RetrogeneDB ID: retro_mdom_190

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 2:371778665..371779142(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMODG00000018021
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

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_190
AAGTCTCTCAAAATGGCATATGACCTGGACTTCGAGACAGGGGATGCAGGGGCATCAGCAACCTTTCCCATGCAGTGCTC
TGCCTTGCCCAAGAATGGCTTTGTGGTGCTCAAAGGCAGGCCCTATAAGATAGTTGAGATGTCCACCTCCAAGACTGGAA
AGCATGGCTGTGCCAAGGTTCATTTGGTTGGTATCAATATCTTTACTGGGAAGAAATATGAAGATATCTGCCCTTCAACC
CACAACATGGATGTGCCCAATATCAAGAGAAATGATTTCCAGCTGATTGGGACTCAGGATGGCTACCTGTCACTGCTCCA
AGACAGTGAGGAGGTGAGGGAGGACCTGTGTTTACCTGAAGGTGACCTAGGCAAGGAGATTGAGCAGAAGTATGATTGTG
GAGAAGAGATTCTGATAACGGTGCTGTCAGCCATAACAGAGGAAGCAGCTGTTGCAATCAAGGCCATGGCAAAGTAA

Alignment

ORF - retro_mdom_190 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.3 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KSLKMADDLDFETGDAGASATFPMQCSALRKNGFVVLKGRPCKIVEMSTSKTGKHGHAKVHLVGIDIFTG
          KSLKMA.DLDFETGDAGASATFPMQCSAL.KNGFVVLKGRP.KIVEMSTSKTGKHG.AKVHLVGI.IFTG
Retrocopy KSLKMAYDLDFETGDAGASATFPMQCSALPKNGFVVLKGRPYKIVEMSTSKTGKHGCAKVHLVGINIFTG

Parental  KKYEDICPSTHNMDVPNIKRNDFQLIGIQDGYLSLLQDSGEVREDLRLPEGDLGKEIEQKYDCGEEILIT
          KKYEDICPSTHNMDVPNIKRNDFQLIG.QDGYLSLLQDS.EVREDL.LPEGDLGKEIEQKYDCGEEILIT
Retrocopy KKYEDICPSTHNMDVPNIKRNDFQLIGTQDGYLSLLQDSEEVREDLCLPEGDLGKEIEQKYDCGEEILIT

Parental  VLSAMTEEAAVAIKAMAK
          VLSA.TEEAAVAIKAMAK
Retrocopy VLSAITEEAAVAIKAMAK

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_190 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_190 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,