RetrogeneDB ID: retro_mdom_99

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 1:267216512..267218420(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMODG00000023945
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000012958
• Aliases: None
• Description: None

Sequence

>retro_mdom_99
ATGTCTGCGCGGGGCCCCGCCATCGGGATCGACCTGGGCACCACTTACTCGTGCGTGGGCGTTTTCCAGCACGGGAAAGT
GGAGATCATCGCCAACGACCAGGGCAACCGCACCACCCCGAGCTATGTGGCCTTCACAGATACCGAGCGCCTCATCGGCG
ACGCCGCCAAGAACCAGGTGGCCATGAACCCCACCAATACCATCTTCGACGCCAAGAGGCTAATCGGGCGCAAGTTTGAA
GACGCGACGGTGCAGTCGGACATGAAACACTGGCCGTTCCGGGTGGTGAGTGAGGGCGGGAAGCCGAAAGTGCAGGTGGA
GTACAAGGGGGAGATTAAGACCTTTTTCCCGGAGGAGATCTCTTCCATGGTCCTGACCAAGATGAAGGAGATCGCCGAGG
CTTATCTGGGGGGGAAGGTGCAAAGCGCCGTCATCACGGTCCCGGCCTACTTCAACGACTCCCAGCGCCAGGCCACTAAG
GACGCCGGTACCATCACCGGCCTTAATGTCCTGAGAATCATCAACGAGCCCACGGCCGCGGCCATTGCCTACGGCCTGGA
CAAAAAAGGGAGCGCAGGGGGAGAAAAGAACGTACTGATCTTTGACCTCGGGGGTGGGACCTTCGATGTGTCCATCCTCA
CCATCGAGGACGGCATCTTCGAGGTGAAGTCGACAGCCGGCGACACCCACCTGGGTGGGGAGGACTTTGACAACCGCATG
GTGAGCCACCTGGCTGAAGAGTTCAAGCGCAAGCACAAGAAAGACATCGGCCCCAACAAGCGAGCGGTCCGGCGCCTCCG
CACCGCTTGTGAACGGGCTAAACGCACACTGAGCTCCTCCACTCAAGCCAGCATTGAAATCGACTCACTCTATGAGGGCG
TGGACTTCTACACCTCTATCACCCGAGCCCGGTTCGAGGAGCTCAATGCCGACCTCTTCCGCGGGACTCTGGAGCCAGTG
GAGAAAGCTCTTCGAGATGCCAAACTAGACAAGGGACAGATCCAGGAGATTGTGCTGGTGGGTGGTTCTACTCGTATCCC
CAAGATCCAAAAGCTGCTGCAAGATTTCTTCAATGGCAAGGAGCTTAACAAGAGCATAAACCCTGATGAGGCTGTAGCAT
ATGGAGCGGCTGTTCAAGCAGCGATTCTTATCGGAGACAAATCTGAGAATGTGCAGGACCTCCTGCTGCTTGATGTTACT
CCGCTGTCTTTGGGTATTGAAACCGCAGGTGGAGTGATGACTCCCCTGATTAAGAGAAACACCACTATTCCCACTAAGCA
GACCCAAACCTTCACAACTTACTCCGACAACCAGAGCAGTGTCTTAGTGCAGGTGTACGAGGGAGAAAGGGCAATGACCA
AGGACAATAACCTGCTCGGCAAGTTCGACCTCACAGGTATCCCTCCTGCTCCCCGTGGGGTGCCCCAAATCGAGGTAACT
TTTGACATAGACGCCAATGGCATCCTCAATGTGACTGCAGCAGACAAAAGCACCGGCAAAGAAAACAAAATTACCATAAC
TAATGACAAAGGCCGTCTAAGTAAGGACGATATCGACCGGATGGTACAAGAGGCAGAAAGGTACAAGTCAGAAGATGAAG
CAAATCGTGATAGAGTTGCTGCTAAAAACGCAGTGGAGTCATATACCTATAACATAAAGCAGACAGTAGAAGACGAGAAA
CTGAGGGGCAAGATAAGCGAACAGGACAAGAACAAGATCCTGGACAAGTGTCAAGAGGTGATAAGCTGGCTAGACCGAAA
CCAAATGGCAGAAAAAGATGAGTTTGAACATAAGCAGAGAGAGCTTGAAAGAGTCTGCAATCCCATCATCAGCAAACTTT
ACCAAGGAGGACCGGGTGGAGGCGGTTCAGGTGCCTCTGGGGGACCAACCATTGAAGAAGTGGACTAA

Alignment

ORF - retro_mdom_99 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.49 %
• Parental protein coverage: 97.06 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SKGPAVGIDLGTTYSCVGVFQHGKVEIIANDQGNRTTPSYVAFTDTERLIGDAAKNQVAMNPTNTVFDAK
          ..GPA.GIDLGTTYSCVGVFQHGKVEIIANDQGNRTTPSYVAFTDTERLIGDAAKNQVAMNPTNT.FDAK
Retrocopy ARGPAIGIDLGTTYSCVGVFQHGKVEIIANDQGNRTTPSYVAFTDTERLIGDAAKNQVAMNPTNTIFDAK

