RetrogeneDB ID: retro_mdom_1574

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 6:28065798..28066173(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: REEP6
• Ensembl ID: ENSMODG00000005050
• Aliases: None
• Description: receptor accessory protein 6 [Source:HGNC Symbol;Acc:30078]

Sequence

>retro_mdom_1574
TCTCTCATACTTGGCTAGGGTGCCTCCAGGTTCTACCATCTCATCAGATTTGTCTTGCCAATGAATACCTCCATCAAGGC
CATTGAAAGCCATGAAATGAAGACACTACCATCTGGCTAGCCAAGTGGATAGTTTATGGCATATTTGACCTGGCTGAATT
TTTCTCGGACATCTTCCTTTTCTGGTTGCACTTTTACTATGCAGTGAAGTTTGCCTTCTTGCTTTGGGACATGCTTCCAA
TGACCTGTAATGGTTTCCAGTTTCCTATATAATCACCTAATCTACTCCATCTTCCTGAGGAAATAGGCTTCTGTGGGCAG
CCACCTGATGATGGGAGGATGAGTCCTGGACACAGCAGCCAGTATTACTTGGGAG

Alignment

ORF - retro_mdom_1574 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.72 %
• Parental protein coverage: 57.8 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  SIYIWYGASLLCNLIGFIYPAYASIKAIES-PDREDDTIWLTYWVVYGMFGLAEFFSDIFLFWFPFYYAG
          S.....GAS....LI.F..P...SIKAIES.P..ED.TIWL..W.VYG.F.LAEFFSDIFLFW..FYYA.
Retrocopy SLILG*GASRFYHLIRFVLPMNTSIKAIES<P*NEDTTIWLAKWIVYGIFDLAEFFSDIFLFWLHFYYAV

Parental  KCAFLLWCMLPLACNG-SQFLYNRLIRPIFLRHQASMDSLVTDLSGRALDTAASITRE
          K.AFLLW.MLP..CNG.S.FLYN.LI..IFLR..AS..S......G..LDTAASIT.E
Retrocopy KFAFLLWDMLPMTCNG>SSFLYNHLIYSIFLRK*ASVGSHLM-MGG*VLDTAASITWE

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_1574 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1574 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 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Microcebus murinus	ENSMICG00000003588	1 retrocopy	retro_mmur_1072,
Monodelphis domestica	ENSMODG00000005050	1 retrocopy	retro_mdom_1574 ,
Sarcophilus harrisii	ENSSHAG00000012645	1 retrocopy	retro_shar_657,
Drosophila melanogaster	FBgn0033906	1 retrocopy	retro_dmel_12,