RetrogeneDB ID: retro_mdom_1706

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 7:11065223..11065543(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPS24
• Ensembl ID: ENSMODG00000025091
• Aliases: None
• Description: ribosomal protein S24 [Source:HGNC Symbol;Acc:10411]

Sequence

>retro_mdom_1706
AATGACACTGTAGCCATAAGAACCAGGAAGTTCATGACAAACAGATTTCTTCAATGTAAACGTGTTACAGATGTCCTTCA
TCCTCAAAAGGCTACAGTACCAAAGACTGAACGTTTGAGAAAAACTGCTCAAGATATAGAAGACAATTCCAGATGCCATT
TTTGTCTTTGGATTGTCAAAAACCATTCTGGGGATGAACAACAGGCTTTGTCATGATTTACGATTCCTTTGACTATGCAA
AGAAAAATGAACCAAAACACAGACTTGCAAGCAATGGCATGAATAATAAGAAAGACATCAAGAAAGCAGCAAAAGGGGAG

Alignment

ORF - retro_mdom_1706 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.55 %
• Parental protein coverage: 53.47 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  NDTVTIRTRKFMTNRLLQRKQMVIDVLHPGKATVPKTE-IREKLAKMYKTTPDVIFVFGF-RTHFGGGKT
          NDTV.IRTRKFMTNR.LQ.K..V.DVLHP.KATVPKTE...EKL.K..KT.PD.IFVFG.....F.G..T
Retrocopy NDTVAIRTRKFMTNRFLQCKR-VTDVLHPQKATVPKTE>V*EKLLKI*KTIPDAIFVFGL>QKPFWG*TT

Parental  TGFGMIYDSLDYAKKNEPKHRLARHGLYEKKKTSRKQRKE
          .GF.MIYDS.DYAKKNEPKHRLA..G...KK........E
Retrocopy -GFVMIYDSFDYAKKNEPKHRLASNGMNNKKDIKKAAKGE

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	641.99 RPM
SRP007412_cerebellum	0.00 RPM	538.32 RPM
SRP007412_heart	0.00 RPM	899.08 RPM
SRP007412_kidney	0.00 RPM	1983.15 RPM
SRP007412_liver	0.00 RPM	1921.31 RPM
SRP007412_testis	0.00 RPM	594.02 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_1706 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1706 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 11 parental genes, and 82 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000010243	18 retrocopies	retro_dnov_1299, retro_dnov_1305, retro_dnov_1394, retro_dnov_1444, retro_dnov_1470, retro_dnov_1471, retro_dnov_168, retro_dnov_1889, retro_dnov_1920, retro_dnov_1985, retro_dnov_2074, retro_dnov_2357, retro_dnov_288, retro_dnov_309, retro_dnov_551, retro_dnov_73, retro_dnov_782, retro_dnov_92,
Equus caballus	ENSECAG00000016939	5 retrocopies	retro_ecab_239, retro_ecab_398, retro_ecab_422, retro_ecab_514, retro_ecab_746,
Echinops telfairi	ENSETEG00000007481	32 retrocopies	retro_etel_1119, retro_etel_1242, retro_etel_1274, retro_etel_1339, retro_etel_1395, retro_etel_1663, retro_etel_1688, retro_etel_1783, retro_etel_1800, retro_etel_1806, retro_etel_183, retro_etel_1901, retro_etel_1934, retro_etel_1978, retro_etel_1991, retro_etel_2040, retro_etel_2104, retro_etel_223, retro_etel_287, retro_etel_289, retro_etel_369, retro_etel_422, retro_etel_476, retro_etel_503, retro_etel_523, retro_etel_67, retro_etel_744, retro_etel_752, retro_etel_815, retro_etel_904, retro_etel_91, retro_etel_94,
Gadus morhua	ENSGMOG00000012595	1 retrocopy	retro_gmor_15,
Microcebus murinus	ENSMICG00000005951	7 retrocopies	retro_mmur_1308, retro_mmur_132, retro_mmur_1338, retro_mmur_1636, retro_mmur_217, retro_mmur_583, retro_mmur_902,
Monodelphis domestica	ENSMODG00000025091	3 retrocopies	retro_mdom_1303, retro_mdom_1706 , retro_mdom_1914,
Ornithorhynchus anatinus	ENSOANG00000006329	1 retrocopy	retro_oana_54,
Pongo abelii	ENSPPYG00000002304	1 retrocopy	retro_pabe_184,
Sarcophilus harrisii	ENSSHAG00000008090	3 retrocopies	retro_shar_276, retro_shar_303, retro_shar_697,
Sus scrofa	ENSSSCG00000010328	8 retrocopies	retro_sscr_1212, retro_sscr_14, retro_sscr_242, retro_sscr_289, retro_sscr_491, retro_sscr_564, retro_sscr_718, retro_sscr_902,
Tursiops truncatus	ENSTTRG00000007845	3 retrocopies	retro_ttru_1462, retro_ttru_740, retro_ttru_86,