RetrogeneDB ID: retro_mdom_13

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: X:52846146..52846638(-)
• Located in intron of: ENSMODG00000014317

Retrocopy information

• Ensembl ID: ENSMODG00000022947
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000000837
• Aliases: None
• Description: None

Sequence

>retro_mdom_13
ATGGCTGGGCGTCTGATCCTAAGCAGATCCTTGGCTTTGGTCATGGCGAGAAAACTGCCTATGTGCCGTTGGGTTTCCCC
TCGCACTGGGGTCCTACAGGCTGCCCACAAGATCCCTGGCACTCCAGCACTAAACCTGATCAAGCCCTTGTATACTACCC
GCATTCACAAGATTACATTTGAAATCCAGGATGGGCCAGATTTTCAGGACAGGGTTCTCAACAGCAACACTCCAGTGGTG
GTGGATTTCCATGCCCAGTGGTGCGGCCCCTGTAAGATCCTGGGACCTCGTCTGGAGAAGATGGTGGCCAGACAGAAGGG
CAAGGTAGTGATGGCTAAGGTTGACATCGATGACAACACCGACCTCGCCATTGCCTTTGAGGTATCTGTAGTGCCAACTG
TTTTGGCCATCAAGAATGGCGATGTGGTAGACAAGTTTGAAGGGATCAAGGATGAAGATCAGCTTGAATGCTTCCTGAAG
AAGCTGATCTAC

Alignment

ORF - retro_mdom_13 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.09 %
• Parental protein coverage: 98.79 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAQRMVLRRFVASLFSRKFPQCHWAPLSPEVLAQGN--PGRPAIVPSLARTFFTSRVCKVTFNVQDGPDF
          MA.R..L.R..A....RK.P.C.W......VL......PG.PA....L.....T.R..K.TF..QDGPDF
Retrocopy MAGRLILSRSLALVMARKLPMCRWVSPRTGVLQAAHKIPGTPAL--NLIKPLYTTRIHKITFEIQDGPDF

Parental  QDRVVNSQTPVVVDFHAQWCGPCKILGPRLEKMVAKQEGKVLMAKVDIDDNTDLAIEYEVSAVPTVLAIK
          QDRV.NS.TPVVVDFHAQWCGPCKILGPRLEKMVA.Q.GKV.MAKVDIDDNTDLAI..EVS.VPTVLAIK
Retrocopy QDRVLNSNTPVVVDFHAQWCGPCKILGPRLEKMVARQKGKVVMAKVDIDDNTDLAIAFEVSVVPTVLAIK

Parental  NGDVVDKFVGIKDEDQLEAFLKKLI
          NGDVVDKF.GIKDEDQLE.FLKKLI
Retrocopy NGDVVDKFEGIKDEDQLECFLKKLI

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_13 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_13 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 9 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000013929	1 retrocopy	retro_ecab_229,
Erinaceus europaeus	ENSEEUG00000010654	2 retrocopies	retro_eeur_554, retro_eeur_67,
Homo sapiens	ENSG00000100348	1 retrocopy	retro_hsap_179,
Gorilla gorilla	ENSGGOG00000028091	1 retrocopy	retro_ggor_260,
Myotis lucifugus	ENSMLUG00000015841	1 retrocopy	retro_mluc_483,
Monodelphis domestica	ENSMODG00000000837	2 retrocopies	retro_mdom_1125, retro_mdom_13 ,
Pteropus vampyrus	ENSPVAG00000002012	1 retrocopy	retro_pvam_1431,
Sarcophilus harrisii	ENSSHAG00000000670	1 retrocopy	retro_shar_61,
Tursiops truncatus	ENSTTRG00000006612	1 retrocopy	retro_ttru_438,