RetrogeneDB ID: retro_mdom_1501

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 5:42993043..42993895(-)
• Located in intron of: ENSMODG00000020626

Retrocopy information

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

Parental gene information

• Parental gene symbol: NMI
• Ensembl ID: ENSMODG00000003594
• Aliases: None
• Description: N-myc (and STAT) interactor [Source:HGNC Symbol;Acc:7854]

Sequence

>retro_mdom_1501
ATCGATGAAATGGTACAAACAAATACTGACCTAAAGATTGAAATTAAAAAAGCTGAAATGGAGTTGCAACGACCTTCATC
ATCTTACCTGGTTAAAAAGAATATTCCTACAAAGGAAATAAAGTTCATATCAGCGGAAAGCCCTAAGGATGACAGTCAGT
ATTCAGATATCTCCTGTTCATTTCAAGTAACAACACAACTTGAATATGAATTGAAGAAAGGACAAGCTCTTATCACCTTT
GAAGATGAAGAAGTTGCCCAGAATGTGATAAAAAGAGGAAAACATCTTGTGACATTTGGCAATGAGGAAATGAAATTGAT
GGCCAAACCTGTCCCACTAAAAACAGGTTTAAGTCTTCAGGTTCATTCAAAGATTTCTAAGAAAAAGATTGATGTTGCCG
GAATACCTAATGAATTACCTGAAGAACAGATGAGAGACAAATTAGCACTGAGCTTCAGTAAATCCCAGAATGGGGGTGGA
GAAGTAAAACATGTGGAGTATAATGTAAATACCCAAAGAGCGGTTATTACATTTCTTAAAAATGGAGTTGCTGATAACAT
TCTCAAGCACAAGAAATATCCTCTTTTTACAAATACCAGCTGCTATCAGGTTGATGTTTCCCCACATATGGAAAAAAATG
TCAAGAAGCTACAGGTATTTTCAGGAATTTCTAAGAGGACTGTTCTTCTGACAGGATTTAGAAATATTCAAGATGATGAA
GAAAATATAGAAGAGGACATTTTTATTCATTTTCAGAAAGGGTCAAATGGAGGAGGGGATGTAGAAGTTGTCAAATGTGC
CCTCAAAAAACCTCAAATAGCATATTTTGAGGCTGATTTAGATCAGGGATGC

Alignment

ORF - retro_mdom_1501 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.18 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  IDEMVQTNTNLKIEIKKAEMELQRPSSSYLVKKNIPTKEIKFISAESPKDDSQYSDISCSFQVTTQLEYE
          IDEMVQTNT.LKIEIKKAEMELQRPSSSYLVKKNIPTKEIKFISAESPKDDSQYSDISCSFQVTTQLEYE
Retrocopy IDEMVQTNTDLKIEIKKAEMELQRPSSSYLVKKNIPTKEIKFISAESPKDDSQYSDISCSFQVTTQLEYE

Parental  LKKGQALITFEDEEVAQNVIKRGKHLVTFGSEEMKLMAKPVPLKTGLSLQVHSKISKKKIDVAGIPNELP
          LKKGQALITFEDEEVAQNVIKRGKHLVTFG.EEMKLMAKPVPLKTGLSLQVHSKISKKKIDVAGIPNELP
Retrocopy LKKGQALITFEDEEVAQNVIKRGKHLVTFGNEEMKLMAKPVPLKTGLSLQVHSKISKKKIDVAGIPNELP

Parental  EEQMRDKLALSFSKSQNGGGEVEHVEYSVNTQRAVITFLKNGVADNILKHKKYPLFTNTSCYQVDVSPHM
          EEQMRDKLALSFSKSQNGGGEV.HVEY.VNTQRAVITFLKNGVADNILKHKKYPLFTNTSCYQVDVSPHM
Retrocopy EEQMRDKLALSFSKSQNGGGEVKHVEYNVNTQRAVITFLKNGVADNILKHKKYPLFTNTSCYQVDVSPHM

Parental  KRNVKKLQVFSGISKRTVLLTGLRNIQDDEESIEEDIFIHFQKGSNGGGDVEVVKCALKKPQIAYFEADL
          ..NVKKLQVFSGISKRTVLLTG.RNIQDDEE.IEEDIFIHFQKGSNGGGDVEVVKCALKKPQIAYFEADL
Retrocopy EKNVKKLQVFSGISKRTVLLTGFRNIQDDEENIEEDIFIHFQKGSNGGGDVEVVKCALKKPQIAYFEADL

Parental  DQGC
          DQGC
Retrocopy DQGC

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_1501 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1501 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Monodelphis domestica	ENSMODG00000003594	1 retrocopy	retro_mdom_1501 ,
Otolemur garnettii	ENSOGAG00000002762	1 retrocopy	retro_ogar_1125,