RetrogeneDB ID: retro_mdom_1638

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 6:2684242..2685260(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000020456
• Aliases: None
• Description: None

Sequence

>retro_mdom_1638
ATGGCAGATATTGACAACAAAGAAACTGAACGTGACCAACAAGACGTGGAGGATGTTCAAGAAGTGGAAGAAGAAATTGG
TGAAGATGCACACAGCAAAGCCCATCAACTGACTGTTCCGATGATGCAGAATTCTCAAATTCTTGCAGCTCTTCAGGAAA
GATTGGCTGGTTTAGTGGGAACATCTACTGGATACATTGAAAGCTTGCCAAAAATAGTTAAGGGATGGGAGCACGCCCTC
ACAAACCTTCAGGGGAAACGTGCACAGAGAGAAGCCAAGTTCTATGAGGAAGTTCATGCTCTTTAAAGAAAGCACGCTGT
TCTTTACCAGGCACTTTTTGGTAAGAGAAGTGAAATCATCAAAGCAATTTGTGAACCTACCGAGGAAGAATGTGAGTGGA
AACTGGATGAAGACATTTCAGAGGAAATGAAAGAGAAGGCTAAGCTTGAAGAGGAGAAAAAAGATGAAGAAAAAGAAGAC
CCTAAGGCAATTCCTGAATTTGGGCTGACTTTTAAAAAATGGTGACTTGCTCAGTGACACGGTTCAGGAGCATGATGAAC
CTATTCTGAAGCATTTGAAAGATATTAAAGTGAAGTTCTCAAATGCTGGACAGTCTATGAGTTTTATGTTAGAATTTCAC
TTTGAACCCAAGGAATATTTCACAAATAAGGTATTGATGAAGACATATTGTATGTGGTCAGAGCCAGATGATCCTGATCC
CGTCTCCTTTGATGGACCAGAAATTAAGAGTTGTCCAGGGTGCCAGGTAGACTGGAAAAAAGGGGAAAATGTTACTTTGA
AAACTATTAAGAAGTAGCGGAAACACAAGGGTCGTGGGACTGTTCAAATTGTGACAAAACCAGTTTCCAATGATTCTTTC
TTCAATTTCTTTTCTCCTTCTGAAGTTCCTGGGAGTGGACACCTGGATGATGATGCAGAGGCTATCCTTGCTGCAGACTT
TAAGATCCGTCACTTTTTCTGTGAGAGTATCATCCCAAGATCAGATTTACACTTCACA

Alignment

ORF - retro_mdom_1638 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.07 %
• Parental protein coverage: 87.47 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MADIDNKETELDQQDMEDVEEVEEEETGEDANSKARQLTVQMMQNPQILAALQERLDGLVGTSTGYIESL
          MADIDNKETE.DQQD.EDV.EVEEE..GEDA.SKA.QLTV.MMQN.QILAALQERL.GLVGTSTGYIESL
Retrocopy MADIDNKETERDQQDVEDVQEVEEE-IGEDAHSKAHQLTVPMMQNSQILAALQERLAGLVGTSTGYIESL

Parental  PKVVKRRVNALKNLQVKCAQIEAKFYEEVHALERKYAVLYQPLFDKRSEIINAIYEPTEEECEWKPDDDE
          PK.VK....AL.NLQ.K.AQ.EAKFYEEVHAL.RK.AVLYQ.LF.KRSEII.AI.EPTEEECEWK.D.D.
Retrocopy PKIVKGWEHALTNLQGKRAQREAKFYEEVHAL*RKHAVLYQALFGKRSEIIKAICEPTEEECEWKLDEDI

Parental  EISEMKEKAKLEEEKKDEEKED-PKGIPEFWLT-VFKNVDLLSDMVQEHDEPILKHLKDIKVKFSDAGQP
          ...EMKEKAKLEEEKKDEEKED.P.G....W.....KN.DLLSD.VQEHDEPILKHLKDIKVKFS.AGQ.
Retrocopy S-EEMKEKAKLEEEKKDEEKED<P*GNS*IWAD<LLKNGDLLSDTVQEHDEPILKHLKDIKVKFSNAGQS

