RetrogeneDB ID: retro_mdom_2010

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: X:19143453..19144721(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000013302
• Aliases: None
• Description: None

Sequence

>retro_mdom_2010
CAGGAGTATGGCGAATTTTATAAGAGTCTCACCAATGATTGGGAAGATCACTTGGCAGTAAAGCATTTCTCTATGGAAGG
TCAGCTGGAATTCAGAGTTCTGCTCTTCATCCCTCACCATGCCCCCTTTGATCTCTTTAAAAACAAAAAGAAGAACAACC
TTAAACTGTATGTGCGACATGTCTTTATCATGGACAGTTGTGATGAGCTTATTCCTGAGTATCTTAATTTTATCCGAGGT
GTGGTAGATTCTGAGGATCTGCCCCTCAACATTTTAAGAGAGATGCTGCAGCAGAGCAAAATCCTGAAGGTCATCTGTAA
GAATATTGTCAAGAAGTGCCCAGAGCTCTTCTCTGAACTGGCAGAAGATAAAGAGAATTACAAAAAGTTCCATGAGGCCT
TCTCAAAAAACCTCAAGCTTGGAATCCATGAGAACTCTACCAACAGGCGCCGTTTATCTAAACTATTGCATTATCACACA
TCTCATTCAGTAGATGAGATGACTTCTTTGTCTGAATATGTGTCCAGAATGAAGGAATCCCAGAAATGCATCTATTATAT
CACTGGTGAGAGCAAGGAACAGGTGGCCAACTCTGCTTTTGTTGAATGGGTACGGAAACATGGTTTTGAAGTAGTATACA
TGACAGAGCCCATTGATGAGTACTGTGTGCAGCACCTAAAGGAGTTTGATGGGAAGACCCTTGTCTCTGTTACTAAGGGT
TAGAACTTCGAGAGGATGAAGAAGAGAAGAAAAAAATGGAGGAAAGCAAGGCAAAATTTGAAAACTTGTGCAAGCTAATG
AAGTAAATTCTGGATAAGAAGGTTGAGAAAGTGACAATCTCTAATCGACTGGTGTCTTTACCCTGTTGCATCGTGACTAG
CACATATGGTTGGAGAGCCAACATGGAATGCTTCATGAAGGCACAGGCGTTGAGAGACAACTCCACAATGGGTTACATGA
TGGCCAAGAATCACTTGGAGATAAACCCAGATCATCCCATTGTGGAGACTCTCAGGCAGAAGGCTGAGGCTGACAAGAAT
GACAAGGCTGTGAAAGATCTGGTGGTGCTGCTTTTTGAGACAGCCCTGTTGTCTTCAGGTTTCTCCCTTGAAGATCCCCA
AACTCACTCAAACCGAATTTATTGCATGATTAAGCTAGGTCTTGGTATTGATGAGGATGAGTTGACAGCAGAGGAGCCCA
GTGCTGCTGTTCCTGATGAGATTCCCCCATTTGAAGGCAATGAAGATGCATCCCTCTTGGAGGAGGTG

Alignment

ORF - retro_mdom_2010 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.7 %
• Parental protein coverage: 63.61 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  EEYGEFYKSLTNDWEDHLAVK--VMEGQLEFRALLFVPRRAPFDLFENRKKKNNIKLYVRRVFIMDNCEE
          .EYGEFYKSLTNDWEDHLAVK...MEGQLEFR.LLF.P..APFDLF.N.KKKNN.KLYVR.VFIMD.C.E
Retrocopy QEYGEFYKSLTNDWEDHLAVKHFSMEGQLEFRVLLFIPHHAPFDLFKN-KKKNNLKLYVRHVFIMDSCDE

Parental  LIPEYLNFIRGVVDSEDLPLNISREMLQQSKILKVIRKNLVKKCLELFTELAEDKENYKKFYEQFSKNIK
          LIPEYLNFIRGVVDSEDLPLNI.REMLQQSKILKVI.KN.VKKC.ELF.ELAEDKENYKKF.E.FSKN.K
Retrocopy LIPEYLNFIRGVVDSEDLPLNILREMLQQSKILKVICKNIVKKCPELFSELAEDKENYKKFHEAFSKNLK

