RetrogeneDB ID: retro_mdom_365

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 1:298031881..298032619(+)
• Located in intron of: ENSMODG00000014580

Retrocopy information

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

Parental gene information

• Parental gene symbol: EIF2S2
• Ensembl ID: ENSMODG00000002805
• Aliases: None
• Description: eukaryotic translation initiation factor 2, subunit 2 beta, 38kDa [Source:HGNC Symbol;Acc:3266]

Sequence

>retro_mdom_365
ATATTTGATATTGATGAAGCTGAAGAAGGTGTTAAGGACCTAAAGATTGAAAGTGTTATGCAAGAACCAGCAGAACCAGA
ATATGGCCTTGATATTATAATCGGCAACAAAAAGAAGAAAAGGAAGAATGTCAAGTTACCAGATGAGGATGAAATCCTAG
AGAAAGATGAAGCCTTAGAAGATGAGGACAGCAAAAAGGATGATGGAATCTCCTTCAGCAATCAGACTGGCCCTGCTTGG
GCATGTTCAGAAAGAGACTATATTTATGATGAGTTGCTGAATTGAGTATTCAACGTAAGGCGGGAAAAGAATCCAGATAT
GGTTGTTGGAGAAAAAAGAAAATTTGTCATGAAATCTCCACAGGTTGTTAGAATAGAAACCAAGAAAACTTCTTTTGTCA
ACTTCACAGATATCTGTAAACTATTGCATCATCAGCCCAAACATCTCCTGGCATTTTTAATGGCTGAGTTGGGTACAAGT
GGTTCCATAGATGGTAATAATCAACTTTTAACCAAAGGAAGATTCCAACAGAAACAGATAGAAAACGTCTTGAGAAGATA
TATCAAGGAATATGTCACATGTCATACATGTTGGTCACCAGACACAATCCTATAGAAAGATATTTGACTCTATTTCTTAG
AGTGTGAGACCTGACATTCTTGCTGCTCTGTCACCAGCATCAAAACTGGGTTCCAGGCCATCATAGGCAAGCGAGCACAG
CTCCATGCCAAAGCTAAT

Alignment

ORF - retro_mdom_365 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.99 %
• Parental protein coverage: 73.87 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  IFDIDEAEEGVKDLKIESDVQEPAEPEDDLDIMLGNKKKKKKNVKFPDEDEILEKDEALEDEDSKKDDGI
          IFDIDEAEEGVKDLKIES..QEPAEPE..LDI..GNKKKK.KNVK.PDEDEILEKDEALEDEDSKKDDGI
Retrocopy IFDIDEAEEGVKDLKIESVMQEPAEPEYGLDIIIGNKKKKRKNVKLPDEDEILEKDEALEDEDSKKDDGI

Parental  SFSNQTGPAWAGSERDYTYDELLNRVFNIMREKNPDMVAGEKRKFVMKPPQVVRVGTKKTSFVNFTDICK
          SFSNQTGPAWA.SERDY.YDELLN.VFN..REKNPDMV.GEKRKFVMK.PQVVR..TKKTSFVNFTDICK
Retrocopy SFSNQTGPAWACSERDYIYDELLN*VFNVRREKNPDMVVGEKRKFVMKSPQVVRIETKKTSFVNFTDICK

Parental  LLHRQPKHLLAFLLAELGTSGSIDGNNQLVIKGRFQQKQIENVLRRYIKEYVTCHTCRSPDTILQKDTRL
          LLH.QPKHLLAFL.AELGTSGSIDGNNQL..KGRFQQKQIENVLRRYIKEYVTCHTC.SPDTIL.KD..L
Retrocopy LLHHQPKHLLAFLMAELGTSGSIDGNNQLLTKGRFQQKQIENVLRRYIKEYVTCHTCWSPDTIL*KDI*L

Parental  YFLQCETCHSRCSVASIKTGFQAVTGKRAQLRAKAN
          YFL.CET.HS.CSV.SIKTGFQA..GKRAQL.AKAN
Retrocopy YFLECET*HSCCSVTSIKTGFQAIIGKRAQLHAKAN

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	0.12 RPM	320.52 RPM
SRP007412_cerebellum	0.00 RPM	255.29 RPM
SRP007412_heart	0.40 RPM	286.87 RPM
SRP007412_kidney	0.00 RPM	377.93 RPM
SRP007412_liver	0.00 RPM	388.69 RPM
SRP007412_testis	0.20 RPM	1198.83 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_365 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_365 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 18 parental genes, and 33 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000007498	1 retrocopy	retro_cfam_2070,
Choloepus hoffmanni	ENSCHOG00000006521	1 retrocopy	retro_chof_271,
Callithrix jacchus	ENSCJAG00000018334	2 retrocopies	retro_cjac_4196, retro_cjac_697,
Cavia porcellus	ENSCPOG00000015439	1 retrocopy	retro_cpor_1143,
Echinops telfairi	ENSETEG00000001922	1 retrocopy	retro_etel_1101,
Homo sapiens	ENSG00000125977	3 retrocopies	retro_hsap_2176, retro_hsap_2260, retro_hsap_713,
Gorilla gorilla	ENSGGOG00000015546	5 retrocopies	retro_ggor_1683, retro_ggor_1726, retro_ggor_2007, retro_ggor_280, retro_ggor_604,
Microcebus murinus	ENSMICG00000006944	1 retrocopy	retro_mmur_1583,
Myotis lucifugus	ENSMLUG00000005335	1 retrocopy	retro_mluc_604,
Macaca mulatta	ENSMMUG00000018095	1 retrocopy	retro_mmul_1483,
Monodelphis domestica	ENSMODG00000002805	5 retrocopies	retro_mdom_1981, retro_mdom_365 , retro_mdom_368, retro_mdom_370, retro_mdom_837,
Mus musculus	ENSMUSG00000074656	1 retrocopy	retro_mmus_3200,
Nomascus leucogenys	ENSNLEG00000010034	2 retrocopies	retro_nleu_2242, retro_nleu_466,
Otolemur garnettii	ENSOGAG00000001417	1 retrocopy	retro_ogar_196,
Pongo abelii	ENSPPYG00000010933	2 retrocopies	retro_pabe_1955, retro_pabe_2421,
Pan troglodytes	ENSPTRG00000013412	2 retrocopies	retro_ptro_1600, retro_ptro_508,
Rattus norvegicus	ENSRNOG00000017447	1 retrocopy	retro_rnor_2395,
Tupaia belangeri	ENSTBEG00000009970	2 retrocopies	retro_tbel_1505, retro_tbel_2508,