RetrogeneDB ID: retro_mdom_326

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 1:144309358..144310392(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: EIF4A1
• Ensembl ID: ENSMODG00000007090
• Aliases: None
• Description: eukaryotic translation initiation factor 4A1 [Source:HGNC Symbol;Acc:3282]

Sequence

>retro_mdom_326
TCAGTAATTCTTTTTATCAAGGGTTATGATGTTATTGCTCAAGCTCAGTCTGGGACCTGGAAGACTGTTACCTTTGCCAT
TTCCATTTTGCAACAGATCAAACTGGTCTTAAAGGCTATACAGGTCTTGGTTTTGGTACCTACTTGAGAGCTTGCTCAGC
AGATCCAAAAGGTAGTGATGTCATTGGGGGACTACATGGGTGCTTCCTGGCATGCCTGTATTGGAGGCACAAATGTTCAG
GCTGAAGTTCAGAACTTGCAGATGGAGGCTCCCCACATCATTGTAGGCATTCCAGGCTGAGTCTTTGACATGCTTAATCA
GAGATACCTATCTCCTAAATATATCAAGATGTTTTTTCTAGATGAAACAGATGAAATGTTGAGTCATGGTTTTAAGGACA
AGATATATGACATATTCCAGAAACTTAGTGGCAGTACTCAGGTGGTACTCCTGTCAGCCACCATGCCCTCAGATGTGCTG
GAAGTGACCAAGAAGTTTATGAGGGATCCTATCAGGATTCTAGTCAAGAAGGAGGAATTGGCATTGGAAGGCATTTGTCA
GTTTTACATAAATGTGGAATGAGAGGAGTGGAAGCTAGATACTTTGTGTGATCTATATGAAACACTGACCCTTACTCAAG
TTTTTATCTTCATCAATACCCACCAAAAGGTGGATTAGCTCACTGAGGAAATGCATGCCCATGATTTTACTGCCTTTGCA
ATTCATGGAGACATGGACCAAAAAGAACATGATGTTATCACAAGGGAGTTTCACTCAGGCTCCAGTTGGGTGCTTATTAC
CACTGACCTATTGGCTAGAAGCATTGATGTTCAGCAAGTATCTTTGGTTATTAATTATGACCTTCCCACTAACTGGGAAA
ATTACATCCATCTAATTGGCTGTGGAGGGCATTTTGGTCATAAAGGTGTGGCATCAACATGGTGACAGAGGAAGACAAGA
GGATCCTTAGAGACATCAAGACCTTCTATAACACCTCCATTGAGGAGATGCCTCTCAATGTGATTGACTTCATC

Alignment

ORF - retro_mdom_326 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.68 %
• Parental protein coverage: 84.98 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  AILPCIKGYDVIAQAQSGTGKTATFAISILQQIELDLKATQALVLAPTRELAQQIQKVVMALGDYMGASC
          .....IKGYDVIAQAQSGT.KT.TFAISILQQI.L.LKA.Q.LVL.PT.ELAQQIQKVVM.LGDYMGAS.
Retrocopy SVILFIKGYDVIAQAQSGTWKTVTFAISILQQIKLVLKAIQVLVLVPT*ELAQQIQKVVMSLGDYMGASW

Parental  HACIGGTNVRAEVQKLQMEAPHIIVGTPGRVFDMLNRRYLSPKYIKMFVLDEADEMLSRGFKDQIYDIFQ
          HACIGGTNV.AEVQ.LQMEAPHIIVG.PG.VFDMLN.RYLSPKYIKMF.LDE.DEMLS.GFKD.IYDIFQ
Retrocopy HACIGGTNVQAEVQNLQMEAPHIIVGIPG*VFDMLNQRYLSPKYIKMFFLDETDEMLSHGFKDKIYDIFQ

Parental  KLSGNTQVVLLSATMPSDVLEVTKKFMRDPIRILVKKEELTLEGIRQFYINVEREEWKLDTLCDLYETLT
          KLSG.TQVVLLSATMPSDVLEVTKKFMRDPIRILVKKEEL.LEGI.QFYINVE.EEWKLDTLCDLYETLT
Retrocopy KLSGSTQVVLLSATMPSDVLEVTKKFMRDPIRILVKKEELALEGICQFYINVE*EEWKLDTLCDLYETLT

Parental  ITQAVIFINTRRKVDWLTEKMHARDFTVSAMHGDMDQKERDVIMREFRSGSSRVLITTDLLARGIDVQQV
          .TQ..IFINT..KVD.LTE.MHA.DFT..A.HGDMDQKE.DVI.REF.SGSS.VLITTDLLAR.IDVQQV
Retrocopy LTQVFIFINTHQKVD*LTEEMHAHDFTAFAIHGDMDQKEHDVITREFHSGSSWVLITTDLLARSIDVQQV

Parental  SLVINYDLPTNRENYIHRIGRGGRFGRKGVA-INMVTEEDKRILRDIETFYNTSIEEMPLNVADLI
          SLVINYDLPTN.ENYIH.IG.GG.FG.KGVA.INMVTEEDKRILRDI.TFYNTSIEEMPLNV.D.I
Retrocopy SLVINYDLPTNWENYIHLIGCGGHFGHKGVA<INMVTEEDKRILRDIKTFYNTSIEEMPLNVIDFI

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_326 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_326 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.

