RetrogeneDB ID: retro_mdom_822

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 2:89292903..89293457(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: EIF3I
• Ensembl ID: ENSMODG00000017481
• Aliases: None
• Description: eukaryotic translation initiation factor 3, subunit I [Source:HGNC Symbol;Acc:3272]

Sequence

>retro_mdom_822
TTTGATTTTAGGGGCAACAGCATCATATTCTCCATAGAGAAGCAAATTGGGTACCAGAGCTTTGTCAATTCTTTGACCTA
TCGTACCCTAGCCAGATAGAAAGCAATGAATCTTCTATAAAAAATCACCTGTAATTCTGATGCTAGGATCACAAGTGTTG
CATGGGTACCTTGGGGGTGTGTATCATTGCTGGTCATGAAAATGGGGAGCTCAACCAGTAAAATGCAAAGTCTGGAGAAG
TGATGGAGAATATTAAGATGCCCACAAGGCAGATTAATAACATTCAGACAACTCAAGATAAGACAAGGTTTGTAGCTGCA
TCAAAAACCCAATACAGCCATGCTTTTTTACTTTAAAACACTTGAGCACCTGAAAATATTCAAAACAAAGTGATCTGTCA
ATTCAGCTGCTCTGTCCTCCATCTTTGACCATTTAGTCCTGAGTAGTGGACAGGAGGCCATTGATATATCACAACCTCCA
CCAGAACTGGAAAGTTTGAAGGCAAGTTCTTCCATTTTATGTTTAAAGAGGTGTTTAGAAGAGCCAAGGATCAC

Alignment

ORF - retro_mdom_822 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.21 %
• Parental protein coverage: 56.75 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  FDFGGNIIMFSTDKQMGYQCFVS-FFDLRDPSQIDSNEPYMK-IPCNADAKITSAVW-GPLGECIIAGHE
          FDF.GN.I.FS..KQ.GYQ.FV..FFDL..PSQI.SNE...K.I.CN.DA.ITS..W.G.LG.CIIAGHE
Retrocopy FDFRGNSIIFSIEKQIGYQSFVN<FFDLSYPSQIESNESSIK>ITCNSDARITSVAW<GTLGVCIIAGHE

Parental  NGELNQYSAKSGEVMVNVKEHSRQINDIQTSRDMTMFVTASKD-NTAKLFDSTTLEHQKTFRTERPVNSA
          NGELNQ..AKSGEVM.N.K...RQIN.IQT..D.T.FV.ASK..NTA.LF...TLEH.K.F.T...VNSA
Retrocopy NGELNQ*NAKSGEVMENIKMPTRQINNIQTTQDKTRFVAASKT>NTAMLFYFKTLEHLKIFKTK*SVNSA

Parental  ALSPIYDHVVLGGGQEAMDVT-TTSTRIGKFEARFFHLAFEEEFGRVKGH
          ALS.I.DH.VL..GQEA.D...TTSTR.GKFE..FFH..F.E.F.R.K.H
Retrocopy ALSSIFDHLVLSSGQEAIDIS<TTSTRTGKFEGKFFHFMFKEVFRRAKDH

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_822 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_822 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 12 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000010674	1 retrocopy	retro_cfam_321,
Callithrix jacchus	ENSCJAG00000006810	1 retrocopy	retro_cjac_3104,
Echinops telfairi	ENSETEG00000008047	1 retrocopy	retro_etel_1497,
Homo sapiens	ENSG00000084623	2 retrocopies	retro_hsap_3888, retro_hsap_3894,
Gorilla gorilla	ENSGGOG00000001579	3 retrocopies	retro_ggor_2540, retro_ggor_2615, retro_ggor_2623,
Loxodonta africana	ENSLAFG00000017026	1 retrocopy	retro_lafr_1073,
Macaca mulatta	ENSMMUG00000006119	2 retrocopies	retro_mmul_1730, retro_mmul_1733,
Monodelphis domestica	ENSMODG00000017481	2 retrocopies	retro_mdom_1054, retro_mdom_822 ,
Mus musculus	ENSMUSG00000028798	2 retrocopies	retro_mmus_1375, retro_mmus_607,
Nomascus leucogenys	ENSNLEG00000002426	2 retrocopies	retro_nleu_1129, retro_nleu_1135,
Pongo abelii	ENSPPYG00000001598	2 retrocopies	retro_pabe_3169, retro_pabe_3175,
Rattus norvegicus	ENSRNOG00000047185	1 retrocopy	retro_rnor_1548,