RetrogeneDB ID: retro_mdom_2019

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: X:47936128..47936546(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: C6orf52
• Ensembl ID: ENSMODG00000028324
• Aliases: None
• Description: chromosome 6 open reading frame 52 [Source:HGNC Symbol;Acc:20881]

Sequence

>retro_mdom_2019
ATGCCTGGGAATTTGAGTTCTGTATATTTTAATTTAACCCAACAAAGTAATTATTTCTGGTACTGGCAATGGACAAAGGC
CAAGTTAAACTTCATCACTATGGTACCTATTACCAACTGCACTAAATCTGCTATTTGCAGTTAGATTTTGAAATTTATTT
TGAATATAAATGTAATTGTATTCATAATGTTCCTTTTGCAAATGAGAACACTAAAGATGTAGCTGAAATTGTGGCTTTGT
CAGGAGTTTAGACTATAAATAATGATGAAGAGCAAACAGAAGATTCACAGGTTCACTTGGTTACCAAGAACCTGAGCAAG
GAGTTTATGGTGGGATGTAAAGAGCTCTATGACTCCTAATGAATTGTCATTGGCAGCTTCTGGATACTGGTGCTTCTAGA
ATTGCAAACATTATCCAA

Alignment

ORF - retro_mdom_2019 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.9 %
• Parental protein coverage: 99.32 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MARSLSSADFDLIQQSNYFWYWQWMKTEL-QLDHSGTYYQQHQTCYLQSDFEPYFEYNYNCVFYGNIQDV
          M...LSS..F.L.QQSNYFWYWQW.K..L..L.H.GTYYQ.H..CYLQ.DFE.YFE..Y.C.....I..V
Retrocopy MPGNLSSVYFNLTQQSNYFWYWQWTKAKL<KLHHYGTYYQLH*ICYLQLDFEIYFE--YKC---NCIHNV

Parental  SSAKENTKDLAEIPVMSEDWTTNNDEEQTEDPQIHLDIENLNKEFMVESEELYDS-LMNCHWQPLDTVAS
          ..A.ENTKD.AEI...S...T.NNDEEQTED.Q.HL...NL.KEFMV...ELYDS.LMNCHWQ.LDT.AS
Retrocopy PFANENTKDVAEIVALSGV*TINNDEEQTEDSQVHLVTKNLSKEFMVGCKELYDS<LMNCHWQLLDTGAS

Parental  WIPNNTQ
          .I.N..Q
Retrocopy RIANIIQ

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_2019 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_2019 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 7 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000002583	1 retrocopy	retro_amel_1114,
Canis familiaris	ENSCAFG00000030234	1 retrocopy	retro_cfam_1098,
Choloepus hoffmanni	ENSCHOG00000010768	2 retrocopies	retro_chof_2530, retro_chof_70,
Equus caballus	ENSECAG00000008229	2 retrocopies	retro_ecab_684, retro_ecab_792,
Monodelphis domestica	ENSMODG00000028324	12 retrocopies	retro_mdom_1372, retro_mdom_2019 , retro_mdom_322, retro_mdom_336, retro_mdom_453, retro_mdom_492, retro_mdom_513, retro_mdom_523, retro_mdom_534, retro_mdom_616, retro_mdom_746, retro_mdom_894,
Tursiops truncatus	ENSTTRG00000003650	1 retrocopy	retro_ttru_927,
Vicugna pacos	ENSVPAG00000003001	2 retrocopies	retro_vpac_198, retro_vpac_609,