RetrogeneDB ID: retro_mdom_227

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 1:329235695..329236400(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMODG00000003840
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000001854
• Aliases: None
• Description: Thymidine kinase [Source:UniProtKB/TrEMBL;Acc:F6SP09]

Sequence

>retro_mdom_227
ATGAACTGCATTAACGTGCCCACCATGCTACCCAGCTCCCCCAGCAAAGTCCGGGGGCAAATCCAGGTGATCCTGGGGCC
TATGTTCTCCAGGAAAAGCACAGAGCTCATGCATAGAGTCCAGCGATTCCAGATTGCCCAGTACAAATGCCTTGTGATCA
AGTATACCAAAGACACTCGATACAGCAAAAATTTCTCCACACATGACCAGAACACTATGGAAGCACTACCAGCCTGCTTG
CTTTGGGATGTGGCGCAGAATGCCCTGGCTGTGACTGTCATTGGTATTGATGAGGGACAGTTTTTCCCAGACATTGTAGA
ATTCAGTGAGACCATGGCAAATGCTGGGAAGACAATAATTGTAGCTGCACTAGATGGGACCTTTCAGAGGAAGGCATTGG
GGAATATCCTAAACTTGATGCCACTGACAGAGAGTATGGTGAAACTGATAGCAGTGTGCATGGAGTGCTTCCGGGAAGCT
GCTTATACCAAGAGACTGGGGATGGAGAAAGAGGTCGAGGTGATCGGTGGCGCTGACAAATATCACTCTGTGTGTCGACT
CTGCTATTTCAAGAAAGTCTCAGGACAATCTACTGGGCTGGAGAACAAGGAGAACTGCCCCCAGAGTGGGAAGCCAGGAG
ATACCACAAGCTATCAGAAACTCTTTCCTACTCAACAGATTTTACAATGTAGTTCAAGCAACTGA

Alignment

ORF - retro_mdom_227 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.88 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSCINLPTVLPGSPSKVRGQIQVILGPMFSGKSTELMRRVRRFQIAQYKCLVIKYAKDTRYSKNFSTHDR
          M.CIN.PT.LP.SPSKVRGQIQVILGPMFS.KSTELM.RV.RFQIAQYKCLVIKY.KDTRYSKNFSTHD.
Retrocopy MNCINVPTMLPSSPSKVRGQIQVILGPMFSRKSTELMHRVQRFQIAQYKCLVIKYTKDTRYSKNFSTHDQ

Parental  NTMEALPACLLRDVAQNALAVTVIGIDEGQFFPDIVEFSETMANAGKTIIVAALDGTFQRKAFGNILNLV
          NTMEALPACLL.DVAQNALAVTVIGIDEGQFFPDIVEFSETMANAGKTIIVAALDGTFQRKA.GNILNL.
Retrocopy NTMEALPACLLWDVAQNALAVTVIGIDEGQFFPDIVEFSETMANAGKTIIVAALDGTFQRKALGNILNLM

Parental  PLAESVVKLTAVCMECFREAAYTKRLGIEKEVEVIGGADKYHSVCRLCYFKKVSGQSTGLENKENCPQSG
          PL.ES.VKL.AVCMECFREAAYTKRLG.EKEVEVIGGADKYHSVCRLCYFKKVSGQSTGLENKENCPQSG
Retrocopy PLTESMVKLIAVCMECFREAAYTKRLGMEKEVEVIGGADKYHSVCRLCYFKKVSGQSTGLENKENCPQSG

Parental  KPGDTTSCRKLFPSQQILQCSSSN
          KPGDTTS..KLFP.QQILQCSSSN
Retrocopy KPGDTTSYQKLFPTQQILQCSSSN

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_227 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_227 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.

---

Parental genes homology:

Parental genes homology involve 5 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Echinops telfairi	ENSETEG00000002133	1 retrocopy	retro_etel_332,
Macropus eugenii	ENSMEUG00000002886	1 retrocopy	retro_meug_129,
Monodelphis domestica	ENSMODG00000001854	2 retrocopies	retro_mdom_227 , retro_mdom_691,
Mus musculus	ENSMUSG00000025574	1 retrocopy	retro_mmus_3238,
Rattus norvegicus	ENSRNOG00000047314	2 retrocopies	retro_rnor_1914, retro_rnor_2057,