RetrogeneDB ID: retro_mdom_1113

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 3:144041471..144041711(-)
• Located in intron of: ENSMODG00000005451

Retrocopy information

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

Parental gene information

• Parental gene symbol: EIF1B
• Ensembl ID: ENSMODG00000011056
• Aliases: None
• Description: eukaryotic translation initiation factor 1B [Source:HGNC Symbol;Acc:30792]

Sequence

>retro_mdom_1113
AGAATCCAACCATGGAAAGACAGAAAGACACTGCATACTGTTCAGGGAATTGCAGATAATTATGAGAAGAAGAAACTTGT
GAAAGCTTTCAAAAAGAAATTTGCTTGTAATGGTACTGTGATTAAACATCCAGAATACAGCAAGGTTATCCAACTTTAAG
GTGACCAGAGAAGGAACATTAGTCAGTTCCTCCTGGAGGTTGGCATTGTCAAGGAGAAGCAGCTTAAGGTTCATGGTTTC

Alignment

ORF - retro_mdom_1113 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.5 %
• Parental protein coverage: 70.8 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RIQQRNGRKTLTTVQGIADDYDKKKLVKAFKKKFACNGTVIEHPEYGEVIQLQGDQRKNICQFLLEVGIV
          RIQ....RKTL.TVQGIAD.Y.KKKLVKAFKKKFACNGTVI.HPEY..VIQL.GDQR.NI.QFLLEVGIV
Retrocopy RIQPWKDRKTLHTVQGIADNYEKKKLVKAFKKKFACNGTVIKHPEYSKVIQL*GDQRRNISQFLLEVGIV

Parental  KEEQLKVHGF
          KE.QLKVHGF
Retrocopy KEKQLKVHGF

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_1113 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1113 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 10 parental genes, and 29 retrocopies.

Species	Parental gene accession	Retrocopies number
Dipodomys ordii	ENSDORG00000013689	4 retrocopies	retro_dord_179, retro_dord_307, retro_dord_626, retro_dord_669,
Echinops telfairi	ENSETEG00000017295	5 retrocopies	retro_etel_1228, retro_etel_1480, retro_etel_1793, retro_etel_31, retro_etel_4,
Microcebus murinus	ENSMICG00000013223	5 retrocopies	retro_mmur_254, retro_mmur_445, retro_mmur_535, retro_mmur_654, retro_mmur_706,
Macaca mulatta	ENSMMUG00000017704	1 retrocopy	retro_mmul_154,
Monodelphis domestica	ENSMODG00000011056	2 retrocopies	retro_mdom_1113 , retro_mdom_1382,
Mus musculus	ENSMUSG00000006941	1 retrocopy	retro_mmus_587,
Otolemur garnettii	ENSOGAG00000025224	1 retrocopy	retro_ogar_1943,
Ictidomys tridecemlineatus	ENSSTOG00000012168	1 retrocopy	retro_itri_1597,
Tupaia belangeri	ENSTBEG00000013185	6 retrocopies	retro_tbel_1861, retro_tbel_1920, retro_tbel_1996, retro_tbel_2954, retro_tbel_3209, retro_tbel_3867,
Tarsius syrichta	ENSTSYG00000006338	3 retrocopies	retro_tsyr_1574, retro_tsyr_2154, retro_tsyr_888,