RetrogeneDB ID: retro_mdom_1281

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 4:270892295..270893162(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMODG00000024272
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000008266
• Aliases: None
• Description: None

Sequence

>retro_mdom_1281
ATGTCAGCTCCAAGCCTGAACAGCGGGAGCAGGAGCTGCTCTCCCAGTGCCGTAGGACCCCCTCGGCCAGGCCACATGGC
TGGTAGCAGCATGCAGGGTAAATGTAAAGCATTGAAGCTGAATTTTGCAAATCTACCTTTCAAATCTACCACATGGTTTA
CCCTGAACCCTTCAGGAGTCCAAAACCCACTAATAGAGAGACTGAGAACACCCAACATTGAATCATCAGGAAAACTGAAT
ATCTCCCCTGAACAGCACTGGAATTTCACTGCAGGGGACTTGAAAGACCTTGGAGAAATTGGATGAGGAGCTTATGGTTC
TGTCAACAAAATGGTCCACAAACCAAGTGGGCAAATAATGTCAATTAAAAGAATTCGGTCTACAGTGGATGTAAAAGAGC
AAAAACAGCTACTTATGGACTTGGATGTGGTGATGTGGAGTAGAGATTGCCTGTATATTGTTCAGTTTTATGGAGCACTC
TTCAGAGAGGGTGACTGTTGGATCTCTATGGAACTCATATCTACCTCGTTTGACAAGTTTTACAAATATGTATATAGTGT
ATTAGATGATGTTATTCCAGAAGAAATTTTAGGCAAAGTCACTTTAGCAACTGTGAAAGCACTAAACCATGTAAAAGAAA
ACTTGAAAATTATTCACAGAGACATCAAACCTTCTAATATTCTGCTGTATAGAAGTGACAATATTAAACTTTGTGATTTT
GGTATTAGTGGACAACTTGTGGACTCCACTGACAAAACAAGAGATTCTGGGTGCAGGCCAAACATGGCACCTGAAAGGAT
AGACCCAAGTGCATTGAGGCAAAGATACTATATCTGTTCTGATGTATGGAGTCTGGGGATCACACTG

Alignment

ORF - retro_mdom_1281 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.81 %
• Parental protein coverage: 72.98 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAAPSPSGGSGSGSPSAVGPPGPGHTAVSSMQGKRKALKLNFANPPFKSTARFTLNPSGVQNPHIERLRT
          M.APS...GS.S.SPSAVGPP.PGH.A.SSMQGK.KALKLNFAN.PFKST..FTLNPSGVQNP.IERLRT
Retrocopy MSAPSLNSGSRSCSPSAVGPPRPGHMAGSSMQGKCKALKLNFANLPFKSTTWFTLNPSGVQNPLIERLRT

Parental  HSIESSGKLKISPEQHWDFTAEDLKDLGEIGRGAYGSVNKMVHKPSGQIMAVKRIRSTVDEKEQKQLLMD
          ..IESSGKL.ISPEQHW.FTA.DLKDLGEIG.GAYGSVNKMVHKPSGQIM..KRIRSTVD.KEQKQLLMD
Retrocopy PNIESSGKLNISPEQHWNFTAGDLKDLGEIG*GAYGSVNKMVHKPSGQIMSIKRIRSTVDVKEQKQLLMD

Parental  LDVVMRSSDCPYIVQFYGALFREGDCWICMELMSTSFDKFYKYVYSVLDDVIPEEILGKITLATVKALNH
          LDVVM.S.DC.YIVQFYGALFREGDCWI.MEL.STSFDKFYKYVYSVLDDVIPEEILGK.TLATVKALNH
Retrocopy LDVVMWSRDCLYIVQFYGALFREGDCWISMELISTSFDKFYKYVYSVLDDVIPEEILGKVTLATVKALNH

Parental  LKENLKIIHRDIKPSNILLDRSGNIKLCDFGISGQLVDSIAKTRDAGCRPYMAPERIDPSASRQGYDVRS
          .KENLKIIHRDIKPSNILL.RS.NIKLCDFGISGQLVDS..KTRD.GCRP.MAPERIDPSA.RQ.Y...S
Retrocopy VKENLKIIHRDIKPSNILLYRSDNIKLCDFGISGQLVDSTDKTRDSGCRPNMAPERIDPSALRQRYYICS

Parental  DVWSLGITL
          DVWSLGITL
Retrocopy DVWSLGITL

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_1281 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1281 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 5 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000065559	1 retrocopy	retro_hsap_4858,
Monodelphis domestica	ENSMODG00000008266	2 retrocopies	retro_mdom_1281 , retro_mdom_957,
Mustela putorius furo	ENSMPUG00000003664	1 retrocopy	retro_mputfur_1419,
Pongo abelii	ENSPPYG00000007993	1 retrocopy	retro_pabe_3775,
Tarsius syrichta	ENSTSYG00000011568	1 retrocopy	retro_tsyr_667,