RetrogeneDB ID: retro_mdom_1547

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 5:199822394..199823030(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: KDELR2
• Ensembl ID: ENSMODG00000007832
• Aliases: None
• Description: KDEL (Lys-Asp-Glu-Leu) endoplasmic reticulum protein retention receptor 2 [Source:HGNC Symbol;Acc:6305]

Sequence

>retro_mdom_1547
ATGAACATTTTCTGGCTGCCTGGGGACCTGTCCCACCTGGCAGCCATCATCATCCTGCTGCTGAAGATCTTGAAAACTCG
CTCCTGCGCCGGTATTTCTGGGAAGAGCCAGCTTCTGTTTGCACTGGTTTTCACTACTCGTTATCTGTATCTCTTTACTT
CATTTATTTCACTGTATAATACATCTATGAAGGTTATCTACATTGCTTGTGCATATGCCACTGTGTACTTAATCTACAAG
AAGTTTAAGGCTATGTATGATGGAAACCACGACACATTCTGAGTGGAGTTTCTGGTGGTCCCTGTTGGAGGGCTATCATT
TCTAGTCAATCACGATTTCTCTCCGCTTGAGATCTTGTGGACCTTCTCAATTTACCTTGAGTCAGTTGCTATCCTCCCAC
AGCTCTTTATGATCAGCAAAACTGGGGAAGCTGAGACCATCACTACTCATTATCTTTTCTTCCTTGGCCTATACTGTGCC
TTGTATCTAATTAATTGGATTTGGCGCTACTATTTTGAGGGTTTCTTTGACCTCATAGCTGTTGTTGCTGGTGTGGTCCA
GACTATTCTCTACTGTGACTTCTTCTATTTGTACGTTACAAAAGTACTCAAGGGAAAGAAGCTCAGTTTGCCAGCG

Alignment

ORF - retro_mdom_1547 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.75 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MNIFRLTGDLSHLAAIIILLLKIWKTRSCAGISGKSQLLFALVFTTRYLDLFTSFISLYNTSMKLIYIAC
          MNIF.L.GDLSHLAAIIILLLKI.KTRSCAGISGKSQLLFALVFTTRYL.LFTSFISLYNTSMK.IYIAC
Retrocopy MNIFWLPGDLSHLAAIIILLLKILKTRSCAGISGKSQLLFALVFTTRYLYLFTSFISLYNTSMKVIYIAC

Parental  AYATVYLIYMKFKATYDGNHDTFRVEFLVVPVGGLSFLVNHDFSPLEILWTFSIYLESVAILPQLFMISK
          AYATVYLIY.KFKA.YDGNHDTF.VEFLVVPVGGLSFLVNHDFSPLEILWTFSIYLESVAILPQLFMISK
Retrocopy AYATVYLIYKKFKAMYDGNHDTF*VEFLVVPVGGLSFLVNHDFSPLEILWTFSIYLESVAILPQLFMISK

Parental  TGEAETITTHYLFFLGLYRALYLINWIWRYYFEGFFDLIAVVAGVVQTILYCDFFYLYVTKVLKGKKLSL
          TGEAETITTHYLFFLGLY.ALYLINWIWRYYFEGFFDLIAVVAGVVQTILYCDFFYLYVTKVLKGKKLSL
Retrocopy TGEAETITTHYLFFLGLYCALYLINWIWRYYFEGFFDLIAVVAGVVQTILYCDFFYLYVTKVLKGKKLSL

Parental  PA
          PA
Retrocopy PA

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_1547 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1547 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 5 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000015746	2 retrocopies	retro_cfam_1944, retro_cfam_318,
Choloepus hoffmanni	ENSCHOG00000000125	1 retrocopy	retro_chof_2624,
Dasypus novemcinctus	ENSDNOG00000009897	1 retrocopy	retro_dnov_2654,
Echinops telfairi	ENSETEG00000016544	1 retrocopy	retro_etel_1867,
Monodelphis domestica	ENSMODG00000007832	1 retrocopy	retro_mdom_1547 ,