Parental  RLIGRRFDDAVVQSDMKHWPFTVVNDAGRPKVQVEYKGETKSFYPEEVSSMVLTKMKEIAEAYLGKTVTN
          RLIGR.F.DA.VQSDMKHWPF.VV...G.PKVQVEYKGE.K.F.PEE.SSMVLTKMKEIAEAYLG..V..
Retrocopy RLIGRKFEDATVQSDMKHWPFRVVSEGGKPKVQVEYKGEIKTFFPEEISSMVLTKMKEIAEAYLGGKVQS

Parental  AVVTVPAYFNDSQRQATKDAGTIAGLNVLRIINEPTAAAIAYGLDKK--VGAERNVLIFDLGGGTFDVSI
          AV.TVPAYFNDSQRQATKDAGTI.GLNVLRIINEPTAAAIAYGLDKK...G.E.NVLIFDLGGGTFDVSI
Retrocopy AVITVPAYFNDSQRQATKDAGTITGLNVLRIINEPTAAAIAYGLDKKGSAGGEKNVLIFDLGGGTFDVSI

Parental  LTIEDGIFEVKSTAGDTHLGGEDFDNRMVNHFIAEFKRKHKKDISENKRAVRRLRTACERAKRTLSSSTQ
          LTIEDGIFEVKSTAGDTHLGGEDFDNRMV.H...EFKRKHKKDI..NKRAVRRLRTACERAKRTLSSSTQ
Retrocopy LTIEDGIFEVKSTAGDTHLGGEDFDNRMVSHLAEEFKRKHKKDIGPNKRAVRRLRTACERAKRTLSSSTQ

Parental  ASIEIDSLYEGIDFYTSITRARFEELNADLFRGTLDPVEKALRDAKLDKSQIHDIVLVGGSTRIPKIQKL
          ASIEIDSLYEG.DFYTSITRARFEELNADLFRGTL.PVEKALRDAKLDK.QI..IVLVGGSTRIPKIQKL
Retrocopy ASIEIDSLYEGVDFYTSITRARFEELNADLFRGTLEPVEKALRDAKLDKGQIQEIVLVGGSTRIPKIQKL

Parental  LQDFFNGKELNKSINPDEAVAYGAAVQAAILSGDKSENVQDLLLLDVTPLSLGIETAGGVMTVLIKRNTT
          LQDFFNGKELNKSINPDEAVAYGAAVQAAIL.GDKSENVQDLLLLDVTPLSLGIETAGGVMT.LIKRNTT
Retrocopy LQDFFNGKELNKSINPDEAVAYGAAVQAAILIGDKSENVQDLLLLDVTPLSLGIETAGGVMTPLIKRNTT

Parental  IPTKQTQTFTTYSDNQPGVLIQVYEGERAMTKDNNLLGKFELTGIPPAPRGVPQIEVTFDIDANGILNVS
          IPTKQTQTFTTYSDNQ..VL.QVYEGERAMTKDNNLLGKF.LTGIPPAPRGVPQIEVTFDIDANGILNV.
Retrocopy IPTKQTQTFTTYSDNQSSVLVQVYEGERAMTKDNNLLGKFDLTGIPPAPRGVPQIEVTFDIDANGILNVT

Parental  AVDKSTGKENKITITNDKGRLSKEDIERMVQEAEKYKAEDEKQRDKVSSKNSLESYAFNMKATVEDEKLQ
          A.DKSTGKENKITITNDKGRLSK.DI.RMVQEAE.YK.EDE..RD.V..KN..ESY..N.K.TVEDEKL.
Retrocopy AADKSTGKENKITITNDKGRLSKDDIDRMVQEAERYKSEDEANRDRVAAKNAVESYTYNIKQTVEDEKLR

Parental  GKIGDEDKQKILDKCNEIINWLDKNQTAEKEEFEHQQKELEKVCNPIITKLYQSAGGMPGGMPGGFPGG
          GKI...DK.KILDKC.E.I.WLD.NQ.AEK.EFEH.Q.ELE.VCNPII.KLYQ...G.PGG...G..GG
Retrocopy GKISEQDKNKILDKCQEVISWLDRNQMAEKDEFEHKQRELERVCNPIISKLYQ---GGPGGGGSGASGG

