RetrogeneDB ID: retro_mdom_798

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 2:3113387..3114621(-)
• Located in intron of: ENSMODG00000029236

Retrocopy information

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

Parental gene information

• Parental gene symbol: PPP2R5D
• Ensembl ID: ENSMODG00000019007
• Aliases: None
• Description: protein phosphatase 2, regulatory subunit B', delta [Source:HGNC Symbol;Acc:9312]

Sequence

>retro_mdom_798
GATGTACCTCCTGATGATCAAGAGAAGCTTTTTATCCAGAAGTTACATCAATGTTGTGTCCTCTTTGACTTTGTTTCTGA
TCCACTAAGTGACCTAAAGTGGAAGGAAGTAAAACGAGCTGCTTTAAGTGAAATGGTAGAATATATTACACAGAATCAAA
ATGTGATCACAGAACCTATTTACCCTGAAGTAGTATATATGTTTGCAGTTAACATGTTTCGAACATTACCACTGTCATCC
AATCCCACGGGAGCAGAATTTGATCCAGAGGAAGATGAGCCAACACTAGTAGCAGCCTGGCCTCATTTACAGCTTGTTTA
TGAATTTTTTTAAAAGACTTTTTAGAATATCCAGAATTCCAACCTAATATAGCAAACAAATATATTGATCAGAAGTTTGT
GTTGCAGCTTTTAGAGCTGTTTGACAGTGAAGATCCTCGAGAAAGAGATTTTCTTAAAACTACCCTTCACAGAATCTATG
GGAAATTCTTAGGCTTAAGAGCTTACATCAGAAAACAGATTAATAATATATTTTATAGGTTTATTTATGAAACAGAGCAT
CATAACGGCATAGCAGAATTGCTGGAAATATTGGGAAGCATAATTAATGGATTTGCCTTACCATTAAAAGAAGAGCACAA
GATTTTCTTATTGAAGGTGTTATTACCTTTGCACAAAGTGAAATCACTGAGTGTCTACCATCCTCAGCTGGCATACTGTG
TAGTTCAATTTTTAGAAAAGGACAGCACATTTACTGAACCAGTGGTGATGGCACTTCTCAAATACTGGCCAAAGACTCAA
AGCCCAAAAGAAGTCATGTTTTTAAATGAATTAGAGGAAATTTTAGATGTTATTGAACCATCTGAATTTGTAAAGGTCAT
GGAACCTCTTTTCAGACAACTAGCCAAATGTGTTTCCAGCCCACATTTCCAGGTGGTAGAGCAGGCACTCTATTACTGGA
ATAATGAATATATTATGAGTTTAATCAGTGACAATGCAGCAAAGATTCTGCCCATCATGTTTCCATCTTTGTATTGTAAT
TCAAAGACCCATTGGAATAAAACAATACATGGTTTGATATACAACGCATTGAAACTCTTTATGGAGATGAACCAAAACTG
TTTTATGACTGCACACAACAATTTAAAGCAGAGAAAATGAAAGAGAAGCTAAAAATGAAGGAATGAGAAGAAGCATGGGT
TAAAACAGAAAATCTAGCCAAATCAAATCCCCAG

Alignment

ORF - retro_mdom_798 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.09 %
• Parental protein coverage: 68.05 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  DSPTPEREELFIQKLRQCCVLFDFVADPLSDLKFKEVKRAGLNEMVEYITHSRDVVTEAIYPEAVIMFSV
          D.P....E.LFIQKL.QCCVLFDFV.DPLSDLK.KEVKRA.L.EMVEYIT....V.TE.IYPE.V.MF.V
Retrocopy DVPPDDQEKLFIQKLHQCCVLFDFVSDPLSDLKWKEVKRAALSEMVEYITQNQNVITEPIYPEVVYMFAV

Parental  NLFRTLPPSSNPTGAEFDPEEDEPTLEAAWPHLQLVYEF-FLR-FLESPDFQPNVAKKYIDQKFVLALLD
          N.FRTLP.SSNPTGAEFDPEEDEPTL.AAWPHLQLVYEF.FL..FLE.P.FQPN.A.KYIDQKFVL.LL.
Retrocopy NMFRTLPLSSNPTGAEFDPEEDEPTLVAAWPHLQLVYEF<FLKDFLEYPEFQPNIANKYIDQKFVLQLLE

Parental  LFDSEDPRERDFLKTILHRIYGKFLGLRAYIRRQINHIFYRFIYETEHHNGIAELLEILGSIINGFALPL
          LFDSEDPRERDFLKT.LHRIYGKFLGLRAYIR.QIN.IFYRFIYETEHHNGIAELLEILGSIINGFALPL
Retrocopy LFDSEDPRERDFLKTTLHRIYGKFLGLRAYIRKQINNIFYRFIYETEHHNGIAELLEILGSIINGFALPL

Parental  KEEHKMFLIRVLLPLHKVKSLSVYHPQLAYCVVQFLEKESSLTEPVIVGLLKFWPKTHSPKEVMFLNELE
          KEEHK.FL..VLLPLHKVKSLSVYHPQLAYCVVQFLEK.S..TEPV...LLK.WPKT.SPKEVMFLNELE
Retrocopy KEEHKIFLLKVLLPLHKVKSLSVYHPQLAYCVVQFLEKDSTFTEPVVMALLKYWPKTQSPKEVMFLNELE

Parental  EILDVIEPSEFSKVMEPLFRQLAKCVSSPHFQVAERALYYWNNEYIMSLISDNAARLLPIMFPALYRNSK
          EILDVIEPSEF.KVMEPLFRQLAKCVSSPHFQV.E.ALYYWNNEYIMSLISDNAA..LPIMFP.LY.NSK
Retrocopy EILDVIEPSEFVKVMEPLFRQLAKCVSSPHFQVVEQALYYWNNEYIMSLISDNAAKILPIMFPSLYCNSK

Parental  SHWNKTIHGLIYNALKLFMEMNQ-KLFDDCTQQYKAEKQKGRFRLKEREEMWHKIEELARLNPQ
          .HWNKTIHGLIYNALKLFMEMNQ.KLF.DCTQQ.KAEK.K.....KE.EE.W.K.E.LA..NPQ
Retrocopy THWNKTIHGLIYNALKLFMEMNQ<KLFYDCTQQFKAEKMKEKLKMKE*EEAWVKTENLAKSNPQ

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_798 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_798 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
Dasypus novemcinctus	ENSDNOG00000015445	1 retrocopy	retro_dnov_1333,
Monodelphis domestica	ENSMODG00000019007	1 retrocopy	retro_mdom_798 ,
Pongo abelii	ENSPPYG00000016625	1 retrocopy	retro_pabe_1434,