RetrogeneDB ID: retro_mdom_1093

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 3:71463603..71464907(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMODG00000011090
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000004576
• Aliases: None
• Description: None

Sequence

>retro_mdom_1093
GGGATGGGGTAGTCCAAAGAAGAGCTGATGCGTAAGAAACAAGAGGAATTCATGCAGAAGCATGGGAGAGGTGCTGAGAA
GTCTAGTAAGTCCTCAAAGTCAGATGCACCAAAGGAGAAAGGCAAAAAGGTACCTCGGGTATGGGCCCTAGATGGCTCTG
CAAATGAAGTCTTGGATTATAGCCCACCTACCACCAATGGAACTCCTGAGATCACTTTGCCAGAGGACATCAACCTGATC
CAAGGAACTCGGGTAGGAGGGCAACTACAAGATCTGGACTGCAGCAGCTCAGATGATGAGGGAGTCATTCAGAACTCGGC
CAAACCCAGTGCTTCAAAGGGAGCTCTGGGTGGCATGTTCGGGATGCTGAAAGGCTTGGTTGGCTCTAAGAGCTTAAGTC
GTGAAGACATGGAATCTGTGTTGGATGAGATGCAGGATCACTTAATTGCTAAGAATGTGGCTGCAGACATCACTCTCCAG
CTCTGTGAGTCTGTCGCCAACAAGTTGGAGGGAAAGGTGATGGGCACATTTAGCACTGTGACCTCCACGGTAAAGCAGGC
ACTGCAGGAGTCATTAGTCCAGATCCTGCAGCCACAGCGCCGTGTGGACATGCTCCGAGATATCATGGATGCTCAGCGCC
GCCAGCGTCCTTATGTTGTTACCTTCTGTGGGGTCAACGGAGTAGGCAAGTCCACAAATCTTGCCAAGATCTCCTTCTGG
CTGTTAGAGAATAACTTCAGTGTCCTCATTGCTGCCTGTGACACATTTTGGGCAGGGGCTGTGGAGCAGCTGTGTACCCA
CACACGGTGTCTTAGTGCTCTGCACCCTCCAGAGAATCATGGAGGCCGAACATGGTGCACCTGTTTGAGAAGGGCAAGGA
TGCTGCTGGCATTGCCATGGAGGCCATTTCTTTTGCTCATAATCAGGCTTTTGGTGTGGTGTTGGTGGATACAGCTGGCC
GAATGCAAGATAATGCGACTTTGATGACTGCTTTGGCCAAACTCATTGCTGTCAACACATCTGACCTGGTGCTGTTTGTT
GGGGAAGCCTTGGTGGGAAATGAGGCTGTGGATCAGCTGGTAAAATTCAACAAAACTCTGGCTGAGCACTCTAGAGCTCA
AAGACCCCTGCTCATTGATGGCATTGCTCTCACCAAATTTGATACCATTGATGACAAGGTGGGTGCTGCCATTTCTATGA
TATACATCACAAGCAAACCCATTGTCTTTTTTGGGACTGGCCAGACTTACAGTGACCTGCATAGCCTCAATGCCAAGGCT
GTGGTGACTGCCCTCATGAAGGCC

Alignment

ORF - retro_mdom_1093 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.01 %
• Parental protein coverage: 68.93 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GVELSKEELMRKKREEFMQKHGRGAEKSSKSSKSDAPKEKGKKAPRVWALGGSANEALDYSPPTTNGTPE
          G...SKEELMRKK.EEFMQKHGRGAEKSSKSSKSDAPKEKGKK.PRVWAL.GSANE.LDYSPPTTNGTPE
Retrocopy GMG*SKEELMRKKQEEFMQKHGRGAEKSSKSSKSDAPKEKGKKVPRVWALDGSANEVLDYSPPTTNGTPE

Parental  TTLPEDINLIRGTQAGGQLQDLDCSSSDDEGVTQNSAKPSASKGALGGMFGMLKGLVGSKSLSREDMESV
          .TLPEDINLI.GT..GGQLQDLDCSSSDDEGV.QNSAKPSASKGALGGMFGMLKGLVGSKSLSREDMESV
Retrocopy ITLPEDINLIQGTRVGGQLQDLDCSSSDDEGVIQNSAKPSASKGALGGMFGMLKGLVGSKSLSREDMESV

Parental  LDKMRDHLIAKNVAADIALQLCESVANKLEGKVMGTFSTVTSTVKQALQESLVQILQPQRRVDMLRDIMD
          LD.M.DHLIAKNVAADI.LQLCESVANKLEGKVMGTFSTVTSTVKQALQESLVQILQPQRRVDMLRDIMD
Retrocopy LDEMQDHLIAKNVAADITLQLCESVANKLEGKVMGTFSTVTSTVKQALQESLVQILQPQRRVDMLRDIMD

Parental  AQRRQRPYVVTFCGVNGVGKSTNLAKISFWLLENNFSVLIAACDTFRAGAVEQLRTHTRRLSALHPPENH
          AQRRQRPYVVTFCGVNGVGKSTNLAKISFWLLENNFSVLIAACDTF.AGAVEQL.THTR.LSALHPPENH
Retrocopy AQRRQRPYVVTFCGVNGVGKSTNLAKISFWLLENNFSVLIAACDTFWAGAVEQLCTHTRCLSALHPPENH

Parental  GGRT-MVHLFEKGYGKDAAGIAMEAISFARNQAFDVVLVDTAGRMQDNAPLMTALAKLIAVNTPDLVLFV
          GGRT.MVHLFEK..GKDAAGIAMEAISFA.NQAF.VVLVDTAGRMQDNA.LMTALAKLIAVNT.DLVLFV
Retrocopy GGRT<MVHLFEK--GKDAAGIAMEAISFAHNQAFGVVLVDTAGRMQDNATLMTALAKLIAVNTSDLVLFV

Parental  GEALVGNEAVDQLVKFNKALADHSMAQTPRLIDGIVLTKFDTIDDKVGAAISMTYITSKPIVFVGTGQTY
          GEALVGNEAVDQLVKFNK.LA.HS.AQ.P.LIDGI.LTKFDTIDDKVGAAISM.YITSKPIVF.GTGQTY
Retrocopy GEALVGNEAVDQLVKFNKTLAEHSRAQRPLLIDGIALTKFDTIDDKVGAAISMIYITSKPIVFFGTGQTY

Parental  SDLRSLNAKAVVAALMKA
          SDL.SLNAKAVV.ALMKA
Retrocopy SDLHSLNAKAVVTALMKA

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_1093 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1093 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Felis catus	ENSFCAG00000011274	1 retrocopy	retro_fcat_775,
Monodelphis domestica	ENSMODG00000004576	1 retrocopy	retro_mdom_1093 ,
Mus musculus	ENSMUSG00000032042	1 retrocopy	retro_mmus_723,