RetrogeneDB ID: retro_mdom_1307

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 4:354117029..354117698(+)
• Located in intron of: ENSMODG00000027711

Retrocopy information

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

Parental gene information

• Parental gene symbol: PIP4K2A
• Ensembl ID: ENSMODG00000009032
• Aliases: None
• Description: phosphatidylinositol-5-phosphate 4-kinase, type II, alpha [Source:HGNC Symbol;Acc:8997]

Sequence

>retro_mdom_1307
CCCAGCAACCTGGTGTCCTCGGTCATGGAGAGCAAGACCAAGACGAAGAAGAAGCACTTCGTTGCGCAGCAAGTGAAGCT
GTTCCGAGCCAGCGACCAGCTGCTCAGCGTCCTCATGTAGGGGGTGAACCACTCGATCAATGAACTGAGCCACGTCCAAA
TCCCTGTGATGCTGATGCCGGATGACTTCAAAGAATATTCAAAGATCAAGGTGGACAATCACCTCTTTAACAAAGAAAAC
ATGCCGAGTCATTTCAAGTTTAAGGAGTACTGCCCCATGGTTTTCCACAACCTGCGAGAAAGGTTTGGAATTGACGATCA
GGATTTTCAGAATTCCTTGACCAGAAGTGCACCACTTCGGAACGACTCCCAGGCACTCAGTGGAGCATGATTTCATACTT
CCTATGACAAAAGATACATCATCAAAACAATTACAAGTGAAGATGTGGCTGAAATGCATAACATTCTCAAGAAGTACCAC
CTGTACATTGTGGAGTGTCACGGAGTCACCCTTCTTCCTCAGTTTTTGGGCATGTACCAGCTTAATGTGGATGGAGTGGA
AATCTATGTGATCGTTACAAGAAATGTGTTCAGCCACCGCTTATCCGTCTATAGGAAATACGACTTAAAGGGGTCCACTG
TGGCCAGAGAAGCTAGCGACAAGGAAAAG

Alignment

ORF - retro_mdom_1307 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.62 %
• Parental protein coverage: 50.11 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PSNLVSSVMASKTKTKKKHFVAQKVKLFRASDPLLSVLMWGVNHSINELSHVQIPVMLMPDDFKAYSKIK
          PSNLVSSVM.SKTKTKKKHFVAQ.VKLFRASD.LLSVLM.GVNHSINELSHVQIPVMLMPDDFK.YSKIK
Retrocopy PSNLVSSVMESKTKTKKKHFVAQQVKLFRASDQLLSVLM*GVNHSINELSHVQIPVMLMPDDFKEYSKIK

Parental  VDNHLFNKENMPSHFKFKEYCPMVFRNLRERFGIDDQDFQNSLTRSAPLPNDSQARSGARFHTSYDKRYV
          VDNHLFNKENMPSHFKFKEYCPMVF.NLRERFGIDDQDFQNSLTRSAPL.NDSQA.SGA.FHTSYDKRY.
Retrocopy VDNHLFNKENMPSHFKFKEYCPMVFHNLRERFGIDDQDFQNSLTRSAPLRNDSQALSGA*FHTSYDKRYI

Parental  IKTITSEDVAEMHNILKKYHQYIVECHGVTLLPQFLGMYRLNVDGVEIYVIVTRNVFSHRLSVYRKYDLK
          IKTITSEDVAEMHNILKKYH.YIVECHGVTLLPQFLGMY.LNVDGVEIYVIVTRNVFSHRLSVYRKYDLK
Retrocopy IKTITSEDVAEMHNILKKYHLYIVECHGVTLLPQFLGMYQLNVDGVEIYVIVTRNVFSHRLSVYRKYDLK

Parental  GSTVAREASDKEK
          GSTVAREASDKEK
Retrocopy GSTVAREASDKEK

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_1307 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1307 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Monodelphis domestica	ENSMODG00000009032	1 retrocopy	retro_mdom_1307 ,