RetrogeneDB ID: retro_mdom_1102

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 3:110510994..110511625(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SLC25A39
• Ensembl ID: ENSMODG00000011561
• Aliases: None
• Description: solute carrier family 25, member 39 [Source:HGNC Symbol;Acc:24279]

Sequence

>retro_mdom_1102
CTCCGTGCAACTCTGGTGATGACTTCTGACCTCTATGCACCCATGGTGGCAGGGGCTATGGCCGGTGCTGGGTACTGTGA
CTGTGATCAGCCCCCTGAAGCTGGTGAGAACAAAACTTCAGACTCAGCATCTGTCCTACCGTGAATGTGGGGGCTGTTTC
CGGGCAGCCATGTCCCAGGGCAGCTGAAGTTCTCTGTGGCTTGGCTGTGGTGCCACTGTGTTAAAGCATGTGCCTTTCTC
ATCCCTGTACTGGTTTAACTATGAGTTAGTGAAGGTATGGCTCTGTAAGATGGTAGCCAAGGACTGGACTTCAGTCGGCA
TCAACTTTGTGTCTGGAGCCTTCTCAGGAACAGTGGCTGCTGTGCTCACACTGCCTTTAGATGTGGTGAAAACTCAGCAT
CAGATGGAGCTGGGAAGCTTGGGAGCCCTGAGAATGACATCTCCATGCTCCACTTCCACCTGGCTGCTGCTCCAGCAGAT
TCAGGCTGAGTCTGGGGCCAGAGGACCCTTTGCAGGCTTCCTCCCATGGATCATCAAGGCATCCCCCTCCTGTGCCATTA
TGATCAGCACCTACGAATTTAGCAAAAAATTTTTCCAGAGATTGAACTTGGAAAATTGCCCCCGGGGACCC

Alignment

ORF - retro_mdom_1102 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.99 %
• Parental protein coverage: 58.33 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LLCSRTVTSDLYAPMVAGAMAR-LGTVTVISPLELVRTKLQAQHLSYRELGACVRAAVSQGGWRSLWLGW
          L......TSDLYAPMVAGAMA..LGTVTVISPL.LVRTKLQ.QHLSYRE.G.C.RAA.SQG...SLWLG.
Retrocopy LRATLVMTSDLYAPMVAGAMAG>LGTVTVISPLKLVRTKLQTQHLSYRECGGCFRAAMSQGS*SSLWLGC

Parental  GATALRDVPFSALYWFNYELVKTWLCKMAAKDRTSVGISFVSGAFSGTVAAVLTLPFDVVKTQRQMELGS
          GAT.L..VPFS.LYWFNYELVK.WLCKM.AKD.TSVGI.FVSGAFSGTVAAVLTLP.DVVKTQ.QMELGS
Retrocopy GATVLKHVPFSSLYWFNYELVKVWLCKMVAKDWTSVGINFVSGAFSGTVAAVLTLPLDVVKTQHQMELGS

Parental  VGALRVTSPRSTSTWLLLRRIQAESGARGLFAGFLPRIIKAAPSCAIMISTYEFSKNFFQRLNLEKCPRG
          .GALR.TSP.STSTWLLL..IQAESGARG.FAGFLP.IIKA.PSCAIMISTYEFSK.FFQRLNLE.CPRG
Retrocopy LGALRMTSPCSTSTWLLLQQIQAESGARGPFAGFLPWIIKASPSCAIMISTYEFSKKFFQRLNLENCPRG

Parental  P
          P
Retrocopy P

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_1102 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1102 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 9 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000008556	1 retrocopy	retro_dnov_1866,
Echinops telfairi	ENSETEG00000002713	1 retrocopy	retro_etel_823,
Homo sapiens	ENSG00000013306	1 retrocopy	retro_hsap_290,
Myotis lucifugus	ENSMLUG00000001925	2 retrocopies	retro_mluc_2296, retro_mluc_646,
Monodelphis domestica	ENSMODG00000011561	1 retrocopy	retro_mdom_1102 ,
Pongo abelii	ENSPPYG00000008333	1 retrocopy	retro_pabe_383,
Pan troglodytes	ENSPTRG00000009272	1 retrocopy	retro_ptro_239,
Rattus norvegicus	ENSRNOG00000020994	2 retrocopies	retro_rnor_1892, retro_rnor_2884,
Ictidomys tridecemlineatus	ENSSTOG00000004189	1 retrocopy	retro_itri_447,