RetrogeneDB ID: retro_mdom_1798

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 7:149727171..149727890(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

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

Sequence

>retro_mdom_1798
GTGTTTGTGGATTTGAACCTGAGGAAGGGCCTAGACACTAAGGCACTTAAAGGGCTTCTGGAAAATGCAGCTCACCTTGG
ATATTCAGCTGTTGCCATTAATCATGTTGTAGACTTTAAGGCAAAGAAACAGGAAACTGACAACCCAATAGTTCCTCCTA
TGTTCTTTTCCTCTCTACCTATTATAGGGAAAATTGGAACCAATTAAAATTATAAGTAGACTGACACTTAAAGTATCAGA
TCCATCACACTGCAATGTTCTGAGAGCATCTTCTTGTGTCAAATTATATGACATTGTTGCAGTTTTTCCTAAAACAGAAA
AACTTTTCCACGTTTCTTACACTAATTTGGATATGGATTTGTTATGCATAACAGTAACAGAGAAGTTGCCATTTTACTTT
AGAAGATTTCCTATTAATGTGGCAATTGAACAAGACATTGAGTTTGAGCTTACTTATTCTTCTGCATTACAGACTCCACA
ATGAGGAGATACACCAATTCCATTGCACCGAGTTTGATGCAGATCTGCAAGGAGAAGAATGTAACTGTATCTACTGGTGC
AGAAAGGCCTTTAGAATAAGAGGACCATATGACATAGAAAATTTAGGCTTGTCATTTGGACTCTCTGAAAGTGATACCAA
GGCAGCAATATCCACAAATTGCAGGACTATACTTATTTATGGAGAAAACAGAAAGACTGCTTTTGGAAGTGCCTTGACT

Alignment

ORF - retro_mdom_1798 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.18 %
• Parental protein coverage: 90.64 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  VFVDLNLRKSSDTKALKGLVENAAHLGYSTVAINHVVDFKEKKQEIDKPIVPSELFSS-LPIVQGKSKPI
          VFVDLNLRK..DTKALKGL.ENAAHLGYS.VAINHVVDFK.KKQE.D.PIVP...F.S.L....GK..PI
Retrocopy VFVDLNLRKGLDTKALKGLLENAAHLGYSAVAINHVVDFKAKKQETDNPIVPP-MFFS>LYLL*GKLEPI

Parental  KILSRLTLIVSDPSHCNVLRATSSRVKLYDIVAVFPKTEKLFHVACTSLDVDLVCITVTEKLPFYFRRPP
          KI.SRLTL.VSDPSHCNVLRA.SS.VKLYDIVAVFPKTEKLFHV..T.LD.DL.CITVTEKLPFYFRR.P
Retrocopy KIISRLTLKVSDPSHCNVLRA-SSCVKLYDIVAVFPKTEKLFHVSYTNLDMDLLCITVTEKLPFYFRRFP

Parental  INVAIERGIGFELTYSSA-IKDSTMRRYTISNALSLMQICKGKNVIVSSGAERPLE-IRGPYDIANLGLL
          INVAIE..I.FELTYSSA.I.DSTMRRYT.S.A.SLMQICK.KNV.VS.GAERPLE.IRGPYDI.NLGL.
Retrocopy INVAIEQDIEFELTYSSA<ITDSTMRRYTNSIAPSLMQICKEKNVTVSTGAERPLE<IRGPYDIENLGLS

Parental  FGLSESDAKAAVSTNCRAILLHGETRKTAFGIIYT
          FGLSESD.KAA.STNCR.IL..GE.RKTAFG...T
Retrocopy FGLSESDTKAAISTNCRTILIYGENRKTAFGSALT

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_1798 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1798 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 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,