RetrogeneDB ID: retro_mdom_62

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 1:150662728..150663970(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMODG00000010455
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000017396
• Aliases: None
• Description: None

Sequence

>retro_mdom_62
ATGTCAAAGGATATGAGCTGTCCCTTAGAATCCCCTCCTGGTTGCCATAGTTCAGGGTGTGGCCAGCATTTCCTGCCTGC
GGCCAGTGCTCCAGGCGCCTCTTGGGCTACAATGGGACCCAATGAAGATGAGTTAGATGATTCCTTACTGGAGCTCTCAG
ATGGAGAAGAGGATGACAGTCTCTTCAGTTACACTGAAGAAGAGATTCAGGAGCTCTTAAAGGATGATGACTCCCTCCAC
GATCAGTCCTCTCTGGGTGGAGGGCTAAGCAATGCAGGTGGTCAAATAGAGAAGCTGGGGAGAAATAGTTCTATGTCACT
TGACTCTCCCCAAGATATAAATTCGCTGTGTAGCTTGGAGCTGGGAGCTGGACCAGCCAGCATCCTCCAGCTACCGCAGG
TAAGTACACCAGCTAGTCCCAGCCTCTCTCCCACCAAAATGTCTAGCAGACACTCTGTACCAGAAAAGAGTCTTTTGAAA
GTAACCACTGTCCCGCCATTTAAGCCAATCGTTTGGAATGGTGCGCTTGGAAAGGATAAGATGGAGTCTTCCAAAGACGC
CTGCAGGAATGCAGACCGCTTGGGAAGACCTTCCCACATGGGGGACGATGGGAACAAAGATGGTACTAGTCGTAATAATA
GCAAACCTTTGACTGGGCATGAAGAAACCACCTGTGTCAGCTCAGTTTGGGAAGGACCTTTGGCTCCTTCTAAAGGTAAC
TCTCAACAGATGGTCTATGGGACCAAAAAACCTTGTCGTGATATGCCCGCCCCTTTAATCTCTCTGACCTTGGAACAGAC
AGGTAGCCCCTCTGATGGGAAAGCATCTTTGGGGAGTAGGAGATCTAAAGCCAGTGGCGCCAGGCAGTCCCCAGCTGTCC
CCTCATCATCAGGCAAACGCATCATCCTAGACAAGGATTCAGGGAAGATGGTGGCACATGAGACAAGAGTAAGCAAAATC
ACCCCACTCCTACCAACCAGAGCAAGGAGTAAGTATCCGAGATTTTCACAAGCGGAGACAGAGCCGAAGATGCAGATTTC
ACTCAAGAATGGCATCAGCCATTTACCAAAATCTAGGGCTCTGCACCAGGGCCCTCTGGGTGAGCTGTATGCCTTGATGG
ACCAAGTCACTAGTGTGGAGTATCAAATCCGGAATTCCAGGTGGCAACACCTGTCAGCCCTCACCATGATAAACTACCCC
CGATTCAGACAGAAGCCTCTCCAGAGGTACAGCCTGACTTAG

Alignment

ORF - retro_mdom_62 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 52.44 %
• Parental protein coverage: 87.47 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LPKDSDPVSSWGRFGQDDDGLDDSLLELSEGEEDDGHFSYTEEEIQELLKDDDSLNEQS-LGGLRKDTGG
          LP..S.P..SW...G...D.LDDSLLELS.GEEDD..FSYTEEEIQELLKDDDSL..QS.LGG.....GG
Retrocopy LPAASAPGASWATMGPNEDELDDSLLELSDGEEDDSLFSYTEEEIQELLKDDDSLHDQSSLGGGLSNAGG

Parental  QAEKLENYSCISFDSPQDINVLCSTGPRAGPASIHNLPQKNIPARHAPIPTKSPSRHFVSEKNLLKITLV
          Q.EKL...S..S.DSPQDIN.LCS....AGPASI..LPQ...PA.....PTK..SRH.V.EK.LLK.T.V
Retrocopy QIEKLGRNSSMSLDSPQDINSLCSLELGAGPASILQLPQVSTPASPSLSPTKMSSRHSVPEKSLLKVTTV

Parental  PPFNTTVCDAFGPKETESSSKDGSSNANCLGTPSSLEKDVNREGHGQNDGKLCTKEISSAC--SVWKGTP
          PPF...V......K....SSKD...NA..LG.PS....D.N..G...N..K..T......C..SVW.G..
Retrocopy PPFKPIVWNGALGKDKMESSKDACRNADRLGRPSHMGDDGNKDGTSRNNSKPLTGHEETTCVSSVWEGPL

Parental  PPKAGPPQGPPRANTPICEES-VPVASPTLGPTPRP-DVALSSGNDGHKLGDTARSPAVQSSSTKPVKLD
          .P..G..Q.........C.....P..S.TL..T..P.D...S.G....K......SPAV.SSS.K...LD
Retrocopy APSKGNSQQMVYGTKKPCRDMPAPLISLTLEQTGSPSDGKASLGSRRSKASGARQSPAVPSSSGKRIILD

Parental  KDSKKKEGYERRLGKVIPLQLAKARSKIQTFSKTELEQKKQIYLKNVIAHLKNPLESNQGALGELCALMD
          KDS.K....E.R..K..PL....ARSK...FS..E.E.K.QI.LKN.I.HL.......QG.LGEL.ALMD
Retrocopy KDSGKMVAHETRVSKITPLLPTRARSKYPRFSQAETEPKMQISLKNGISHLPKSRALHQGPLGELYALMD

Parental  QVANGEYQKQNQRWQHPSDLTMRNYPRFRQKPLQRYSLT
          QV...EYQ..N.RWQH.S.LTM.NYPRFRQKPLQRYSLT
Retrocopy QVTSVEYQIRNSRWQHLSALTMINYPRFRQKPLQRYSLT

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	12.38 RPM	0.00 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_62 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_62 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 5 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000000537	1 retrocopy	retro_dnov_1346,
Erinaceus europaeus	ENSEEUG00000006053	1 retrocopy	retro_eeur_439,
Myotis lucifugus	ENSMLUG00000000764	1 retrocopy	retro_mluc_1691,
Monodelphis domestica	ENSMODG00000017396	2 retrocopies	retro_mdom_1633, retro_mdom_62 ,
Tursiops truncatus	ENSTTRG00000014993	1 retrocopy	retro_ttru_89,