RetrogeneDB ID: retro_mdom_1471

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 5:199813499..199814186(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMODG00000000081
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: ANXA2
• Ensembl ID: ENSMODG00000011604
• Aliases: None
• Description: annexin A2 [Source:HGNC Symbol;Acc:537]

Sequence

>retro_mdom_1471
ATGTCTACAGTTCACAAAATTCTATGCAAGGTCAGTTTGGAGAGTGATCATTCCACATTCCAAGTGCATATGGCTCCATC
AAGGCTTATAACAACTTTGATGCTGAGAGGGATGCTTTAAACATTGAGGCAGCTATCAAGACCAAAGTGGTGGATGAAGT
TACTATAGTCAACGTTCTGATAAATGGCAGCATTGAACAAAGGCAGGACATTGCCTTTGCTTATCAGAGAAGGACCAGAA
AGGAATTTACATCAGGACTGAAATCTGCCTCATCTGGCCACCTGGAAGCAGTGATTTGGGTCCTTTTGAAGACTCCACCT
CAGTGTGATGCTTCGGAGCTGAAAGCCTCCATGAAGGGCCTGGGCTCTGATGAAGATTCCCTCATTGAGATCATCTTCTC
ACAACAAACCAGGAGCTCTATGAAATTGATAAAGTCTACAGAGAAATGTTCAAGACAGAGTTGGAGAAGGATTTTATTTC
GGACACATCTGGTGACTTCTGCAAATTGATGGTTGCCCTGCTAAAGGGCAAAGGACAGAAGATGGGTCTTTAATTGATTA
TGAGCTAATTGACCAAGAGGCTCAGGACCTCTATGATGCAGGAGTGAAGAGGAAGGGAACTGATGTCCCTAAATGGATCG
GCATTATGACTGAGAGGAGTGTGTGCCACCTGCAGAAAGTATTTGAG

Alignment

ORF - retro_mdom_1471 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.98 %
• Parental protein coverage: 67.85 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MSTVHEILCKLNLEGDHST-PPSAYGSVKAYNNFDAERDALNIEAAIKTKGVDEVTIVNILTNRSNEQRQ
          MSTVH.ILCK..LE.DHST..PSAYGS.KAYNNFDAERDALNIEAAIKTK.VDEVTIVN.L.N.S.EQRQ
Retrocopy MSTVHKILCKVSLESDHST<IPSAYGSIKAYNNFDAERDALNIEAAIKTKVVDEVTIVNVLINGSIEQRQ

Parental  DIAFAYQRRTKKELTSALKSALSGHLEAVILGLLKTPAQYDASELKASMKGLGTDEDSLIEIICSR-TNQ
          DIAFAYQRRT.KE.TS.LKSA.SGHLEAVI..LLKTP.Q.DASELKASMKGLG.DEDSLIEII.S..TNQ
Retrocopy DIAFAYQRRTRKEFTSGLKSASSGHLEAVIWVLLKTPPQCDASELKASMKGLGSDEDSLIEIIFSQ<TNQ

Parental  ELYEINKVYREMYKTELEKDIISDTSGDFRKLMVAL-AKGRRAEDGSVIDYELIDQDARDLYDAGVKRKG
          ELYEI.KVYREM.KTELEKD.ISDTSGDF.KLMVAL.AKG.R.EDGS.IDYELIDQ.A.DLYDAGVKRKG
Retrocopy ELYEIDKVYREMFKTELEKDFISDTSGDFCKLMVAL<AKGQRTEDGSLIDYELIDQEAQDLYDAGVKRKG

Parental  TDVPKWISIMTERSVCHLQKVFE
          TDVPKWI.IMTERSVCHLQKVFE
Retrocopy TDVPKWIGIMTERSVCHLQKVFE

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	150.31 RPM
SRP007412_cerebellum	0.00 RPM	76.72 RPM
SRP007412_heart	0.00 RPM	270.92 RPM
SRP007412_kidney	0.00 RPM	532.00 RPM
SRP007412_liver	0.00 RPM	708.91 RPM
SRP007412_testis	0.00 RPM	95.07 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_1471 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1471 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 21 parental genes, and 41 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000008055	2 retrocopies	retro_amel_1531, retro_amel_1836,
Bos taurus	ENSBTAG00000009615	2 retrocopies	retro_btau_634, retro_btau_985,
Canis familiaris	ENSCAFG00000016686	3 retrocopies	retro_cfam_1631, retro_cfam_367, retro_cfam_707,
Choloepus hoffmanni	ENSCHOG00000012143	3 retrocopies	retro_chof_1028, retro_chof_1965, retro_chof_815,
Equus caballus	ENSECAG00000012670	1 retrocopy	retro_ecab_759,
Felis catus	ENSFCAG00000007862	2 retrocopies	retro_fcat_594, retro_fcat_709,
Homo sapiens	ENSG00000182718	3 retrocopies	retro_hsap_3114, retro_hsap_4150, retro_hsap_580,
Gorilla gorilla	ENSGGOG00000009738	3 retrocopies	retro_ggor_2137, retro_ggor_2788, retro_ggor_515,
Macropus eugenii	ENSMEUG00000008980	3 retrocopies	retro_meug_1000, retro_meug_312, retro_meug_389,
Myotis lucifugus	ENSMLUG00000002464	3 retrocopies	retro_mluc_1569, retro_mluc_2223, retro_mluc_2431,
Monodelphis domestica	ENSMODG00000011604	1 retrocopy	retro_mdom_1471 ,
Mustela putorius furo	ENSMPUG00000000762	2 retrocopies	retro_mputfur_73, retro_mputfur_79,
Nomascus leucogenys	ENSNLEG00000011678	2 retrocopies	retro_nleu_769, retro_nleu_802,
Otolemur garnettii	ENSOGAG00000009952	1 retrocopy	retro_ogar_3510,
Pongo abelii	ENSPPYG00000006526	2 retrocopies	retro_pabe_2572, retro_pabe_607,
Pan troglodytes	ENSPTRG00000007132	2 retrocopies	retro_ptro_2106, retro_ptro_81,
Pteropus vampyrus	ENSPVAG00000011401	1 retrocopy	retro_pvam_389,
Tupaia belangeri	ENSTBEG00000001276	1 retrocopy	retro_tbel_3335,
Tarsius syrichta	ENSTSYG00000003719	1 retrocopy	retro_tsyr_2086,
Tursiops truncatus	ENSTTRG00000007705	1 retrocopy	retro_ttru_1725,
Vicugna pacos	ENSVPAG00000007888	2 retrocopies	retro_vpac_241, retro_vpac_27,