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	202.04 RPM	0.00 RPM
SRP007412_cerebellum	130.91 RPM	0.00 RPM
SRP007412_heart	71.57 RPM	0.00 RPM
SRP007412_kidney	325.26 RPM	0.00 RPM
SRP007412_liver	2.01 RPM	0.00 RPM
SRP007412_testis	13908.50 RPM	0.00 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_99 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_99 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 35 parental genes, and 119 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000004884	2 retrocopies	retro_acar_21, retro_acar_6,
Ailuropoda melanoleuca	ENSAMEG00000008425	1 retrocopy	retro_amel_126,
Anas platyrhynchos	ENSAPLG00000010667	1 retrocopy	retro_apla_6,
Bos taurus	ENSBTAG00000013162	1 retrocopy	retro_btau_354,
Canis familiaris	ENSCAFG00000011666	3 retrocopies	retro_cfam_140, retro_cfam_191, retro_cfam_509,
Ciona intestinalis	ENSCING00000009665	1 retrocopy	retro_cint_12,
Callithrix jacchus	ENSCJAG00000007648	5 retrocopies	retro_cjac_2388, retro_cjac_3306, retro_cjac_3898, retro_cjac_4057, retro_cjac_721,
Cavia porcellus	ENSCPOG00000004169	3 retrocopies	retro_cpor_1072, retro_cpor_619, retro_cpor_938,
Ciona savignyi	ENSCSAVG00000008588	1 retrocopy	retro_csav_3,
Dipodomys ordii	ENSDORG00000015467	1 retrocopy	retro_dord_16,
Equus caballus	ENSECAG00000013510	2 retrocopies	retro_ecab_291, retro_ecab_628,
Echinops telfairi	ENSETEG00000010996	1 retrocopy	retro_etel_43,
Ficedula albicollis	ENSFALG00000005812	1 retrocopy	retro_falb_18,
Felis catus	ENSFCAG00000001132	6 retrocopies	retro_fcat_132, retro_fcat_1331, retro_fcat_1571, retro_fcat_1775, retro_fcat_556, retro_fcat_79,
Homo sapiens	ENSG00000109971	8 retrocopies	retro_hsap_2384, retro_hsap_2710, retro_hsap_2758, retro_hsap_340, retro_hsap_3698, retro_hsap_4892, retro_hsap_4896, retro_hsap_68,
Gallus gallus	ENSGALG00000006512	1 retrocopy	retro_ggal_8,
Gorilla gorilla	ENSGGOG00000008381	8 retrocopies	retro_ggor_1053, retro_ggor_1810, retro_ggor_1888, retro_ggor_1918, retro_ggor_2501, retro_ggor_3054, retro_ggor_3057, retro_ggor_360,
Loxodonta africana	ENSLAFG00000030312	4 retrocopies	retro_lafr_1218, retro_lafr_391, retro_lafr_790, retro_lafr_797,
Meleagris gallopavo	ENSMGAG00000001929	1 retrocopy	retro_mgal_9,
Myotis lucifugus	ENSMLUG00000004834	3 retrocopies	retro_mluc_1800, retro_mluc_2300, retro_mluc_777,
Macaca mulatta	ENSMMUG00000004696	7 retrocopies	retro_mmul_1536, retro_mmul_2188, retro_mmul_2628, retro_mmul_2632, retro_mmul_580, retro_mmul_778, retro_mmul_963,
Monodelphis domestica	ENSMODG00000012958	2 retrocopies	retro_mdom_127, retro_mdom_99 ,
Mustela putorius furo	ENSMPUG00000005810	9 retrocopies	retro_mputfur_1048, retro_mputfur_1056, retro_mputfur_1144, retro_mputfur_131, retro_mputfur_188, retro_mputfur_309, retro_mputfur_627, retro_mputfur_694, retro_mputfur_958,
Mus musculus	ENSMUSG00000015656	8 retrocopies	retro_mmus_2244, retro_mmus_2584, retro_mmus_26, retro_mmus_2621, retro_mmus_2840, retro_mmus_316, retro_mmus_351, retro_mmus_620,
Nomascus leucogenys	ENSNLEG00000007419	8 retrocopies	retro_nleu_119, retro_nleu_1258, retro_nleu_1261, retro_nleu_1582, retro_nleu_175, retro_nleu_1781, retro_nleu_370, retro_nleu_64,
Oryctolagus cuniculus	ENSOCUG00000015533	4 retrocopies	retro_ocun_1308, retro_ocun_53, retro_ocun_584, retro_ocun_753,
Oreochromis niloticus	ENSONIG00000004759	1 retrocopy	retro_onil_2,
Pongo abelii	ENSPPYG00000003987	9 retrocopies	retro_pabe_183, retro_pabe_2193, retro_pabe_2254, retro_pabe_2260, retro_pabe_2261, retro_pabe_3153, retro_pabe_355, retro_pabe_3804, retro_pabe_3808,
Pelodiscus sinensis	ENSPSIG00000012450	2 retrocopies	retro_psin_17, retro_psin_5,
Pan troglodytes	ENSPTRG00000004404	5 retrocopies	retro_ptro_1743, retro_ptro_2507, retro_ptro_272, retro_ptro_3259, retro_ptro_3264,
Ictidomys tridecemlineatus	ENSSTOG00000003756	1 retrocopy	retro_itri_51,
Taeniopygia guttata	ENSTGUG00000000491	1 retrocopy	retro_tgut_7,
Takifugu rubripes	ENSTRUG00000005265	1 retrocopy	retro_trub_30,
Tursiops truncatus	ENSTTRG00000011139	6 retrocopies	retro_ttru_1507, retro_ttru_1650, retro_ttru_1696, retro_ttru_35, retro_ttru_741, retro_ttru_808,
Xiphophorus maculatus	ENSXMAG00000001602	1 retrocopy	retro_xmac_20,