RetrogeneDB ID: retro_mdom_1310

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 4:402546835..402547472(+)
• Located in intron of: ENSMODG00000029397

Retrocopy information

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

Parental gene information

• Parental gene symbol: IMPA1
• Ensembl ID: ENSMODG00000006271
• Aliases: None
• Description: inositol(myo)-1(or 4)-monophosphatase 1 [Source:HGNC Symbol;Acc:6050]

Sequence

>retro_mdom_1310
TCTCACAGTTTCATTGGTGAGGAATCAGTGGCTGCTGGGGACCACAGTGTCTTGACTGATAATCCCACATGGATAATTGA
TCCTATTGATGGAACTATTAACTTCGTGCACAGATTTCCATTTGTAGCTATTTCCATTGGCTTTGATGTGGGCAAAAAGA
TGGAATTTGGAGTTGTATACAGTTGTATAGAAGATAAAATGTACACTGGCAGGAAAGGAAAATGGACTTTTTGCAATGAT
CAAAAACTTCATGTGTCAGGACAAAAAGATTTTGCTAAAATTGGTGACAGAATTGGTAGTTAACCGACAACCAGAGGTGG
TAAAAACTTTTCTTTCAAATATGGAGATACTTTTTTATATTCCTATTCATGGAATAAGGGGTGCTGGTACAGCAGCAATA
AATCTGTTCCTGGTGGCAACTGGAGGAGCAGATGCATGTTAGGAAATGGGCATTCACTGCTGGGATACGGCAGGAGCTGG
TGTTATCATTAATGAAGCTGGTGGAGTGTTTTTGGATATAACAGGGGGACCTTTTGACTTGATGTCATGAAGAATAATTG
CTGCAAGCATCAGAGTCTTAGCAGAAAGAATTGCCAAAGAAATTCAGCTAATACCTCTTCAGCGAGATGATGAAGAG

Alignment

ORF - retro_mdom_1310 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.93 %
• Parental protein coverage: 77.26 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SHSFIGEESVAAGEHSVLTDNPTWIIDPIDGTTNFVHRFPFVAISIGFVVGKKMEFGVVYSCIEDKMYTG
          SHSFIGEESVAAG.HSVLTDNPTWIIDPIDGT.NFVHRFPFVAISIGF.VGKKMEFGVVYSCIEDKMYTG
Retrocopy SHSFIGEESVAAGDHSVLTDNPTWIIDPIDGTINFVHRFPFVAISIGFDVGKKMEFGVVYSCIEDKMYTG

Parental  R-KGKGAFCNDQKLHVSGQEDITKSLLVTELGSNRQPEVVKTILSNMERLLCIPIHGIRAAGTAAINMCL
          R.K..G.F...............K..LVTEL..NRQPEVVKT.LSNME.L..IPIHGIR.AGTAAIN..L
Retrocopy R>KENGLFAMIKNFMCQDKKILLK--LVTELVVNRQPEVVKTFLSNMEILFYIPIHGIRGAGTAAINLFL

Parental  VATGGADAYYEMGIHCWDMAGAGVIVTEAGGVLLDITGGPFDLMSQRIIAASSRVLAERIAKEIQLIPLQ
          VATGGADA..EMGIHCWD.AGAGVI..EAGGV.LDITGGPFDLMS.RIIAAS.RVLAERIAKEIQLIPLQ
Retrocopy VATGGADAC*EMGIHCWDTAGAGVIINEAGGVFLDITGGPFDLMS*RIIAASIRVLAERIAKEIQLIPLQ

Parental  RDDEE
          RDDEE
Retrocopy RDDEE

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_1310 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1310 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
Equus caballus	ENSECAG00000023030	1 retrocopy	retro_ecab_438,
Macaca mulatta	ENSMMUG00000002628	1 retrocopy	retro_mmul_467,
Monodelphis domestica	ENSMODG00000006271	1 retrocopy	retro_mdom_1310 ,