RetrogeneDB ID: retro_mdom_1152

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 3:261046869..261047252(-)
• Located in intron of: ENSMODG00000021499

Retrocopy information

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

Parental gene information

• Parental gene symbol: ICT1
• Ensembl ID: ENSMODG00000007126
• Aliases: None
• Description: immature colon carcinoma transcript 1 [Source:HGNC Symbol;Acc:5359]

Sequence

>retro_mdom_1152
CTATCTTATTCCAAAAGCGGAGGCCCTGAAGACAGAATGTTAAAGAAGTAAATATCAAGGCTGAAGTGCAGTTCCATTTA
ACAACAGCAGACTGGATTACAGAGCCTGTCTGACAAAAGATTGAAAACTTGTTCAAAAACAAGATCTGCAAATCAGGAGA
GCTGACCATCATCTCTGACTCCTGCCTTTATCAGTTTTGAAGTTTGGCAGATTGCCTCCAGAATATCTGAGACATGATTG
CCCAGGCTAGCCAAGTTCCCAAGGAGCTGTCCAAAGAAGATGCTGGGCTTTGAAGACTCAGGGTAGAAATCATGAATCAT
GAAAAGCTAAGACAGAAGAGAATCCATTCTTCCATAAACACAAGCAAGAAAGAAGATACTGAC

Alignment

ORF - retro_mdom_1152 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.77 %
• Parental protein coverage: 61.54 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VSYSKSSGPGG-QNVNKVNTKAEVRFHLATADWIAEPVRQKISVLFKNKISKSGELIITSDSSRYQFRNL
          .SYSKS.GP...QNV..VN.KAEV.FHL.TADWI.EPV.QKI..LFKNKI.KSGEL.I.SDS..YQF..L
Retrocopy LSYSKSGGPED<QNVKEVNIKAEVQFHLTTADWITEPV*QKIENLFKNKICKSGELTIISDSCLYQF*SL

Parental  ADCLQKIRDMIAQASQVPKEPSKEDAVLRRIRIENSNRERLRQKRIHSSTKANRKIDMD
          ADCLQ.I.DMIAQASQVPKE.SKEDA.L.R.R.E..N.E.LRQKRIHSS.....K.D.D
Retrocopy ADCLQNI*DMIAQASQVPKELSKEDAGL*RLRVEIMNHEKLRQKRIHSSINTSKKEDTD

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_1152 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1152 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 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Dipodomys ordii	ENSDORG00000006439	1 retrocopy	retro_dord_539,
Macaca mulatta	ENSMMUG00000011644	1 retrocopy	retro_mmul_181,
Monodelphis domestica	ENSMODG00000007126	1 retrocopy	retro_mdom_1152 ,