RetrogeneDB ID: retro_mdom_353

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 1:263494405..263495037(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000016808
• Aliases: None
• Description: None

Sequence

>retro_mdom_353
TCTCTAGCAGGATGTGTAACAATTTTCCTTCACAATCAAAATAAAGAGACTCTCTCAGAAAAGCAGAAATTGGCAAGAGT
TCACTTCAACATTCATCTAGGTAGCTCTTCCTATAGGAATGCATGGTACATAAGTATTGTGTGCTCTTGTTCATACATTT
TAACTCTTGGAGAAGCTGTCAGAAAAAGGGCTTTTAAGAACTAATTCCCAAGAAACTGTTTGGAGCATAGATAATGCAAG
CAACAATATGTTCCTTGAATTGACCTTCCTTCCAACTCCTGAGATTTTCACGGTAAATTCAATTGGACAGTTAAAGATAG
GACTTTTCAGATAGGCAGGAGAAAGAACCTTCTCAGATAATGTCACTGACTGGAGACAGAGTTCCACTCCACTCTGTTGA
TAGACATTCTAATCAGCAACACATTGTTTGTAGTGAAGATGGAATGTTGAGTATTTGGGATATTAGACTAGGTAGCATGT
TAGTGTCTCTATTAAAGACACATGAAGCAAAAATGTGAGCTCACTTTCACCCATACAACCTAGATCATCTGTTTACTTTT
TCTAAAAATTAATCCCTCTGTCACTAGAATGTTTCCACGTACCTTTCAGAAAAGTCCTCTCTTTTTCACCAA

Alignment

ORF - retro_mdom_353 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.67 %
• Parental protein coverage: 56.05 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  SSTGCVTVFLHHPNNQTLSVSQEWIGAHYHIGPCSPSYRSAPCTGIVCNSPEIVTVGEDGRINLF-RVGY
          S..GCVT.FLH..N..TLS..Q.....H..I...S.SYR.A....IVC....I.T.GE..R...F.R...
Retrocopy SLAGCVTIFLHNQNKETLSEKQKLARVHFNIHLGSSSYRNAWYISIVCSCSYILTLGEAVRKRAF>RTNS

Parental  KEAVRTIDNADSSTLHAVAFLRTPEILTVNSIGQLKIWDFR-QQGNEPSQILSLTGDRVPLHCVDRHPNQ
          .E.V..IDNA.........FL.TPEI.TVNSIGQLKI..FR..Q..EPSQI.SLTGDRVPLH.VDRH.NQ
Retrocopy QETVWSIDNASNNMFLELTFLPTPEIFTVNSIGQLKIGLFR>RQEKEPSQIMSLTGDRVPLHSVDRHSNQ

Parental  QHVVATGGQDGMLSIWDVRQGSMPVSLLKAHEAEMWEVHFHPSNPDHLFTCSEDGSLWHWDASTDVPEKS
          QH.V.....DGMLSIWD.R.GSM.VSLLK.HEA.M...HFHP.N.DHLFT.S...SL.H...ST...EKS
Retrocopy QHIVCS--EDGMLSIWDIRLGSMLVSLLKTHEAKM-*AHFHPYNLDHLFTFSKN*SLCH*NVSTYLSEKS

Parental  SLFHQ
          SLFHQ
Retrocopy SLFHQ

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_353 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_353 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 6 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000009426	1 retrocopy	retro_chof_1765,
Cavia porcellus	ENSCPOG00000010815	1 retrocopy	retro_cpor_481,
Macaca mulatta	ENSMMUG00000009830	1 retrocopy	retro_mmul_1962,
Monodelphis domestica	ENSMODG00000016808	2 retrocopies	retro_mdom_199, retro_mdom_353 ,
Ictidomys tridecemlineatus	ENSSTOG00000013449	1 retrocopy	retro_itri_990,
Tarsius syrichta	ENSTSYG00000000944	1 retrocopy	retro_tsyr_267,