, retro_mluc_2220, retro_mluc_600, retro_mluc_636,
Macaca mulatta	ENSMMUG00000021023	4 retrocopies	retro_mmul_1345, retro_mmul_170, retro_mmul_1951, retro_mmul_777,
Monodelphis domestica	ENSMODG00000013661	6 retrocopies	retro_mdom_1549, retro_mdom_1552, retro_mdom_1732, retro_mdom_1970, retro_mdom_2020 , retro_mdom_415,
Mustela putorius furo	ENSMPUG00000017619	2 retrocopies	retro_mputfur_103, retro_mputfur_189,
Mus musculus	ENSMUSG00000001403	5 retrocopies	retro_mmus_1344, retro_mmus_1593, retro_mmus_1770, retro_mmus_2881, retro_mmus_3512,
Oryctolagus cuniculus	ENSOCUG00000012176	3 retrocopies	retro_ocun_1005, retro_ocun_1294, retro_ocun_348,
Otolemur garnettii	ENSOGAG00000004989	3 retrocopies	retro_ogar_2347, retro_ogar_249, retro_ogar_3067,
Ochotona princeps	ENSOPRG00000014284	4 retrocopies	retro_opri_1009, retro_opri_1055, retro_opri_222, retro_opri_50,
Pongo abelii	ENSPPYG00000011071	4 retrocopies	retro_pabe_1155, retro_pabe_1221, retro_pabe_1589, retro_pabe_2519,
Pan troglodytes	ENSPTRG00000013564	1 retrocopy	retro_ptro_38,
Pteropus vampyrus	ENSPVAG00000000369	1 retrocopy	retro_pvam_423,
Rattus norvegicus	ENSRNOG00000015131	5 retrocopies	retro_rnor_1390, retro_rnor_2131, retro_rnor_2470, retro_rnor_719, retro_rnor_864,
Sus scrofa	ENSSSCG00000007423	1 retrocopy	retro_sscr_643,
Tursiops truncatus	ENSTTRG00000015987	1 retrocopy	retro_ttru_1752,