RetrogeneDB ID: retro_mdom_336

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 1:210047472..210047746(+)
• Located in intron of: ENSMODG00000017552

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_336
TACTGGCATGGGAACAGATCTAGACTGACTTACAGCTTGAACACTCTTGTACCTATTACCAACAGCACCAACTTGCTATT
TTTAGTTAGATTTTGACCCTTATTTTGAATATAACTATAGCTGTGTGTTTTATGGGAACGTCCAGAATGTTTACATTGCA
AAGGAGAACCCTGAGATCTAGCTGTGTCAGTAGCTTGGACTTACAAAAAATGATGAGGAGCAAACTGAAGATCCATAAGT
TCATTTGGATATTGAGTATCTGAACAAGGAATTT

Alignment

ORF - retro_mdom_336 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65. %
• Parental protein coverage: 65.75 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  FWY-WQWMKTELQLDHSGTYYQQHQ-TCYLQSDFEPYFEYNYNCVFYGNIQDVSSAKENTK-DLAEIPVM
          .W..W....T.LQL.HS.TYYQQHQ.TCY...DF.PYFEYNY.CVFYGN.Q.V..AKEN...DLA.....
Retrocopy YWH<WEQI*TDLQLEHSCTYYQQHQ<TCYF*LDFDPYFEYNYSCVFYGNVQNVYIAKENPE<DLA----V

Parental  SEDWT-TNNDEEQTEDPQIHLDIENLNKEF
          S..WT.T.NDEEQTEDP..HLDIE.LNKEF
Retrocopy SVAWT>TKNDEEQTEDP*VHLDIEYLNKEF

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_336 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_336 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.

---

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,