RetrogeneDB ID: retro_mdom_1717

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 7:64614298..64614697(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: EIF4E2
• Ensembl ID: ENSMODG00000002680
• Aliases: None
• Description: eukaryotic translation initiation factor 4E family member 2 [Source:HGNC Symbol;Acc:3293]

Sequence

>retro_mdom_1717
TCCGTGGAGCAGTTCTGGAGGTTTTATAGCCACATGGCATGTCCCGGGGACCTGACAGGCCATAGTGATTTCCATCTCTT
CAAAGAGGGAATCAAACCCATGTGGGAGGATGATGCTAATAAAAATGGTGGTAAATGGATTATTCCGCTCCATAAGGGTT
TAGCTTCCTGGTGCTGGGAGAATCTGATACGTGCCATGTTGGGGGAAGAGTTCATGGTGGGCAAAGAGATCTGTGGGGCA
ATCATCTCTGTCCATTTCCAGGAGGACATTATTTCAATATGGAACAAGACTGCCAGCGACCAAGATATGCCACAGACCAT
ATCTGGGACATGCTACGTCGAGTGCTTAACCTACCTCCCAAATGGAATGGAATACAAAACACACACCGACAGCATCAAG

Alignment

ORF - retro_mdom_1717 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.1 %
• Parental protein coverage: 54.29 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SVEQFWRFYSHMVRPGDLTGHSDFHLFKEGIKPMWEDDANKNGGKWIIRLRKGLASRCWENLILAMLGEQ
          SVEQFWRFYSHM..PGDLTGHSDFHLFKEGIKPMWEDDANKNGGKWII.L.KGLAS.CWENLI.AMLGE.
Retrocopy SVEQFWRFYSHMACPGDLTGHSDFHLFKEGIKPMWEDDANKNGGKWIIPLHKGLASWCWENLIRAMLGEE

Parental  FMVGEEICGAVVSVRFQEDIISIWNKTASDQATTARIRDTLR-RVLNLPPNTIMEYKTHTDSIK
          FMVG.EICGA..SV.FQEDIISIWNKTASDQ.....I..T.....L...PN..MEYKTHTDSIK
Retrocopy FMVGKEICGAIISVHFQEDIISIWNKTASDQDMPQTISGTCYVECLTYLPNG-MEYKTHTDSIK

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_1717 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1717 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 11 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000011328	1 retrocopy	retro_cfam_183,
Callithrix jacchus	ENSCJAG00000013786	2 retrocopies	retro_cjac_1061, retro_cjac_2717,
Macropus eugenii	ENSMEUG00000015519	2 retrocopies	retro_meug_445, retro_meug_644,
Microcebus murinus	ENSMICG00000015082	2 retrocopies	retro_mmur_806, retro_mmur_975,
Myotis lucifugus	ENSMLUG00000011269	1 retrocopy	retro_mluc_60,
Monodelphis domestica	ENSMODG00000002680	1 retrocopy	retro_mdom_1717 ,
Monodelphis domestica	ENSMODG00000005097	3 retrocopies	retro_mdom_1779, retro_mdom_47, retro_mdom_710,
Monodelphis domestica	ENSMODG00000020716	1 retrocopy	retro_mdom_701,
Otolemur garnettii	ENSOGAG00000009155	1 retrocopy	retro_ogar_104,
Pteropus vampyrus	ENSPVAG00000007494	4 retrocopies	retro_pvam_1147, retro_pvam_340, retro_pvam_541, retro_pvam_720,
Tursiops truncatus	ENSTTRG00000010927	2 retrocopies	retro_ttru_1799, retro_ttru_1920,