RetrogeneDB ID: retro_mdom_1388

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 4:255186085..255186889(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMODG00000000415
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000006863
• Aliases: None
• Description: None

Sequence

>retro_mdom_1388
ATGGCTGTGTTTGTGGATTTGAACCTAAGGAAGAGCTCAGACACTAAAGCACTTAAAGGGCTTGTGGAGAATGCAGCTCA
CCTTGGATATTCAACTGTTGCCATTTATCATGTTGTGGACTTTAAGAAAAAGAAACAGGAAATTGACAAACCAATAGTTC
CTTCTGAGCTCTTTTCCTCTTTACCTATTGTACAGGGGAAATCGAAACCAATTAAAATTTTAAGTAGACTGACACTTATA
ATATCAGAACCATCACCCTGCAATGTTCTGAGAGCAACATCTTCTCGTGCCAAGCTATATGACATTGTTGCAGTTTTTCC
TAAGACAGAAAAACTTTTCCATGTTGCTTGCACTAGTTTGGATGTGGATTTAGTTTGCATAACAGTAACAGAGAAGTTGC
CTTTTTACTTTAGAAGACCTCCTATTAATGTTATGGCAATTGAACGAGGCATTGGGTTTGAGCTTACTTATTCTTCTGCC
ATTAAAGACTCCACGATGAGGAGATACACCATTTCCAATGCACTTAGTTTGATGCAGATCTGCAAAGGGAAGAATGTAAT
TGTATATAGTGGTGCAGAAAGGCCTTTAGAAATAAGAGGACCATATGACATAGCAAATTTAGGCTTGTTATTTGGACTCT
CTGAAAGTGATGCCAAGGCAGCAGTATCCACAAATTGCAGGGCAATACTTCTTCATGGAGAAACCAGAAAGACTGCTTTT
GGTATTATTTATACAACAAAGAAGCCAAGAACAACTGAAGAGGATGACAATGTTCCAGCATGCAAAAAAGCCAAATGTGA
GGAC

Alignment

ORF - retro_mdom_1388 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.64 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAVFVDLNLRKSSDTKALKGLVENAAHLGYSTVAINHVVDFKEKKQEIDKPIVPSELFSSLPIVQGKSKP
          MAVFVDLNLRKSSDTKALKGLVENAAHLGYSTVAI.HVVDFK.KKQEIDKPIVPSELFSSLPIVQGKSKP
Retrocopy MAVFVDLNLRKSSDTKALKGLVENAAHLGYSTVAIYHVVDFKKKKQEIDKPIVPSELFSSLPIVQGKSKP

Parental  IKILSRLTLIVSDPSHCNVLRATSSRVKLYDIVAVFPKTEKLFHVACTSLDVDLVCITVTEKLPFYFRRP
          IKILSRLTLI.S.PS.CNVLRATSSR.KLYDIVAVFPKTEKLFHVACTSLDVDLVCITVTEKLPFYFRRP
Retrocopy IKILSRLTLIISEPSPCNVLRATSSRAKLYDIVAVFPKTEKLFHVACTSLDVDLVCITVTEKLPFYFRRP

Parental  PINV-AIERGIGFELTYSSAIKDSTMRRYTISNALSLMQICKGKNVIVSSGAERPLEIRGPYDIANLGLL
          PINV.AIERGIGFELTYSSAIKDSTMRRYTISNALSLMQICKGKNVIV.SGAERPLEIRGPYDIANLGLL
Retrocopy PINVMAIERGIGFELTYSSAIKDSTMRRYTISNALSLMQICKGKNVIVYSGAERPLEIRGPYDIANLGLL

Parental  FGLSESDAKAAVSTNCRAILLHGETRKTAFGIIYTTKKPRTTEEDDSVPACKKAKCED
          FGLSESDAKAAVSTNCRAILLHGETRKTAFGIIYTTKKPRTTEEDD.VPACKKAKCED
Retrocopy FGLSESDAKAAVSTNCRAILLHGETRKTAFGIIYTTKKPRTTEEDDNVPACKKAKCED

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	19.31 RPM
SRP007412_cerebellum	0.00 RPM	12.41 RPM
SRP007412_heart	0.00 RPM	17.94 RPM
SRP007412_kidney	0.00 RPM	36.87 RPM
SRP007412_liver	0.00 RPM	19.13 RPM
SRP007412_testis	0.00 RPM	7.66 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_1388 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1388 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 3 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Monodelphis domestica	ENSMODG00000006863	2 retrocopies	retro_mdom_1388 , retro_mdom_1798,
Ochotona princeps	ENSOPRG00000007367	1 retrocopy	retro_opri_855,
Tursiops truncatus	ENSTTRG00000014708	1 retrocopy	retro_ttru_1152,