RetrogeneDB ID: retro_mdom_779

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 2:453537625..453538020(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPS12
• Ensembl ID: ENSMODG00000017520
• Aliases: None
• Description: ribosomal protein S12 [Source:HGNC Symbol;Acc:10385]

Sequence

>retro_mdom_779
ATGGCTGAGGAAAGCACTGCTGCTGCAGGTATAACAGACATTAACACTTCTCTAAAAGAAATACTGAAGCTTGAACTCAG
TCATGATGACTTAGCTCATGGAATTGGTGATGTTGCCAAAGCCTTAGATCAATGCCAAGCCCATCTTAGTGTTCTTCCTT
CCAACTGGATGAACCTACATAAGTAAAGTTGGTTGAAACCCTGTGTGCTGAGCACCAAATCAACTTAATCTAAGTTGATG
CCCAAAGAAGCTGGCTGGATGGGTAGGAGTTTGTAAAATTGACAGAGAGAGAAAGCCCCATAAAATGGTTGGCTGTAGTT
GTGTTGTTGTTAAGGACCATGGCAAGGAAACTCTGGTGAAAGAAGTTTATTGAAGGATATTTTAAAAGTAAAAAA

Alignment

ORF - retro_mdom_779 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.41 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MAEEGIAAGGVMDVNTALQEVLKTALIHDGLARGIREAAKALDKRQAHLCVLASN-CDEPMYVKLVEALC
          MAEE..AA.G..D.NT.L.E.LK..L.HD.LA.GI...AKALD..QAHL.VL.SN..DEP..VKLVE.LC
Retrocopy MAEESTAAAGITDINTSLKEILKLELSHDDLAHGIGDVAKALDQCQAHLSVLPSN<LDEPT*VKLVETLC

Parental  AEHQINLIKVDDN-KKLGEWVGLCKIDREGKPRKVVGCSCVVVKDYGKESQAKDV-IEEYFKCKK
          AEHQINLI.VD...KKL..WVG.CKIDRE.KP.K.VGCSCVVVKD.GKE...K.V.IE.YFK.KK
Retrocopy AEHQINLI*VDAQ<KKLAGWVGVCKIDRERKPHKMVGCSCVVVKDHGKETLVKEV>IEGYFKSKK