Parental  MSFTLEFHFEPNEYFTNEVLMKTYRMRSEPDDSDPFSFDGPEIMSCTGCQVDWKKGKNVTLKTIKKKQKH
          MSF.LEFHFEP.EYFTN.VLMKTY.M.SEPDD.DP.SFDGPEI.SC.GCQVDWKKG.NVTLKTIKK..KH
Retrocopy MSFMLEFHFEPKEYFTNKVLMKTYCMWSEPDDPDPVSFDGPEIKSCPGCQVDWKKGENVTLKTIKK*RKH

Parental  KGRGTVRTVTKTVSNDSFFNFFSPPEVPESGDLDDDAEAILAADFEIGHFLRERIVPRSVLYFT
          KGRGTV..VTK.VSNDSFFNFFSP.EVP.SG.LDDDAEAILAADF.I.HF..E.I.PRS.L.FT
Retrocopy KGRGTVQIVTKPVSNDSFFNFFSPSEVPGSGHLDDDAEAILAADFKIRHFFCESIIPRSDLHFT

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_1638 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1638 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 52 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000020908	8 retrocopies	retro_btau_1319, retro_btau_1324, retro_btau_1462, retro_btau_1487, retro_btau_474, retro_btau_652, retro_btau_70, retro_btau_935,
Choloepus hoffmanni	ENSCHOG00000003210	2 retrocopies	retro_chof_1095, retro_chof_2057,
Callithrix jacchus	ENSCJAG00000001115	1 retrocopy	retro_cjac_534,
Felis catus	ENSFCAG00000000279	1 retrocopy	retro_fcat_1037,
Homo sapiens	ENSG00000187109	3 retrocopies	retro_hsap_1199, retro_hsap_2696, retro_hsap_833,
Gorilla gorilla	ENSGGOG00000003883	3 retrocopies	retro_ggor_1879, retro_ggor_686, retro_ggor_934,
Macropus eugenii	ENSMEUG00000013702	2 retrocopies	retro_meug_1031, retro_meug_604,
Macaca mulatta	ENSMMUG00000015583	1 retrocopy	retro_mmul_233,
Monodelphis domestica	ENSMODG00000020456	4 retrocopies	retro_mdom_1476, retro_mdom_1638 , retro_mdom_520, retro_mdom_724,
Mustela putorius furo	ENSMPUG00000017474	1 retrocopy	retro_mputfur_505,
Mus musculus	ENSMUSG00000058799	1 retrocopy	retro_mmus_263,
Nomascus leucogenys	ENSNLEG00000004682	4 retrocopies	retro_nleu_1192, retro_nleu_2085, retro_nleu_265, retro_nleu_2766,
Oryctolagus cuniculus	ENSOCUG00000013857	1 retrocopy	retro_ocun_834,
Otolemur garnettii	ENSOGAG00000010319	4 retrocopies	retro_ogar_1278, retro_ogar_1281, retro_ogar_3357, retro_ogar_666,
Pongo abelii	ENSPPYG00000004786	2 retrocopies	retro_pabe_2287, retro_pabe_999,
Pan troglodytes	ENSPTRG00000005240	4 retrocopies	retro_ptro_1820, retro_ptro_582, retro_ptro_694, retro_ptro_819,
Pteropus vampyrus	ENSPVAG00000016032	2 retrocopies	retro_pvam_1282, retro_pvam_306,
Rattus norvegicus	ENSRNOG00000003890	1 retrocopy	retro_rnor_150,
Ictidomys tridecemlineatus	ENSSTOG00000003046	2 retrocopies	retro_itri_1007, retro_itri_416,
Tursiops truncatus	ENSTTRG00000017062	2 retrocopies	retro_ttru_160, retro_ttru_1921,
Vicugna pacos	ENSVPAG00000007290	3 retrocopies	retro_vpac_435, retro_vpac_441, retro_vpac_601,