RetrogeneDB ID: retro_mdom_1214

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 3:501006888..501007236(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000023689
• Aliases: None
• Description: None

Sequence

>retro_mdom_1214
ATGAATTCTCTGATGTTGAATAAGTTTTATCTTTCCTCTAAAGGCCTTCCCAAATTCATCACATTTAAAAAGTTTCTTAG
ACATATGACTTGTTTGATGTTGACTAAGCTGTCCTTTTAGTCGGAAAGCCTTTCCACAGCCATCACAATCATAAGGTTTC
TCACCAGTATGAATTCTCTGATGCTAATAAGTCTTATCTTCCAGCTGAATGACTTCCCATATTCATTCCATTCATAAATT
TTTCTAACCAGTATGACTTCTCTGGTGTTTAGTACTCCAGTGGAAAGTCTTCCCACATTCATTACATTCATATGGTTTCT
CCACAGTATGAATTCTCTCATGTTGAGT

Alignment

ORF - retro_mdom_1214 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 50.41 %
• Parental protein coverage: 98.35 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MNSLMSSKVCAQSKGLSTFITFKRFLSSMNYQMSSKLFSPAKGLSTFITFIRFLSRMNSLMY-NKTGPLT
          MNSLM..K....SKGL..FITFK.FL..M...M..KL......LST.IT.IRFL..MNSLM..NK.....
Retrocopy MNSLMLNKFYLSSKGLPKFITFKKFLRHMTCLMLTKLSF*SESLSTAITIIRFLTSMNSLML<NKSYLPA

Parental  KCLSTLLAFMRF-LTSLHSLMYSKMGARIKGLSTFITFIRLLPSMNYLMLS
          ..L.....F..F.LTS..SL..S........L.TFITFI..L.SMN.LMLS
Retrocopy E*LPIFIPFINF>LTSMTSLVFS---TPVESLPTFITFIWFLHSMNSLMLS

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_1214 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1214 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 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000007018	1 retrocopy	retro_dnov_33,
Monodelphis domestica	ENSMODG00000023141	4 retrocopies	retro_mdom_1425, retro_mdom_1832, retro_mdom_1972, retro_mdom_797,
Monodelphis domestica	ENSMODG00000023689	1 retrocopy	retro_mdom_1214 ,