RetrogeneDB ID: retro_mdom_209

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 1:500417531..500418665(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMODG00000016206
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000018283
• Aliases: None
• Description: None

Sequence

>retro_mdom_209
ATGGTGATGACCTTGGTTGCATTGAGTCCCCGGATCCTGACAATTTCACAATCTGGAATAACTTCTGTAGCCACATCTCT
GTTTCTTGCACAGTCCCACCGCCATCTTCATCATGCTTTTATTCCTCATGGGAAAGGAGGACGTTCTTCATTCAGTGGGA
TTGTGGCTACTGTATTTGGAGCAACAGGATTCTTGGGTCGATATGTTGTCAGTCACCTTGGGCGCATAGGATCACAGGTG
ATTATCCCCTATCGGTGTGAGCCTTATGATATTACATATCTCAAACCCATGGGTGACCTGGGACAGCTTATTTTTCTGGA
ATGGAATGCCAAGATTAGAAGTTCTATCCAGAGGGCTCTGGAGCACAGTAATGTTGTCATCAATCTTATAGGACGAGACT
GGGAAACCAATAACTTTGATTTTTCAGATGTCTTTGCTACCATTCCCCAGTCAATAGCCCGGTTGGCCAAGGAGGCTGGA
GTAGAAACATTTATTCATGTTTCTCATCTCAATGCTGATCTCAGAAGTACTTCTAAATACTTGAGAAATAAAGCTGTTGG
AGAGATAGCAGTGAAAGATGAATTTCCTGAAGCCATTATCCTGAAACCCTCTGACATTTTTGGTAGAGAGGATAGATTAC
TCAATTACTTTGCAAATATCCGTTGGTTTGGTGGTGTTCCTCTCATTTCATTAGGCAGAAATACAGTGAAACAACCAGTT
TATGTGGTGGATGTATCCAAAGCCATCATCAATGCAATTAAGGATCCAGGTGCCCGAGGAAAGACTTATGCCATCACTGG
GCCTCATAGGTACCTTTTGTGTGATTTGGTACAGTATATCTTTGCTGTGGCTCACAGACCATACGTACCATACTACATGC
CACGTTTTGCCTATCATTTGATGGCAAGAATCTTTGAGATGAATCCATTTGAACCCTGGACCACAAGGGACAAAGTGGAA
CGAATGCATATCACTGACAGGAAATTGCCTCACCTGCCTGGCTTGGCTGACCTTGGTGTAGAGGCTACTCCCTTAGAACT
CAAAGCCATTGAAGTTCTTCGGCGTCATCGCACTTACCGATGGCTGTCTGCTGAAATCAAAGATACAAAGCCACCCAAAA
CAGTTGACTTTTAA

Alignment

ORF - retro_mdom_209 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.23 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAAALVARSPRFLTMSRTGTTAIATSLFLAQSHRQLHHAVIPHGKGGRSSVSGIVATVFGATGFLGRYVV
          M...LVA.SPR.LT.S..G.T..ATSLFLAQSHR.LHHA.IPHGKGGRSS.SGIVATVFGATGFLGRYVV
Retrocopy MVMTLVALSPRILTISQSGITSVATSLFLAQSHRHLHHAFIPHGKGGRSSFSGIVATVFGATGFLGRYVV

Parental  NHLGRMGSQVIVPYRCEPYDFTYLRPMGDLGQIIFLEWNSKDKSSIQRALEHSNVVINLVGRDWETRNFD
          .HLGR.GSQVI.PYRCEPYD.TYL.PMGDLGQ.IFLEWN.K..SSIQRALEHSNVVINL.GRDWET.NFD
Retrocopy SHLGRIGSQVIIPYRCEPYDITYLKPMGDLGQLIFLEWNAKIRSSIQRALEHSNVVINLIGRDWETNNFD

Parental  FTDVFADIPESIAQLAKEAGVETFIHVSHLNADIKSTSKYLRNKAVGEKAVREAFPEAIILKPADIFGRE
          F.DVFA.IP.SIA.LAKEAGVETFIHVSHLNAD..STSKYLRNKAVGE.AV...FPEAIILKP.DIFGRE
Retrocopy FSDVFATIPQSIARLAKEAGVETFIHVSHLNADLRSTSKYLRNKAVGEIAVKDEFPEAIILKPSDIFGRE

Parental  DRLLNYFANNRWFGGVPLISMGKKTVKQPVYVVDVSRAIVNAIKDPDSRGKTYAITGPNRYLLHDFVQYI
          DRLLNYFAN.RWFGGVPLIS.G..TVKQPVYVVDVS.AI.NAIKDP..RGKTYAITGP.RYLL.D.VQYI
Retrocopy DRLLNYFANIRWFGGVPLISLGRNTVKQPVYVVDVSKAIINAIKDPGARGKTYAITGPHRYLLCDLVQYI

Parental  FAVSHRPYFPYSMPRFTYQLVAKIFEMSPFEPWTTRDKIERIHISDKKLPHLPGLEDLGVEPTPLELKAI
          FAV.HRPY.PY.MPRF.Y.L.A.IFEM.PFEPWTTRDK.ER.HI.D.KLPHLPGL.DLGVE.TPLELKAI
Retrocopy FAVAHRPYVPYYMPRFAYHLMARIFEMNPFEPWTTRDKVERMHITDRKLPHLPGLADLGVEATPLELKAI

Parental  EILRRHRTYRWLSAESEDIKPAKTVSF
          E.LRRHRTYRWLSAE..D.KP.KTV.F
Retrocopy EVLRRHRTYRWLSAEIKDTKPPKTVDF

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	0.12 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	220.59 RPM	0.00 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_209 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_209 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 11 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000009588	1 retrocopy	retro_acar_16,
Danio rerio	ENSDARG00000070723	1 retrocopy	retro_drer_1,
Homo sapiens	ENSG00000139180	1 retrocopy	retro_hsap_2585,
Gorilla gorilla	ENSGGOG00000006076	1 retrocopy	retro_ggor_1618,
Macaca mulatta	ENSMMUG00000020813	1 retrocopy	retro_mmul_648,
Monodelphis domestica	ENSMODG00000018283	1 retrocopy	retro_mdom_209 ,
Nomascus leucogenys	ENSNLEG00000003252	1 retrocopy	retro_nleu_1520,
Otolemur garnettii	ENSOGAG00000005225	1 retrocopy	retro_ogar_2244,
Pongo abelii	ENSPPYG00000004171	1 retrocopy	retro_pabe_1905,
Pan troglodytes	ENSPTRG00000004557	1 retrocopy	retro_ptro_1511,
Ictidomys tridecemlineatus	ENSSTOG00000006504	1 retrocopy	retro_itri_543,