RetrogeneDB ID: retro_mdom_950

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 3:6474415..6474754(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000019309
• Aliases: None
• Description: None

Sequence

>retro_mdom_950
ATGCAACAAGGACAGCCCCTGGTCATTGTGACTCAGCCCCAGCGTGGTGTTTATCCACAAAGCTCCAACTGGCAGACAGG
CCTTTTAGACTGTTGCAGTGACTGTGGAGTCTGTCTTTGTGGGATATTCTGTCCCCTTTGCCTCTCCTGCCAAGTAGCTT
CTGACATGAATGAATGCTGTTTGTGTGGCTCAAGCGTGGCCATGAGGACCCTCTACCGCACCAGATATGGCATCACTGGA
TCCATCTGCAGTGACTTCATGATGACTACTTGTTGTACTGTGTGTTCTCTTTGCCAACTTAAGAGAGACATTAATAGAAG
GAGGGGAATGAATGCTTTC

Alignment

ORF - retro_mdom_950 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.46 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MQQGQPVVIVTQPQGGVYPQSSNWQTGLLDCCSDCGVCLCGIFCPLCLSCQIASDMNECCLCGSSVAMRT
          MQQGQP.VIVTQPQ.GVYPQSSNWQTGLLDCCSDCGVCLCGIFCPLCLSCQ.ASDMNECCLCGSSVAMRT
Retrocopy MQQGQPLVIVTQPQRGVYPQSSNWQTGLLDCCSDCGVCLCGIFCPLCLSCQVASDMNECCLCGSSVAMRT

Parental  LYRTRYGITGSICSDFMVTTCCTVCSLCQLKRDINRRRGMNAF
          LYRTRYGITGSICSDFM.TTCCTVCSLCQLKRDINRRRGMNAF
Retrocopy LYRTRYGITGSICSDFMMTTCCTVCSLCQLKRDINRRRGMNAF

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_950 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_950 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 7 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000145287	1 retrocopy	retro_hsap_1165,
Gorilla gorilla	ENSGGOG00000007464	1 retrocopy	retro_ggor_910,
Monodelphis domestica	ENSMODG00000019309	1 retrocopy	retro_mdom_950 ,
Mus musculus	ENSMUSG00000029322	1 retrocopy	retro_mmus_1051,
Otolemur garnettii	ENSOGAG00000017232	1 retrocopy	retro_ogar_714,
Pan troglodytes	ENSPTRG00000016226	1 retrocopy	retro_ptro_800,
Rattus norvegicus	ENSRNOG00000002217	2 retrocopies	retro_rnor_1489, retro_rnor_1878,