RetrogeneDB ID: retro_mdom_341

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 1:221810928..221811287(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: UBE2A
• Ensembl ID: ENSMODG00000010209
• Aliases: None
• Description: ubiquitin-conjugating enzyme E2A [Source:HGNC Symbol;Acc:12472]

Sequence

>retro_mdom_341
GCCTTATCAGAGAATAGCATCATGATGTAGATTCGAGTTGTTTTGGGGCTCAAGGGAACCCCATTTGAAGATGTCATATT
TAAACTTAGAAGAGAATTCACCAAAGAATATTTAAACAAACCATCCATTGTAAGATTTGCCCCTCGAATATTTCATACAA
AAATCTATGAGGATGGTAATATATGCCCAGATATACTTCAAAATCATTGGAATCCAACCTATGACGTCTCCTCTATTTCA
ATATCCTTAAGGTCTTTATTAAATGGGCCTGATCCCAACAGTGTAGCCAACAGCTGGGATACTCAGCTATAGCAGGGAAC
AAGTAAGAATATCAGGCTGTGACCAGCGAGATTGCACAA

Alignment

ORF - retro_mdom_341 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.02 %
• Parental protein coverage: 78.95 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  APSENNIMVWNAVIFGPEGTPFEDGTFKLTIEFTEEYPNKPPTVRFVSKMFHPNVYADGSICLDILQNRW
          A.SEN.IM....V..G..GTPFED..FKL..EFT.EY.NKP..VRF....FH...Y.DG.IC.DILQN.W
Retrocopy ALSENSIMM*IRVVLGLKGTPFEDVIFKLRREFTKEYLNKPSIVRFAPRIFHTKIYEDGNICPDILQNHW

Parental  SPTYDVSSILTSIQSLLDEPNPNSPANSQAAQLYQ-ENKREYEKRVSAIVE
          .PTYDVSSI..S..SLL..P.PNS.ANS...QL.Q..NK.EY....S.I..
Retrocopy NPTYDVSSISISLRSLLNGPDPNSVANSWDTQL*Q<GNK*EYQAVTSEIAQ

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_341 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_341 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 12 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000001079	1 retrocopy	retro_chof_1316,
Callithrix jacchus	ENSCJAG00000005098	2 retrocopies	retro_cjac_1180, retro_cjac_3862,
Cavia porcellus	ENSCPOG00000011908	1 retrocopy	retro_cpor_489,
Dasypus novemcinctus	ENSDNOG00000007060	1 retrocopy	retro_dnov_215,
Macropus eugenii	ENSMEUG00000003026	1 retrocopy	retro_meug_2180,
Monodelphis domestica	ENSMODG00000010209	1 retrocopy	retro_mdom_341 ,
Monodelphis domestica	ENSMODG00000014209	1 retrocopy	retro_mdom_1218,
Oryctolagus cuniculus	ENSOCUG00000016739	1 retrocopy	retro_ocun_183,
Otolemur garnettii	ENSOGAG00000024335	1 retrocopy	retro_ogar_3203,
Procavia capensis	ENSPCAG00000005045	1 retrocopy	retro_pcap_222,
Sus scrofa	ENSSSCG00000012621	1 retrocopy	retro_sscr_29,
Tarsius syrichta	ENSTSYG00000000888	1 retrocopy	retro_tsyr_676,