RetrogeneDB ID: retro_mdom_1415

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 4:360536802..360537653(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMODG00000013023
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: CHMP7
• Ensembl ID: ENSMODG00000009093
• Aliases: None
• Description: charged multivesicular body protein 7 [Source:HGNC Symbol;Acc:28439]

Sequence

>retro_mdom_1415
ATGTGGTCCCCGGGGCAGGAGTCCGAAGCCTCAGCCGGGGGAGAACCGGCGGGGGATGCTGCCCCCCGAGTGGGAGGAAG
ATGAAGAACGGATGTCCTTGTTCTCCGCCTTCAAGAGGAGTCGGGAGGTGAACAGCACGGACTGGGATAGCAAGATAGGC
TTCTGGGCACCGCTAGTGCTGAGCCACAGTCGCCGCCAGGGGGCGGTGCGTTTGCGCCTGCGCGACCTTCAGGAGGCCTT
CCAGCGCAAGGGGAGCGTCCCGCTCGGGTTGGCCACAGTGCTTCAGGGATCTGCTCCGCCGAGGGGAGCTACCACGGGAG
TCTGATTTCATGGCCAGTGTGGACAGCAGCTGGATTTCATGGGGTGTAGGTGTCTTCCTTTTGAAGCCTCTCAAATGGAC
TCTTTCTAATGTGCTAGGGGACAATGAAGTCCCTGCTGAAGAAGTGCTGGTGGCTGTGGAGCTGCTTAAGGAAAAAGCAG
AGGATGTATATCGTCTGTATCAGAACTCTCCAATCTCCTCTCATCCTTTGGTGGCCCTATCAGAGTTGAGCACCTTCTGT
GCTAGTTCCTGCCCAGATGAACGAACCTTCTATTTGGTATTGTTACAGCTGCAGAAAGAGAAGAGAGGCACTGTTTTAGA
ACAGAATGGTGAGAAAATTGTGAAGTTTGCCCGAGGGCTACATGCCAAGGTCTCCCCGGTAAATGATGTAGATGTCGGGG
TGTACCAGTTGATGCAGAATGAACGGCTGCTCTCACGCAAGGTGGAGTCCCTGTCCCAGGAATCAGAGAGATGTAAAGAA
GATGCCCGACAAGCATGTCAAGCTAGAAAGAAGCAACTGGCACTAAGGCAT

Alignment

ORF - retro_mdom_1415 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.1 %
• Parental protein coverage: 62.97 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MWSPGQESEAPAGGEPAG-LLPPEWEEDEERMSFLFSAFKRSREVNSTDWDSKMGFWAPLVLSHSRRQGA
          MWSPGQESEA.AGGEPAG..LPPEWEEDEERMS.LFSAFKRSREVNSTDWDSK.GFWAPLVLSHSRRQGA
Retrocopy MWSPGQESEASAGGEPAG>MLPPEWEEDEERMS-LFSAFKRSREVNSTDWDSKIGFWAPLVLSHSRRQGA

Parental  VRLRLRDLQEAFQRKGSVPLGLATVLQ-DLLRRGELQRESDFMASVDSSWISWGVGVFLLKPLKWTLSNV
          VRLRLRDLQEAFQRKGSVPLGLATVLQ.DLLRRGEL.RESDFMASVDSSWISWGVGVFLLKPLKWTLSNV
Retrocopy VRLRLRDLQEAFQRKGSVPLGLATVLQ>DLLRRGELPRESDFMASVDSSWISWGVGVFLLKPLKWTLSNV

Parental  LGDNKVPAEEVLVAVELLKEKAEDVYRLYQNSPISSHPVVALSELSTLCASSCPDERTFYLVLLQLQKEK
          LGDN.VPAEEVLVAVELLKEKAEDVYRLYQNSPISSHP.VALSELST.CASSCPDERTFYLVLLQLQKEK
Retrocopy LGDNEVPAEEVLVAVELLKEKAEDVYRLYQNSPISSHPLVALSELSTFCASSCPDERTFYLVLLQLQKEK

Parental  RVTVLEQNGEKIVKFARGLHAKVSPVNDVDVGVYQLMQSERLLSRKVESLSQESERCKEDARQACRAGKK
          R.TVLEQNGEKIVKFARGLHAKVSPVNDVDVGVYQLMQ.ERLLSRKVESLSQESERCKEDARQAC.A.KK
Retrocopy RGTVLEQNGEKIVKFARGLHAKVSPVNDVDVGVYQLMQNERLLSRKVESLSQESERCKEDARQACQARKK

Parental  QLALRH
          QLALRH
Retrocopy QLALRH

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	123.37 RPM
SRP007412_cerebellum	0.00 RPM	139.72 RPM
SRP007412_heart	0.00 RPM	136.36 RPM
SRP007412_kidney	0.00 RPM	183.04 RPM
SRP007412_liver	0.00 RPM	123.86 RPM
SRP007412_testis	0.00 RPM	76.61 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_1415 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1415 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Monodelphis domestica	ENSMODG00000009093	1 retrocopy	retro_mdom_1415 ,