RetrogeneDB ID: retro_mdom_1158

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 3:271090317..271091191(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000020916
• Aliases: None
• Description: None

Sequence

>retro_mdom_1158
ATACTGCCATTGAAAAAGAATGACCAGATCTATGCCTTGAATGTAGTGAAAAACATTTGGTACATGATGACAAAGAAATT
GACTGTGTGCAGACAGAGAAGCATGTATGTGAACAGGCTTCTGGTAACCCATTCCCTGTTGTTCTCCACTCCTGCTTCCA
AATTACTAGTTGGTTATTCCTTGTCATTGAGTATGCAAATAGAGAGGATCTCATCCTTCCAAGAAAGCTTCCAGAGGAGC
ACACCAAGTTTTATGTTGCTGAAATACATCTTGCACTAGATTTCATCCACAAATGAAAAATTATCTATAGAGACTTAAAA
CTAGATAACCTCTTCTTGGATGCTGAAGATCACATAAATTTAATAGATTATGACAAGCACAGGGAAGGATTGGACCCAGG
AGACATGGTTAGCACTTTCTGTGGGACACCAAGTTATATTGCACCTGAAATACTAAGGGGAGAAGAATATGGATACAGTG
TGGACTGGAGGGCTCCTGCCCCTTGATGTTTGAGATGATGGCAGGAAGACTGCCATTTGATATAATCACCGATTATCCAG
ACTTGAACACTGAAGATTACCCCTTCCAAGTTCTTTTTGAGAAGCCTATTCAAATCCCAAGATTTCTCTCTGTCAAAGTT
TCTTTCATTTTAAAAGTATTTTAAAATAAGGATCCTAAAAAGAGGTTTAGCTGCCAACAACAAATGGAATTTTCAGATAT
CAAGTCTCACATGTTCCTCCACAGTATAGATTGGGATCTGCTGGAGAAGAAGCAAGATCTCCCTCTATTTCACTCTAAGA
TAACCAATGATTATGGTCTGGAAAACTTCAATGCACAGTTCATCAGTGAACCTGTGCAGCTAATCTCAGGTGAT

Alignment

ORF - retro_mdom_1158 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.46 %
• Parental protein coverage: 51.93 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LVRLKKNDQIYAMKVVK-KELVHDDEDIDWVQTEKHVFEQASSNPFLVGLHSCFQTTSRLFLVIEYVNGG
          ...LKKNDQIYA..VVK.K.LVHDD..ID.VQTEKHV.EQAS.NPF.V.LHSCFQ.TS.LFLVIEY.N..
Retrocopy ILPLKKNDQIYALNVVK<KHLVHDDKEIDCVQTEKHVCEQASGNPFPVVLHSCFQITSWLFLVIEYANRE

Parental  DLMFHMQRQRKLPEEHARFYAAEICIALNFLHERGIIYRDLKLDNVLLDSEGHIKLTDYGMCKEGLGPGD
          DL.......RKLPEEH..FY.AEI..AL.F.H...IIYRDLKLDN..LD.E.HI.L.DY....EGL.PGD
Retrocopy DLIL----PRKLPEEHTKFYVAEIHLALDFIHK*KIIYRDLKLDNLFLDAEDHINLIDYDKHREGLDPGD

Parental  TTSTFCGTPNYIAPEILRGEEYGFSVDWWALGV-LMFEMMAGRSPFDIITDNPDMNTEDYLFQVILEKPI
          ..STFCGTP.YIAPEILRGEEYG.SVDW.A....LMFEMMAGR.PFDIITD.PD.NTEDY.FQV..EKPI
Retrocopy MVSTFCGTPSYIAPEILRGEEYGYSVDWRAPAP<LMFEMMAGRLPFDIITDYPDLNTEDYPFQVLFEKPI

Parental  RIPRFLSVKASHVLKGFLNKDPKERLGCQPQTGFSDIMSHTFFRSIDWDLLEKKQALPPFQPQITDDYGL
          .IPRFLSVK.S..LK.F.NKDPK.R..CQ.Q..FSDI.SH.F..SIDWDLLEKKQ.LP.F...IT.DYGL
Retrocopy QIPRFLSVKVSFILKVF*NKDPKKRFSCQQQMEFSDIKSHMFLHSIDWDLLEKKQDLPLFHSKITNDYGL

Parental  DNFDTQFTSEPVQLTPDD
          .NF..QF.SEPVQL...D
Retrocopy ENFNAQFISEPVQLISGD

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_1158 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1158 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 2 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Monodelphis domestica	ENSMODG00000020916	3 retrocopies	retro_mdom_1158 , retro_mdom_1336, retro_mdom_1463,
Mus musculus	ENSMUSG00000029053	1 retrocopy	retro_mmus_3013,