RetrogeneDB ID: retro_mdom_817

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 2:71058470..71059805(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMODG00000024962
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

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

Sequence

>retro_mdom_817
GAAGAGCTGAACAAGACCAAACCCATCTGGACATGGAACCCTGATGATATCAGCCAAGAGGAGTATGGCAAGTTTTATAA
GAGTCTCACCAATGATTGGGAAGATCACTTGGCAGTAAAGCACTTCTCTGTGGAAGGTCAGCTGGAATTCAGAGCTCTGC
TCTTCATCCCCCGTCATGTCCCCTTTGACCTCTTTGAAAACAAAAAGAAGAAGAACAACATTAAACTGTACGTTCGACGA
GTCTTTATCATGGACAGTTGTGATGAGCTTATTCCTGAGTATCTTAATTTTATCTGAGGTGTGGTAGATTCTGAGGATCT
GCCCCTCAACATTTCAAGAGAGATGTTGCAGCAGAGCAAAATCCTGAAGGTCATCCATAAAAATATTGTCAAGAAGTGCC
TAGAGCTCTTCTCTGAACTGGCAGAAGATAAAGAGAATTATAAAAAGTTCTATGAGGCCTTCTCAAAAAACCTCAAACTT
GGAATCCATGAGGACTCTACCAATAGGCACCGTTTATCTGAACTATTGCGTTATCATACATCTCAGTCTGGAGATGAGAT
GACTTCTTTGTCTCAATATGTGTCCAGAATGAAGGAATCCCAGAAATGCATCTATTATATCACTGGTGAGAGCAAGGAAC
AAGTGGCCAACTCTGCTTTTGTTGAATGGGTATGGAAATGTGGTTTTGAAGTAGTATACATGACAGAGCCCATTGATGAG
TACTGTGTGCAGCAGCTAAAGGAGTTTGATGGGAAGACCCTTGTCTCTGTTACTAAGGAAGGTTTAGAACTTCCAGAGGA
TGAAGAAGAGAAGAAAAAAATGGAGGAAAGCAAGGCAAAATTTGAAAACTTGTGCAAGCTAATGAAGGAAATTCTGGATA
AGAAGGTTGAGAAAGTGACAATCTCTAATCGGCTGGTGTCTTCACCCTGTTGCATTGTGACTAGCACATATGGTTGGACA
ACCAACATGGAATGCATCATGAAGGCACAGGCATTGAGAGACAACTCCACAATGGGTTACATGATGGCCAAGAAGCACTT
GGAGATAAACCCAGATCACCCCATTGTGGAGACTCTCAGGCAGAAGGCTGAGGCTGACAAGAATGACAAGGCTGTGAAAG
ATCTGGTGGTGCTGCTTTTTGAGACAGCTCTGCTGTCTTCAGGTTTCTCCCTTGAAGATCCCCAGACTCACTCAAAGCAA
ATTTATCACATGATTAAGCGAGGGCTTGGCATTGATGAGGATGAGGTGACAGCAGAGGAGCCCAGTGCTGCTGTTCCTGA
TGAGATTCCCCCACTTGAAGGCGATGAAGATGCATCCCGCATGGAGGAGGTGGAT

Alignment

ORF - retro_mdom_817 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.92 %
• Parental protein coverage: 66.62 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KELNKTKPIWTRNPDDITNEEYGEFYKSLTNDWEDHLAVK--VMEGQLEFRALLFVPRRAPFDLFENRKK
          .ELNKTKPIWT.NPDDI..EEYG.FYKSLTNDWEDHLAVK....EGQLEFRALLF.PR..PFDLFEN.KK
Retrocopy EELNKTKPIWTWNPDDISQEEYGKFYKSLTNDWEDHLAVKHFSVEGQLEFRALLFIPRHVPFDLFENKKK

Parental  KNNIKLYVRRVFIMDNCEELIPEYLNFIRGVVDSEDLPLNISREMLQQSKILKVIRKNLVKKCLELFTEL
          KNNIKLYVRRVFIMD.C.ELIPEYLNFI.GVVDSEDLPLNISREMLQQSKILKVI.KN.VKKCLELF.EL
Retrocopy KNNIKLYVRRVFIMDSCDELIPEYLNFI*GVVDSEDLPLNISREMLQQSKILKVIHKNIVKKCLELFSEL

Parental  AEDKENYKKFYEQFSKNIKLGIHEDSQNRKKLSELLRYYTSASGDEMVSLKDYCTRMKENQKHIYYITGE
          AEDKENYKKFYE.FSKN.KLGIHEDS.NR..LSELLRY.TS.SGDEM.SL..Y..RMKE.QK.IYYITGE
Retrocopy AEDKENYKKFYEAFSKNLKLGIHEDSTNRHRLSELLRYHTSQSGDEMTSLSQYVSRMKESQKCIYYITGE

Parental  TKDQVANSAFVERLRKHGLEVIYMIEPIDEYCVQQLKEFEGKTLVSVTKEGLELPEDEDEKKKQEEKKAK
          .K.QVANSAFVE...K.G.EV.YM.EPIDEYCVQQLKEF.GKTLVSVTKEGLELPEDE.EKKK.EE.KAK
Retrocopy SKEQVANSAFVEWVWKCGFEVVYMTEPIDEYCVQQLKEFDGKTLVSVTKEGLELPEDEEEKKKMEESKAK

Parental  FENLCKIMKDILEKKVEKVVVSNRLVTSPCCIVTSTYGWTANMERIMKAQALRDNSTMGYMAAKKHLEIN
          FENLCK.MK.IL.KKVEKV..SNRLV.SPCCIVTSTYGWT.NME.IMKAQALRDNSTMGYM.AKKHLEIN
Retrocopy FENLCKLMKEILDKKVEKVTISNRLVSSPCCIVTSTYGWTTNMECIMKAQALRDNSTMGYMMAKKHLEIN

Parental  PDHSIIETLRQKAEADKNDKSVKDLVILLYETALLSSGFSLEDPQTHANRIYRMIKLGLGIDEDDSTTEE
          PDH.I.ETLRQKAEADKNDK.VKDLV.LL.ETALLSSGFSLEDPQTH...IY.MIK.GLGIDED..T.EE
Retrocopy PDHPIVETLRQKAEADKNDKAVKDLVVLLFETALLSSGFSLEDPQTHSKQIYHMIKRGLGIDEDEVTAEE

Parental  TNAAITEEMPPLEGDDDTSRMEEVD
          ..AA...E.PPLEGD.D.SRMEEVD
Retrocopy PSAAVPDEIPPLEGDEDASRMEEVD

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_817 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_817 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,