RetrogeneDB ID: retro_mdom_373

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 1:305230729..305231163(+)
• Located in intron of: ENSMODG00000014131

Retrocopy information

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

Parental gene information

• Parental gene symbol: SOD2
• Ensembl ID: ENSMODG00000007521
• Aliases: None
• Description: superoxide dismutase 2, mitochondrial [Source:HGNC Symbol;Acc:11180]

Sequence

>retro_mdom_373
ATGATGATCGGGGTGATGAGCAGGAGGACCAGTAAGCTAGTACTGGCTTTGGGATGTCTGGGCTCCAGGCAAAGGCACAG
CCTTCCTGAATTGCCTGATAATTATGGTGCACTGTAGCCTCACATTAATGCACAGATCATGCAACTGCACCACAGCAAAA
ATCATGCCACTTAAGTGAATAACTTGAATGCTACAGAGGAGAAATATAAAGAGGCCCTGGAAAAGGGTGATGTTACTTCT
CAGGTAGCTCTCCAGCCTGCATTATGGTTCAATGGTGGTGGTCGTATCAATCATACGATTTTCTGAACAAACCTTTGCCA
AAATGGTAGAGGAGAACCTAAAGGGGAATTGATGAAAGCCATCATACGTGATTTGGGTTCTTTTGAAAATTATAAGGAGA
GTTGACAATTGTGTCAGTTGGTGTTCAAGGTTCA

Alignment

ORF - retro_mdom_373 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.88 %
• Parental protein coverage: 65.32 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MLCRVMSRRTSKLVPALGCLGSRQKHSLPDLPYDYGALEPHINAQIMQLHHSKHHATYVNNLNATEEKYK
          M...VMSRRTSKLV.ALGCLGSRQ.HSLP.LP..YGAL.PHINAQIMQLHHSK.HAT.VNNLNATEEKYK
Retrocopy MMIGVMSRRTSKLVLALGCLGSRQRHSLPELPDNYGAL*PHINAQIMQLHHSKNHAT*VNNLNATEEKYK

Parental  EALAKGDVTSQVALQPALRFNGGGHINHTIFWTNLCPNGGGEPKGELMEAIKRDFGSFEKFKE-KLTAVS
          EAL.KGDVTSQVALQPAL.FNGGG.INHTIF.TNLC.NG.GEPKGELM.AI.RD.GSFE..KE..LT.VS
Retrocopy EALEKGDVTSQVALQPALWFNGGGRINHTIF*TNLCQNGRGEPKGELMKAIIRDLGSFENYKE<ELTIVS

Parental  VGVQGS
          VGVQGS
Retrocopy VGVQGS

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	0.00 RPM
SRP007412_cerebellum	0.33 RPM	0.00 RPM
SRP007412_heart	0.00 RPM	0.00 RPM
SRP007412_kidney	0.00 RPM	0.00 RPM
SRP007412_liver	0.50 RPM	0.00 RPM
SRP007412_testis	0.20 RPM	0.00 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_373 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_373 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 24 parental genes, and 28 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000015466	1 retrocopy	retro_amel_786,
Canis familiaris	ENSCAFG00000000671	1 retrocopy	retro_cfam_1795,
Choloepus hoffmanni	ENSCHOG00000003215	4 retrocopies	retro_chof_1952, retro_chof_1966, retro_chof_2620, retro_chof_937,
Callithrix jacchus	ENSCJAG00000011664	1 retrocopy	retro_cjac_3032,
Dasypus novemcinctus	ENSDNOG00000007907	1 retrocopy	retro_dnov_1653,
Equus caballus	ENSECAG00000011797	2 retrocopies	retro_ecab_70, retro_ecab_840,
Echinops telfairi	ENSETEG00000016400	1 retrocopy	retro_etel_731,
Felis catus	ENSFCAG00000002843	1 retrocopy	retro_fcat_1200,
Homo sapiens	ENSG00000112096	1 retrocopy	retro_hsap_430,
Gorilla gorilla	ENSGGOG00000008212	1 retrocopy	retro_ggor_419,
Myotis lucifugus	ENSMLUG00000012242	1 retrocopy	retro_mluc_528,
Monodelphis domestica	ENSMODG00000007521	1 retrocopy	retro_mdom_373 ,
Mustela putorius furo	ENSMPUG00000005045	1 retrocopy	retro_mputfur_1382,
Nomascus leucogenys	ENSNLEG00000011061	1 retrocopy	retro_nleu_1023,
Otolemur garnettii	ENSOGAG00000017100	1 retrocopy	retro_ogar_1123,
Pongo abelii	ENSPPYG00000017143	1 retrocopy	retro_pabe_292,
Pan troglodytes	ENSPTRG00000018757	1 retrocopy	retro_ptro_327,
Pteropus vampyrus	ENSPVAG00000005302	1 retrocopy	retro_pvam_288,
Rattus norvegicus	ENSRNOG00000019048	1 retrocopy	retro_rnor_2221,
Sarcophilus harrisii	ENSSHAG00000014795	1 retrocopy	retro_shar_210,
Ictidomys tridecemlineatus	ENSSTOG00000008738	1 retrocopy	retro_itri_1432,
Tupaia belangeri	ENSTBEG00000002100	1 retrocopy	retro_tbel_665,
Tarsius syrichta	ENSTSYG00000000457	1 retrocopy	retro_tsyr_183,
Tursiops truncatus	ENSTTRG00000014364	1 retrocopy	retro_ttru_265,