RetrogeneDB ID: retro_mdom_1641

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 6:15862133..15862439(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: EIF5A
• Ensembl ID: ENSMODG00000006652
• Aliases: None
• Description: eukaryotic translation initiation factor 5A [Source:HGNC Symbol;Acc:3300]

Sequence

>retro_mdom_1641
AATGACCTGAACTTCCATATTGGTCTGCAGGAGTCTCAGGTACTTTTCACACACAGCATCCACCTTGAAAAAGAATCACT
GCAGAATTCTCAAAGGCCAGCCCTGTAAAATAGTTGGGGTATTTACTTCTAAGAGTATAAAGCATGACCGTTTCATCATC
CATCTAGTTCATGTTAATATCTTTATTAGGAAGAAATTGAAAGATACCTATTCTTCTACTTACAACATGGTTGTGCTCAA
TATCAAGAGAAATGACTTCCATTGATTGTGATCCTGAATGGTCACTTCTTGATATTGCTCCAGGAT

Alignment

ORF - retro_mdom_1641 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 52.83 %
• Parental protein coverage: 64.56 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  DDLDFETG-DAGASATFPMQ-CSALRKNGFVVLKGRPCKIVEMSTSKTGKHGHAKVHLVGIDIFTGKKYE
          .DL.F..G..AG.S.TF..Q..S.L.KN....LKG.PCKIV...TSK..KH.....HLV...IF..KK..
Retrocopy NDLNFHIG<SAGVSGTFHTQ<ASTLKKNHCRILKGQPCKIVGVFTSKSIKHDRFIIHLVHVNIFIRKKLK

Parental  DICPSTHNMDVPNIKRNDFQ-LIGIQDG-YLSLLQD
          D...ST.NM.V.NIKRNDF..LI.I..G..L.LLQD
Retrocopy DTYSSTYNMVVLNIKRNDFH<LIVILNGHFLILLQD

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_1641 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1641 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 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000132507	3 retrocopies	retro_hsap_1788, retro_hsap_2004, retro_hsap_9,
Gorilla gorilla	ENSGGOG00000012032	2 retrocopies	retro_ggor_1448, retro_ggor_159,
Microcebus murinus	ENSMICG00000012459	1 retrocopy	retro_mmur_711,
Macaca mulatta	ENSMMUG00000006206	1 retrocopy	retro_mmul_1379,
Monodelphis domestica	ENSMODG00000006652	2 retrocopies	retro_mdom_1641 , retro_mdom_190,
Otolemur garnettii	ENSOGAG00000014230	1 retrocopy	retro_ogar_2414,
Pongo abelii	ENSPPYG00000007907	1 retrocopy	retro_pabe_1468,
Pan troglodytes	ENSPTRG00000008674	3 retrocopies	retro_ptro_1198, retro_ptro_442, retro_ptro_504,
Rattus norvegicus	ENSRNOG00000016478	3 retrocopies	retro_rnor_1627, retro_rnor_1947, retro_rnor_671,
Sus scrofa	ENSSSCG00000017939	1 retrocopy	retro_sscr_1204,
Tursiops truncatus	ENSTTRG00000009783	1 retrocopy	retro_ttru_1526,