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_779 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_779 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 25 parental genes, and 196 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000010479	1 retrocopy	retro_acar_102,
Ailuropoda melanoleuca	ENSAMEG00000008015	2 retrocopies	retro_amel_79, retro_amel_92,
Bos taurus	ENSBTAG00000001360	7 retrocopies	retro_btau_106, retro_btau_1097, retro_btau_1306, retro_btau_1495, retro_btau_1514, retro_btau_1630, retro_btau_1802,
Callithrix jacchus	ENSCJAG00000002865	34 retrocopies	retro_cjac_1038, retro_cjac_1044, retro_cjac_1205, retro_cjac_1291, retro_cjac_1528, retro_cjac_1602, retro_cjac_1778, retro_cjac_1994, retro_cjac_2039, retro_cjac_2058, retro_cjac_2065, retro_cjac_2101, retro_cjac_2112, retro_cjac_2155, retro_cjac_2337, retro_cjac_2406, retro_cjac_2421, retro_cjac_2461, retro_cjac_2681, retro_cjac_2694, retro_cjac_2858, retro_cjac_301, retro_cjac_3310, retro_cjac_4149, retro_cjac_427, retro_cjac_466, retro_cjac_494, retro_cjac_592, retro_cjac_773, retro_cjac_805, retro_cjac_806, retro_cjac_807, retro_cjac_836, retro_cjac_977,
Cavia porcellus	ENSCPOG00000000429	4 retrocopies	retro_cpor_1096, retro_cpor_304, retro_cpor_32, retro_cpor_380,
Equus caballus	ENSECAG00000001599	8 retrocopies	retro_ecab_1012, retro_ecab_1131, retro_ecab_133, retro_ecab_744, retro_ecab_80, retro_ecab_828, retro_ecab_875, retro_ecab_959,
Echinops telfairi	ENSETEG00000006854	14 retrocopies	retro_etel_1129, retro_etel_1512, retro_etel_1580, retro_etel_2016, retro_etel_205, retro_etel_2082, retro_etel_2099, retro_etel_2169, retro_etel_26, retro_etel_280, retro_etel_29, retro_etel_55, retro_etel_578, retro_etel_915,
Felis catus	ENSFCAG00000028402	7 retrocopies	retro_fcat_1084, retro_fcat_1314, retro_fcat_1446, retro_fcat_1880, retro_fcat_537, retro_fcat_664, retro_fcat_796,
Homo sapiens	ENSG00000112306	26 retrocopies	retro_hsap_1241, retro_hsap_1522, retro_hsap_1738, retro_hsap_1771, retro_hsap_1797, retro_hsap_1962, retro_hsap_1992, retro_hsap_2249, retro_hsap_2264, retro_hsap_2667, retro_hsap_2722, retro_hsap_3043, retro_hsap_3079, retro_hsap_3249, retro_hsap_3347, retro_hsap_3428, retro_hsap_3467, retro_hsap_3640, retro_hsap_3680, retro_hsap_3994, retro_hsap_4130, retro_hsap_599, retro_hsap_661, retro_hsap_702, retro_hsap_824, retro_hsap_895,
Gorilla gorilla	ENSGGOG00000012234	22 retrocopies	retro_ggor_1164, retro_ggor_1287, retro_ggor_1322, retro_ggor_139, retro_ggor_1426, retro_ggor_1441, retro_ggor_1686, retro_ggor_1861, retro_ggor_1894, retro_ggor_2115, retro_ggor_2241, retro_ggor_2261, retro_ggor_2339, retro_ggor_2456, retro_ggor_2489, retro_ggor_2680, retro_ggor_3076, retro_ggor_530, retro_ggor_595, retro_ggor_673, retro_ggor_724, retro_ggor_971,
Gadus morhua	ENSGMOG00000019455	1 retrocopy	retro_gmor_11,
Microcebus murinus	ENSMICG00000005252	5 retrocopies	retro_mmur_1260, retro_mmur_1527, retro_mmur_391, retro_mmur_491, retro_mmur_98,
Myotis lucifugus	ENSMLUG00000001137	5 retrocopies	retro_mluc_1479, retro_mluc_1552, retro_mluc_1987, retro_mluc_1988, retro_mluc_582,
Macaca mulatta	ENSMMUG00000013237	1 retrocopy	retro_mmul_12,
Monodelphis domestica	ENSMODG00000017520	1 retrocopy	retro_mdom_779 ,
Mustela putorius furo	ENSMPUG00000014771	1 retrocopy	retro_mputfur_6,
Mus musculus	ENSMUSG00000061983	1 retrocopy	retro_mmus_36,
Nomascus leucogenys	ENSNLEG00000014611	4 retrocopies	retro_nleu_2717, retro_nleu_543, retro_nleu_588, retro_nleu_86,
Pelodiscus sinensis	ENSPSIG00000003457	1 retrocopy	retro_psin_52,
Rattus norvegicus	ENSRNOG00000016411	5 retrocopies	retro_rnor_177, retro_rnor_186, retro_rnor_241, retro_rnor_295, retro_rnor_300,
Sorex araneus	ENSSARG00000003170	2 retrocopies	retro_sara_356, retro_sara_8,
Sarcophilus harrisii	ENSSHAG00000008905	6 retrocopies	retro_shar_187, retro_shar_226, retro_shar_475, retro_shar_492, retro_shar_621, retro_shar_671,
Tarsius syrichta	ENSTSYG00000010097	24 retrocopies	retro_tsyr_1010, retro_tsyr_102, retro_tsyr_1123, retro_tsyr_1188, retro_tsyr_129, retro_tsyr_1313, retro_tsyr_1345, retro_tsyr_1398, retro_tsyr_1486, retro_tsyr_1668, retro_tsyr_1955, retro_tsyr_1993, retro_tsyr_205, retro_tsyr_249, retro_tsyr_303, retro_tsyr_419, retro_tsyr_453, retro_tsyr_556, retro_tsyr_645, retro_tsyr_733, retro_tsyr_764, retro_tsyr_801, retro_tsyr_970, retro_tsyr_99,
Tursiops truncatus	ENSTTRG00000000609	11 retrocopies	retro_ttru_1290, retro_ttru_206, retro_ttru_233, retro_ttru_304, retro_ttru_559, retro_ttru_64, retro_ttru_667, retro_ttru_727, retro_ttru_787, retro_ttru_955, retro_ttru_990,
Vicugna pacos	ENSVPAG00000011504	3 retrocopies	retro_vpac_133, retro_vpac_267, retro_vpac_339,