RetrogeneDB ID: retro_mdom_1679

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 6:143296075..143296695(-)
• Located in intron of: ENSMODG00000016289

Retrocopy information

• Ensembl ID: ENSMODG00000016293
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: UBE2E3
• Ensembl ID: ENSMODG00000010301
• Aliases: None
• Description: ubiquitin-conjugating enzyme E2E 3 [Source:HGNC Symbol;Acc:12479]

Sequence

>retro_mdom_1679
ATGTCCAGTGATAGGCAAAGGTCAGATGATGAAAGTCCAAGTACCAGCAGTGGTAGTTCAGATGCAGATCAGAGGGACCT
AGCAGCACCAGAACCTGAAGAACAAGAAGAAAGAAAACCCTCTGCCACCCAGCAGAAGAAAAACACCAAACTCTCTAGCA
AAACCACTGCTAAGTTATCCACTAGTGCTAAAAGAATTCAGAAAGAACTAGCTGAAATAACCCTTGATCTACCTCCGAAC
TGCAGTGCTGGGCCTAAAGGAGATAACATTTATGAATGGAGATCAACCATACTTGGACCACCAGGTTCTGTTTATGAAGG
TGGCGTGTTTTTTTCTGGATATCACATTTTCATTAGATTATCCATTTAAGCCACCAAAGGTTACTTTCCGTACCAGAATT
TATCACTGCAACATCAACAAGTCAGGGCGTCATCTGTCTTGATATTCTTAAAGACAACTGGAGTCCTGCTCTGACTATTT
CAAAGGTTTTGCTGTCTATTTGTTCCCTCTTGACAGACTGCAACCCTGCTGATCCTCTGGTTGGAAGCATAGCCACTCAG
TATTTGACCAACAGAGCAGAACATGACAGGATAGCCAGACAGTGGACCAAGAGATACGCA

Alignment

ORF - retro_mdom_1679 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.6 %
• Parental protein coverage: 99.52 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MSSDRQRSDDESPSTSSGSSDADQRDPAAPEPEEQEERKPSATQQKKNTKLSSKTTAKLSTSAKRIQKEL
          MSSDRQRSDDESPSTSSGSSDADQRD.AAPEPEEQEERKPSATQQKKNTKLSSKTTAKLSTSAKRIQKEL
Retrocopy MSSDRQRSDDESPSTSSGSSDADQRDLAAPEPEEQEERKPSATQQKKNTKLSSKTTAKLSTSAKRIQKEL

Parental  AEITLDPPPNCSAGPKGDNIYEWRSTILGPPGSVYEGGV-FFLDITFSSDYPFKPPKVTFRTRIYHCNIN
          AEITLD.PPNCSAGPKGDNIYEWRSTILGPPGSVYEGGV.FFLDITFS.DYPFKPPKVTFRTRIYHCNIN
Retrocopy AEITLDLPPNCSAGPKGDNIYEWRSTILGPPGSVYEGGV>FFLDITFSLDYPFKPPKVTFRTRIYHCNIN

Parental  -SQGVICLDILKDNWSPALTISKVLLSICSLLTDCNPADPLVGSIATQYLTNRAEHDRIARQWTKRYA
          .SQGVICLDILKDNWSPALTISKVLLSICSLLTDCNPADPLVGSIATQYLTNRAEHDRIARQWTKRYA
Retrocopy >SQGVICLDILKDNWSPALTISKVLLSICSLLTDCNPADPLVGSIATQYLTNRAEHDRIARQWTKRYA

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_1679 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1679 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 19 parental genes, and 41 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000014163	3 retrocopies	retro_cfam_2076, retro_cfam_2161, retro_cfam_27,
Choloepus hoffmanni	ENSCHOG00000007325	3 retrocopies	retro_chof_1756, retro_chof_2077, retro_chof_2358,
Ciona intestinalis	ENSCING00000006860	1 retrocopy	retro_cint_33,
Callithrix jacchus	ENSCJAG00000011559	3 retrocopies	retro_cjac_3194, retro_cjac_3911, retro_cjac_3967,
Equus caballus	ENSECAG00000007233	1 retrocopy	retro_ecab_196,
Echinops telfairi	ENSETEG00000019324	2 retrocopies	retro_etel_314, retro_etel_848,
Homo sapiens	ENSG00000170035	1 retrocopy	retro_hsap_4653,
Macaca mulatta	ENSMMUG00000008069	2 retrocopies	retro_mmul_1382, retro_mmul_1834,
Monodelphis domestica	ENSMODG00000010301	2 retrocopies	retro_mdom_1679 , retro_mdom_1688,
Monodelphis domestica	ENSMODG00000011783	2 retrocopies	retro_mdom_17, retro_mdom_884,
Monodelphis domestica	ENSMODG00000017665	2 retrocopies	retro_mdom_2029, retro_mdom_956,
Mus musculus	ENSMUSG00000027011	4 retrocopies	retro_mmus_2814, retro_mmus_3123, retro_mmus_3416, retro_mmus_3571,
Nomascus leucogenys	ENSNLEG00000006290	1 retrocopy	retro_nleu_2068,
Otolemur garnettii	ENSOGAG00000014956	4 retrocopies	retro_ogar_1343, retro_ogar_2512, retro_ogar_2682, retro_ogar_3443,
Pongo abelii	ENSPPYG00000012987	1 retrocopy	retro_pabe_3614,
Rattus norvegicus	ENSRNOG00000004544	1 retrocopy	retro_rnor_1236,
Tupaia belangeri	ENSTBEG00000009932	2 retrocopies	retro_tbel_1986, retro_tbel_3294,
Tarsius syrichta	ENSTSYG00000002281	5 retrocopies	retro_tsyr_1393, retro_tsyr_1809, retro_tsyr_1842, retro_tsyr_1942, retro_tsyr_457,
Tursiops truncatus	ENSTTRG00000001361	1 retrocopy	retro_ttru_1056,