RetrogeneDB ID: retro_mdom_1245

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 4:74338994..74339370(+)
• Located in intron of: ENSMODG00000018120

Retrocopy information

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

Parental gene information

• Parental gene symbol: RHOC
• Ensembl ID: ENSMODG00000000981
• Aliases: None
• Description: ras homolog family member C [Source:HGNC Symbol;Acc:669]

Sequence

>retro_mdom_1245
GAAGTCTATGGTGGACTCTAGCCACTCTTTTACACTGATACTGAGATCATCCTTTTGTACTTCTCCACTGATAGCCCAGT
CAGTCCTAAGAAATAGACATCAGAAGTGAAGCCCTTCTGTCCCCAAGTGCCCAACATCATGTGGGGAATAAGAAGGACCT
GAGACATGATGAGCATAGCATAGGGAAAGCTAGTGAAGGTGAAGTAGGAACTTGTGAGGTCAAAGGAGTGCTGGGACATG
ACCAATGAGATCAGCCTTTAGCCACCTTGAGTGTTTCGCCAAAACCAAAGAAAGTGTCTGAAAAGTGTTTGAGATGGCCA
CACGAGCTGGCCAGTACATTCAAAAGAACAAGTGGCAGCAGGGGTTGCCTTCTCTT

Alignment

ORF - retro_mdom_1245 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.48 %
• Parental protein coverage: 67.36 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  EDYDRLRPLSYPDTDVILMCFSIDSPDSLENIPEKWTPEVKHFCPNVPIIL-VGNKKDLRQDEHTR-REL
          E.Y..L.PL.Y.DT..IL..FS.DSP.S....P.K.T.EVK.FCP.VP.I..VGNKKDLR.DEH.....L
Retrocopy EVYGGL*PLFYTDTEIILLYFSTDSPVS----PKK*TSEVKPFCPQVPNIM<VGNKKDLRHDEHSI>GKL

Parental  AKMKQEPVRSEEGRDMANRIS-AFGYLECSAKTK-EGVREVFEMATRAGLQVRKNKRRRGCPLL
          .K.K.E.VRS.E..DM.N.IS.....L..S.K.K.E.V..VFEMATRAG....KNK...G.P.L
Retrocopy VKVK*ELVRSKECWDMTNEIS<PLATLSVSPKPK<ESV*KVFEMATRAGQYIQKNKWQQGLPSL

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_1245 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1245 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 15 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000014299	1 retrocopy	retro_btau_1171,
Canis familiaris	ENSCAFG00000013413	1 retrocopy	retro_cfam_1152,
Callithrix jacchus	ENSCJAG00000013657	2 retrocopies	retro_cjac_1657, retro_cjac_2027,
Equus caballus	ENSECAG00000010174	3 retrocopies	retro_ecab_112, retro_ecab_257, retro_ecab_932,
Ficedula albicollis	ENSFALG00000000736	1 retrocopy	retro_falb_11,
Gorilla gorilla	ENSGGOG00000002741	2 retrocopies	retro_ggor_18, retro_ggor_732,
Macropus eugenii	ENSMEUG00000004807	1 retrocopy	retro_meug_37,
Monodelphis domestica	ENSMODG00000000981	1 retrocopy	retro_mdom_1245 ,
Monodelphis domestica	ENSMODG00000012981	2 retrocopies	retro_mdom_19, retro_mdom_294,
Otolemur garnettii	ENSOGAG00000027678	3 retrocopies	retro_ogar_2606, retro_ogar_3360, retro_ogar_58,
Sarcophilus harrisii	ENSSHAG00000001981	1 retrocopy	retro_shar_455,
Taeniopygia guttata	ENSTGUG00000017533	1 retrocopy	retro_tgut_11,
Tetraodon nigroviridis	ENSTNIG00000015041	1 retrocopy	retro_tnig_2,
Xenopus tropicalis	ENSXETG00000006898	1 retrocopy	retro_xtro_15,
Xiphophorus maculatus	ENSXMAG00000008103	1 retrocopy	retro_xmac_13,