RetrogeneDB ID: retro_mdom_1045

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 3:363377077..363377785(+)
• Located in intron of: ENSMODG00000006474

Retrocopy information

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

Parental gene information

• Parental gene symbol: SDE2
• Ensembl ID: ENSMODG00000005979
• Aliases: None
• Description: SDE2 telomere maintenance homolog (S. pombe) [Source:HGNC Symbol;Acc:26643]

Sequence

>retro_mdom_1045
ACTAATCAAGAAGCATGTTATGATCTCAGTGGAAGGAGACTTCGCGATGTCAACCATGAAAAGGCAATGGCTGAATGGGT
AAAACAGCAAGCTGATTGAGAAGCAGAAAAAGAACAAAGACTCCTGGAGAGGCTGCAGTGGAAGCTGGTGGAACCAAAGC
ACCACTTTACCAGTCCTGACTATCAGCAGCAGTGTCATGAGATGGCTGAGCGCTTGGAGGACTCAGTCCTCAAAGGTATG
CAGAATGCCTCCAGCAAGATGGTGTCACCTGAAATTAGTGATAATAGAAAGTAACCTAGTGAACCTGAGATAAGTGGTGG
AAACAAATCAAGGAAAAGGAAATGCTTTTGGATGGGTATAGAAGAACTAGAGGACGCTGCTGGAAGTTCAGATGATGGGG
ACAGTGAAGAAGTCCCCAGCACTTCAGGAATGAGCTTCCACTCACCAAATGACTGTCACAGTAATGCTGACAAGTCAGCA
GAATCCATGAGTTGTAAGAATTCTGTAGGAATGAGTCCTGGCATCAGTGTATCAGAAAAACTACAGGTGTCCACGGTTAA
TTCTGAGACCATTGCCACAACAGAAATGTGTGGTGAGCTGGGTGAGAAGCCCACACAGAAGCAGGAGAAATCAGAAGAGA
TGGATATAGAGAGAAAAATCAGCATGGAGCAGGAAGCATATATGACAGAAATTACAGCACAAACTACA

Alignment

ORF - retro_mdom_1045 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.56 %
• Parental protein coverage: 54.13 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  TNREACRDLSGRRLRDVNHEKAMAEWVKQQAEREAEKEQRRLERLQRKLVEPKHHFTSPDYQQQCHEMAE
          TN.EAC.DLSGRRLRDVNHEKAMAEWVKQQA..EAEKEQR.LERLQ.KLVEPKHHFTSPDYQQQCHEMAE
Retrocopy TNQEACYDLSGRRLRDVNHEKAMAEWVKQQAD*EAEKEQRLLERLQWKLVEPKHHFTSPDYQQQCHEMAE

Parental  RLEDSVLKGMQAASSKMVSPEISDNRKRPSEPEIIGGNKSRKRKCFWMGMEGLEDAAGSSDDGDSEEVPS
          RLEDSVLKGMQ.ASSKMVSPEISDNRK.PSEPEI.GGNKSRKRKCFWMG.E.LEDAAGSSDDGDSEEVPS
Retrocopy RLEDSVLKGMQNASSKMVSPEISDNRK*PSEPEISGGNKSRKRKCFWMGIEELEDAAGSSDDGDSEEVPS

Parental  TSGMSFHSPNDCHSNADKSAESMSCKDSVGMSPGISVSEKLQVPTVNSEAIAITEVCGELGEKPTQKQEK
          TSGMSFHSPNDCHSNADKSAESMSCK.SVGMSPGISVSEKLQV.TVNSE.IA.TE.CGELGEKPTQKQEK
Retrocopy TSGMSFHSPNDCHSNADKSAESMSCKNSVGMSPGISVSEKLQVSTVNSETIATTEMCGELGEKPTQKQEK

Parental  AEEMDVDRKISMEQEACVTGKKEETS
          .EEMD..RKISMEQEA..T.....T.
Retrocopy SEEMDIERKISMEQEAYMTEITAQTT

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_1045 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1045 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Monodelphis domestica	ENSMODG00000005979	1 retrocopy	retro_mdom_1045 ,
Monodelphis domestica	ENSMODG00000017729	1 retrocopy	retro_mdom_269,