---

Parental genes homology:

Parental genes homology involve 26 parental genes, and 96 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016753	1 retrocopy	retro_amel_1300,
Bos taurus	ENSBTAG00000000132	1 retrocopy	retro_btau_1207,
Callithrix jacchus	ENSCJAG00000015114	8 retrocopies	retro_cjac_1876, retro_cjac_2046, retro_cjac_2521, retro_cjac_2679, retro_cjac_3086, retro_cjac_3203, retro_cjac_395, retro_cjac_727,
Cavia porcellus	ENSCPOG00000004900	1 retrocopy	retro_cpor_1088,
Dipodomys ordii	ENSDORG00000014225	1 retrocopy	retro_dord_732,
Erinaceus europaeus	ENSEEUG00000003581	1 retrocopy	retro_eeur_610,
Felis catus	ENSFCAG00000024897	1 retrocopy	retro_fcat_370,
Homo sapiens	ENSG00000161960	10 retrocopies	retro_hsap_1004, retro_hsap_1182, retro_hsap_1252, retro_hsap_1270, retro_hsap_1796, retro_hsap_2520, retro_hsap_4836, retro_hsap_4873, retro_hsap_4931, retro_hsap_610,
Gorilla gorilla	ENSGGOG00000024702	8 retrocopies	retro_ggor_1321, retro_ggor_1572, retro_ggor_3015, retro_ggor_537, retro_ggor_798, retro_ggor_920, retro_ggor_983, retro_ggor_998,
Loxodonta africana	ENSLAFG00000001107	1 retrocopy	retro_lafr_1210,
Macropus eugenii	ENSMEUG00000010780	2 retrocopies	retro_meug_158, retro_meug_179,
Microcebus murinus	ENSMICG00000014759	2 retrocopies	retro_mmur_1164, retro_mmur_1477,
Myotis lucifugus	ENSMLUG00000003415	3 retrocopies	retro_mluc_1047, retro_mluc_1229, retro_mluc_1805,
Macaca mulatta	ENSMMUG00000013499	1 retrocopy	retro_mmul_1280,
Monodelphis domestica	ENSMODG00000002190	1 retrocopy	retro_mdom_202,
Monodelphis domestica	ENSMODG00000007090	3 retrocopies	retro_mdom_1282, retro_mdom_326 , retro_mdom_711,
Mus musculus	ENSMUSG00000059796	7 retrocopies	retro_mmus_1810, retro_mmus_1853, retro_mmus_2320, retro_mmus_2473, retro_mmus_3122, retro_mmus_325, retro_mmus_527,
Nomascus leucogenys	ENSNLEG00000009547	7 retrocopies	retro_nleu_2109, retro_nleu_2117, retro_nleu_230, retro_nleu_2470, retro_nleu_2769, retro_nleu_440, retro_nleu_701,
Oryctolagus cuniculus	ENSOCUG00000010375	5 retrocopies	retro_ocun_1020, retro_ocun_1326, retro_ocun_1375, retro_ocun_475, retro_ocun_934,
Otolemur garnettii	ENSOGAG00000008132	2 retrocopies	retro_ogar_1375, retro_ogar_1862,
Ochotona princeps	ENSOPRG00000008591	2 retrocopies	retro_opri_155, retro_opri_985,
Pongo abelii	ENSPPYG00000007926	7 retrocopies	retro_pabe_1090, retro_pabe_1474, retro_pabe_3759, retro_pabe_3792, retro_pabe_548, retro_pabe_846, retro_pabe_987,
Pan troglodytes	ENSPTRG00000008694	10 retrocopies	retro_ptro_1201, retro_ptro_1465, retro_ptro_2954, retro_ptro_3112, retro_ptro_3247, retro_ptro_450, retro_ptro_750, retro_ptro_810, retro_ptro_862, retro_ptro_870,
Rattus norvegicus	ENSRNOG00000030628	3 retrocopies	retro_rnor_1059, retro_rnor_2213, retro_rnor_2306,
Sorex araneus	ENSSARG00000006017	7 retrocopies	retro_sara_224, retro_sara_383, retro_sara_461, retro_sara_567, retro_sara_6, retro_sara_605, retro_sara_89,
Ictidomys tridecemlineatus	ENSSTOG00000024814	1 retrocopy	retro_itri_610,