RetrogeneDB ID: retro_mdom_1218

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 3:519909434..519909731(-)
• Located in intron of: ENSMODG00000027556

Retrocopy information

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

Parental gene information

• Parental gene symbol: UBE2B
• Ensembl ID: ENSMODG00000014209
• Aliases: None
• Description: ubiquitin-conjugating enzyme E2B [Source:HGNC Symbol;Acc:12473]

Sequence

>retro_mdom_1218
AGGATGGTAATAGAATTCTCAGAAGAGTATTCGAATAAACCTCCCACTGTTAGGTGCTTATCAAATATGTTTCACCCAAA
TGTCTATGTCATGGTAGCATATGTTTAGATATCCTCTAGAATCATGGGAGTCCAATGTATGGTGTGTCTTCTATTTTAAC
ATCAATTCAGTCTCTGCTGGATGAACCTAATCCCAACAATCCTGCCAATAGCCAAGCAGTGCAGCTTTATCAGGAAAACA
AACTAGAATATGAGAAAAGAGTTTCAGCTATTATTGAACAAAAGCTGGACCGATTCA

Alignment

ORF - retro_mdom_1218 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.19 %
• Parental protein coverage: 65.13 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  KLVIEFSEEYPNKPPTVRFLSKMFHPNVYA-DGSICLDILQNRWSPTYDVSSILTSIQSLLDEPNPNSPA
          ..VIEFSEEY.NKPPTVR.LS.MFHPNVY...GSICLDIL.N..SP.Y.VSSILTSIQSLLDEPNPN.PA
Retrocopy RMVIEFSEEYSNKPPTVRCLSNMFHPNVYV<HGSICLDIL*NHGSPMYGVSSILTSIQSLLDEPNPNNPA

Parental  NSQAAQLYQENKREYEKRVSAIVEQ-SWNDS
          NSQA.QLYQENK.EYEKRVSAI.EQ.SW.DS
Retrocopy NSQAVQLYQENKLEYEKRVSAIIEQ>SWTDS

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	174.98 RPM
SRP007412_cerebellum	0.00 RPM	113.61 RPM
SRP007412_heart	0.00 RPM	405.68 RPM
SRP007412_kidney	0.00 RPM	158.02 RPM
SRP007412_liver	0.00 RPM	158.60 RPM
SRP007412_testis	0.00 RPM	188.77 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_1218 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1218 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.

---

Parental genes homology:

Parental genes homology involve 14 parental genes, and 46 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000001019	2 retrocopies	retro_cfam_2099, retro_cfam_216,
Dipodomys ordii	ENSDORG00000002525	1 retrocopy	retro_dord_646,
Echinops telfairi	ENSETEG00000006522	2 retrocopies	retro_etel_1531, retro_etel_771,
Macropus eugenii	ENSMEUG00000004740	1 retrocopy	retro_meug_718,
Myotis lucifugus	ENSMLUG00000012910	4 retrocopies	retro_mluc_1319, retro_mluc_1520, retro_mluc_2216, retro_mluc_478,
Monodelphis domestica	ENSMODG00000010209	1 retrocopy	retro_mdom_341,
Monodelphis domestica	ENSMODG00000014209	1 retrocopy	retro_mdom_1218 ,
Mus musculus	ENSMUSG00000020390	1 retrocopy	retro_mmus_736,
Ochotona princeps	ENSOPRG00000006668	1 retrocopy	retro_opri_1186,
Pteropus vampyrus	ENSPVAG00000012430	1 retrocopy	retro_pvam_141,
Sarcophilus harrisii	ENSSHAG00000016143	2 retrocopies	retro_shar_12, retro_shar_173,
Tupaia belangeri	ENSTBEG00000010294	26 retrocopies	retro_tbel_2107, retro_tbel_2133, retro_tbel_2137, retro_tbel_2157, retro_tbel_2285, retro_tbel_2286, retro_tbel_2287, retro_tbel_2288, retro_tbel_2385, retro_tbel_2616, retro_tbel_2945, retro_tbel_3251, retro_tbel_3252, retro_tbel_3253, retro_tbel_3284, retro_tbel_3878, retro_tbel_4086, retro_tbel_4087, retro_tbel_4238, retro_tbel_4289, retro_tbel_4443, retro_tbel_4585, retro_tbel_4680, retro_tbel_4684, retro_tbel_4685, retro_tbel_4693,
Tarsius syrichta	ENSTSYG00000011148	2 retrocopies	retro_tsyr_151, retro_tsyr_553,
Tursiops truncatus	ENSTTRG00000016861	1 retrocopy	retro_ttru_700,