RetrogeneDB ID: retro_meug_585

Retrocopy location

• Organism: Wallaby (Macropus eugenii)
• Coordinates: Scaffold14149:21580..22630(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: EIF4B
• Ensembl ID: ENSMEUG00000012341
• Aliases: None
• Description: eukaryotic translation initiation factor 4B [Source:HGNC Symbol;Acc:3285]

Sequence

>retro_meug_585
CGAGACAATAGTTCCTTTGGCGGTGACCGGGATCGAAATCAGGATTCTGACAAGGTCGACACAGACTGGAGGGCTTGCCC
TGCCACACACAGCTTTGATGACTACCCTCCTCGGAGGGGTGATGACAGCTTTGGAGACAAGTATTGTGATCTTTATGATT
CAGACCAGTACCGTGATGGTCCTTGGTGTGACACGGACCGATATAGAGTCTGGGATCAATATGATGACAGGGGCAGCAGA
GACTATGATAGAGGTTTTGATTCTAGGATAGGCAGTGGCAGAAGAGCATTTGGTAGTGGGTACCGTCTGGATGATGATTA
CAGAGGAGGAGGAGATCGCTATGAAGACAGATATAACAGACGAGATGATCAGTCACGGAACTCGAGAGATTATTACAGAA
GGGATGATTTTAGGCATGAAGACACAGGTTCTCCCCCCGCCCCTGAGAGACCCAAACTGAATCTGAAGCCGCGGAGTGCA
CCCAAGAACGAAGATTCATCAGCTAGCACCTCGCAGTCTAGCTGAGTTGCCTCCATCTTTGGGGGGCAAAGCCAGTGGAT
ACAGCTGCTAGGGAACGAGAAGTAGAGAAACGACTACAAAAGGAGCAAGAGAAACTACAATGACAGCTGGAGGAGCCGAA
ACTAGAAAGACAGCCCCGGGAGAGACACCCAAGTTGGCAAAGTGAGGAAATGCAGGAACGGTCAAGGGCGGGAAGTGAAT
CTTCACAGTCTGGGAATACAGCACCATCTGGCAGAAACACAGGAAGGAGGGAGAGTGAGAAATCCCTCGAAAATGAAACA
TTCAACAAGGAAGAGGGTTCTCAGTCTCCAGCTTCCAAGCCTTCTAGGGGAAGATCAGCTTCCCCTAAAGGTGATGCCTG
CATCCTCACCAAAGGAAAACGCCTGGGTGAAAAGAAGCTCCAACCCTCCTGTCCAATCTCAGAGCTCCGACTCTTCAGAG
CAGCAATCCCCCACAAGTGATGGAGGAAAGGTAACATCCCAGCAGTCTGAGGAAGGACCAGCTAATATTTCAAGGAAAGA
TGAGAATAAG

Alignment

ORF - retro_meug_585 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.33 %
• Parental protein coverage: 63.15 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  RDDRSFGRDRDRNRDSDKTDTDWRARPATDSFDDYPPRRGDDSFGDKYRDRYDSDRYRDGPRRDMDRYGG
          RD..SFG.DRDRN.DSDK.DTDWRA.PAT.SFDDYPPRRGDDSFGDKY.D.YDSD.YRDGP..D.DRY..
Retrocopy RDNSSFGGDRDRNQDSDKVDTDWRACPATHSFDDYPPRRGDDSFGDKYCDLYDSDQYRDGPWCDTDRYRV

Parental  RDRYDDRGSRDYDRGFDSRIGSGRRAFGSGYRRDDDYRGGGDRYEDRYDRRDDRSWNSRDDYSRDDFRRE
          .D.YDDRGSRDYDRGFDSRIGSGRRAFGSGYR.DDDYRGGGDRYEDRY.RRDD.S.NSRD.Y.RDDFR.E
Retrocopy WDQYDDRGSRDYDRGFDSRIGSGRRAFGSGYRLDDDYRGGGDRYEDRYNRRDDQSRNSRDYYRRDDFRHE

