RetrogeneDB ID: retro_mdom_957

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 3:24783263..24784130(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMODG00000019588
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

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

Sequence

>retro_mdom_957
ATGGCAGCTCCAAGCCCAATCGGCGGTAGCGGGAGCGGCTCTCCTAGCGCCCTAGGGCCCCCCTGGCCAGGCCACATGGC
CATCAGCAGCATGCAGGGTAAACGCAAAGCATTGAAGCTGAATTTTGCAAATCCACCTTTCAAATCTACTGCACGGTTTA
CCCTGAATCCTTCAGGAGTCCAAAACCCACACATAGAGAGACTGAGAACACACAGCATTGAATCATCAGGAAAACTGAAG
ATCTCCCCTGAACAGCACTGGGATTTCACTGCAGAGGACTTGAAAGACCTTGGAGAAATTGGACGAGAAGCTTATGGTTC
TGTCAACAAAATGGTCCACAAACCAAGTGGGAAAATATTGGCAGTTAAAAGAATTCGGTCTACAGTGGATGAAAAAGAGC
AAAAACAGCTACTTATGGACTTGGATGTGGTGATGCGGAGTAGTGATTGCCCGTATATTGTTCAGTTTTATGGAGCACTC
TTCAGAGAGGGTGACTGTTGGATCTGTATGGAACTCATGTCTACTTCGTTTGACAAGTTTTACAAATATGTATATAGTGT
ATTAGATGATGTTATTCCAGAAGAAATTTTAGGCAAAGTCACTTTAGCAACTGCGAAAGCACTAAACCACTTAAAAGAAA
ACTTGAAAATTATTCACAGAGACATCAAACCTTCTAATATTCTTCTGGATAGAAGTGGCAATATTAAACGTTGTGATTTT
GGTATAAGTGGACAACTTGTGGACTCCATTGCCAAAACAAGAGATGCTGGGTGCAGGCCATACATGGCAACTGAAAGGAT
AGACCCAAGTGCATCGAGGCAAGGATACGATGTCCGTTCTGATGTATGGAGTCTGGGGATCACACTG

Alignment

ORF - retro_mdom_957 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.85 %
• Parental protein coverage: 72.98 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAAPSPSGGSGSGSPSAVGPPGPGHTAVSSMQGKRKALKLNFANPPFKSTARFTLNPSGVQNPHIERLRT
          MAAPSP.GGSGSGSPSA.GPP.PGH.A.SSMQGKRKALKLNFANPPFKSTARFTLNPSGVQNPHIERLRT
Retrocopy MAAPSPIGGSGSGSPSALGPPWPGHMAISSMQGKRKALKLNFANPPFKSTARFTLNPSGVQNPHIERLRT

Parental  HSIESSGKLKISPEQHWDFTAEDLKDLGEIGRGAYGSVNKMVHKPSGQIMAVKRIRSTVDEKEQKQLLMD
          HSIESSGKLKISPEQHWDFTAEDLKDLGEIGR.AYGSVNKMVHKPSG.I.AVKRIRSTVDEKEQKQLLMD
Retrocopy HSIESSGKLKISPEQHWDFTAEDLKDLGEIGREAYGSVNKMVHKPSGKILAVKRIRSTVDEKEQKQLLMD

Parental  LDVVMRSSDCPYIVQFYGALFREGDCWICMELMSTSFDKFYKYVYSVLDDVIPEEILGKITLATVKALNH
          LDVVMRSSDCPYIVQFYGALFREGDCWICMELMSTSFDKFYKYVYSVLDDVIPEEILGK.TLAT.KALNH
Retrocopy LDVVMRSSDCPYIVQFYGALFREGDCWICMELMSTSFDKFYKYVYSVLDDVIPEEILGKVTLATAKALNH

Parental  LKENLKIIHRDIKPSNILLDRSGNIKLCDFGISGQLVDSIAKTRDAGCRPYMAPERIDPSASRQGYDVRS
          LKENLKIIHRDIKPSNILLDRSGNIK.CDFGISGQLVDSIAKTRDAGCRPYMA.ERIDPSASRQGYDVRS
Retrocopy LKENLKIIHRDIKPSNILLDRSGNIKRCDFGISGQLVDSIAKTRDAGCRPYMATERIDPSASRQGYDVRS

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_957 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_957 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,