Parental  LGIHEDSQNRKKLSELLRYYTSASGDEMVSLKDYCTRMKENQKHIYYITGETKDQVANSAFVERLRKHGL
          LGIHE.S.NR..LS.LL.Y.TS.S.DEM.SL..Y..RMKE.QK.IYYITGE.K.QVANSAFVE..RKHG.
Retrocopy LGIHENSTNRRRLSKLLHYHTSHSVDEMTSLSEYVSRMKESQKCIYYITGESKEQVANSAFVEWVRKHGF

Parental  EVIYMIEPIDEYCVQQLKEFEGKTLVSVTKEGLELPEDEDEKKK-QEEKKAKFENLCKIMKDILEKKVEK
          EV.YM.EPIDEYCVQ.LKEF.GKTLVSVTK.G..........KK..EE.KAKFENLCK.MK.IL.KKVEK
Retrocopy EVVYMTEPIDEYCVQHLKEFDGKTLVSVTK-G*NFERMKKRRKK<MEESKAKFENLCKLMK*ILDKKVEK

Parental  VVVSNRLVTSPCCIVTSTYGWTANMERIMKAQALRDNSTMGYMAAKKHLEINPDHSIIETLRQKAEADKN
          V..SNRLV..PCCIVTSTYGW.ANME..MKAQALRDNSTMGYM.AK.HLEINPDH.I.ETLRQKAEADKN
Retrocopy VTISNRLVSLPCCIVTSTYGWRANMECFMKAQALRDNSTMGYMMAKNHLEINPDHPIVETLRQKAEADKN

Parental  DKSVKDLVILLYETALLSSGFSLEDPQTHANRIYRMIKLGLGIDEDDSTTEETNAAITEEMPPLEGDDDT
          DK.VKDLV.LL.ETALLSSGFSLEDPQTH.NRIY.MIKLGLGIDED..T.EE..AA...E.PP.EG..D.
Retrocopy DKAVKDLVVLLFETALLSSGFSLEDPQTHSNRIYCMIKLGLGIDEDELTAEEPSAAVPDEIPPFEGNEDA

Parental  SRMEEV
          S..EEV
Retrocopy SLLEEV

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	528.88 RPM
SRP007412_cerebellum	0.00 RPM	401.87 RPM
SRP007412_heart	0.00 RPM	49.04 RPM
SRP007412_kidney	0.00 RPM	175.14 RPM
SRP007412_liver	0.00 RPM	116.31 RPM
SRP007412_testis	0.00 RPM	898.09 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_2010 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_2010 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 12 parental genes, and 26 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000006270	1 retrocopy	retro_btau_501,
Canis familiaris	ENSCAFG00000018036	1 retrocopy	retro_cfam_1094,
Callithrix jacchus	ENSCJAG00000033945	8 retrocopies	retro_cjac_1818, retro_cjac_2300, retro_cjac_2835, retro_cjac_3514, retro_cjac_3596, retro_cjac_3601, retro_cjac_3626, retro_cjac_502,
Cavia porcellus	ENSCPOG00000002015	1 retrocopy	retro_cpor_1372,
Homo sapiens	ENSG00000080824	2 retrocopies	retro_hsap_237, retro_hsap_859,
Macaca mulatta	ENSMMUG00000011073	2 retrocopies	retro_mmul_1526, retro_mmul_2313,
Monodelphis domestica	ENSMODG00000013302	3 retrocopies	retro_mdom_1653, retro_mdom_2010 , retro_mdom_817,
Mus musculus	ENSMUSG00000021270	1 retrocopy	retro_mmus_2139,
Nomascus leucogenys	ENSNLEG00000015925	3 retrocopies	retro_nleu_714, retro_nleu_822, retro_nleu_854,
Pongo abelii	ENSPPYG00000006153	1 retrocopy	retro_pabe_1760,
Pan troglodytes	ENSPTRG00000006736	2 retrocopies	retro_ptro_207, retro_ptro_596,
Rattus norvegicus	ENSRNOG00000007219	1 retrocopy	retro_rnor_860,