Parental  DRGPP---QRPKLNLKPRSAPKDEDSSASTSQSSRAASIFG-GAKPVDTAAREREVEERLQKEQEKLQRQ
          D.G.P....RPKLNLKPRSAPK.EDSSASTSQSS..ASIFG.GAKPVDTAAREREVE.RLQKEQEKLQ.Q
Retrocopy DTGSPPAPERPKLNLKPRSAPKNEDSSASTSQSS*VASIFG<GAKPVDTAAREREVEKRLQKEQEKLQ*Q

Parental  LEEPKLERRPRERHPSWRSEETQERSRTGSESSQTGNIAPSGRNTRRRESEKSLENEAFNKEEDSQSPTS
          LEEPKLER.PRERHPSW.SEE.QERSR.GSESSQ.GN.APSGRNT.RRESEKSLENE.FNKEE.SQSP.S
Retrocopy LEEPKLERQPRERHPSWQSEEMQERSRAGSESSQSGNTAPSGRNTGRRESEKSLENETFNKEEGSQSPAS

Parental  KPSK-SDQLPLKVMPAPPPKENAWVKRSSNPPARSQSSDSSEQQSPTENKVDGVSVLKGQSGNSNRGPVD
          KPS...DQLPLKVMPA..PKENAWVKRSSNPP..SQSSDSSEQQSPT....DG..V...QS.....GP..
Retrocopy KPSR>EDQLPLKVMPASSPKENAWVKRSSNPPVQSQSSDSSEQQSPTS---DGGKVTSQQS---EEGPAN

Parental  GGSKDHWK
          ...KD..K
Retrocopy ISRKDENK

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Macropus eugenii was not studied using RNA-Seq expression data.

ChIP-Seq

Macropus eugenii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_meug_585 retrocopy.

TSS

Macropus eugenii was not studied using FANTOM5 data.

Lab

retro_meug_585 was not experimentally validated.

Homology

Retrocopy orthology:

Macropus eugenii 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 17 parental genes, and 48 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000012023	2 retrocopies	retro_amel_1107, retro_amel_559,
Canis familiaris	ENSCAFG00000007117	2 retrocopies	retro_cfam_1447, retro_cfam_936,
Choloepus hoffmanni	ENSCHOG00000001608	2 retrocopies	retro_chof_1310, retro_chof_366,
Callithrix jacchus	ENSCJAG00000018176	2 retrocopies	retro_cjac_1717, retro_cjac_2001,
Cavia porcellus	ENSCPOG00000005595	3 retrocopies	retro_cpor_278, retro_cpor_752, retro_cpor_937,
Homo sapiens	ENSG00000063046	7 retrocopies	retro_hsap_1686, retro_hsap_2639, retro_hsap_2698, retro_hsap_3767, retro_hsap_4196, retro_hsap_4848, retro_hsap_4891,
Gorilla gorilla	ENSGGOG00000013695	5 retrocopies	retro_ggor_1233, retro_ggor_1263, retro_ggor_1882, retro_ggor_1883, retro_ggor_3024,
Loxodonta africana	ENSLAFG00000009534	1 retrocopy	retro_lafr_294,
Macropus eugenii	ENSMEUG00000012341	2 retrocopies	retro_meug_1054, retro_meug_585 ,
Macaca mulatta	ENSMMUG00000001062	5 retrocopies	retro_mmul_1428, retro_mmul_2384, retro_mmul_2589, retro_mmul_731, retro_mmul_783,
Mus musculus	ENSMUSG00000058655	1 retrocopy	retro_mmus_3686,
Nomascus leucogenys	ENSNLEG00000017727	3 retrocopies	retro_nleu_2371, retro_nleu_2601, retro_nleu_721,
Pongo abelii	ENSPPYG00000025848	7 retrocopies	retro_pabe_1388, retro_pabe_1560, retro_pabe_2283, retro_pabe_260, retro_pabe_3532, retro_pabe_3768, retro_pabe_506,
Rattus norvegicus	ENSRNOG00000010103	2 retrocopies	retro_rnor_2467, retro_rnor_2972,
Ictidomys tridecemlineatus	ENSSTOG00000006800	1 retrocopy	retro_itri_604,
Tupaia belangeri	ENSTBEG00000005423	2 retrocopies	retro_tbel_2363, retro_tbel_4167,
Tarsius syrichta	ENSTSYG00000012880	1 retrocopy	retro_tsyr_452,