RetrogeneDB ID: retro_mdom_605

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 1:495178055..495178697(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CHMP2B
• Ensembl ID: ENSMODG00000016939
• Aliases: None
• Description: charged multivesicular body protein 2B [Source:HGNC Symbol;Acc:24537]

Sequence

>retro_mdom_605
ATGGCCTCCCTTTTCAAGAAGAAGACAGTAGATGATGTAATAAAGGAGCAGAATTGAGAGTTACGAGGTACACAGAGGGC
TATAATGAGAGATCGAGCAGCATTAGAAAAACAGGAAAAACAGCTGGAATTAGAAATTAAGAAAATGGCCAAGATTGGTA
ACAAAGAAGCCTGCAGAGTTTTGGCTAAACAGCTTGTGCAACTGAGGAAACAGAAAACTAGAATTTTTGCTGTAAGTTCA
AAAGTCACTTCTATGTCTACCCAGACTAAAGTCATGAACTCTCAGATGAAGATGGCTGGAGCCATGTCAACTACTGCCAA
AACAATGCAGGCAGTTAACAAGAAGATGGATCCACAAAAGACATTGCAAACAATGCAAAATTTCCAGAAGGAAAACATGA
AAATGGAAATGACTGAAGAAATGATCAATGATACACTGGATGACATCTTTGATGGATCTGATGATGAAGAAGAAAGCCAG
GATATTGTGAACCAGGTGCTTGATGAAACTGGAATTGAAATCTCTGGAAAGATGGCCAAAGCACCATCAGCCGCCCGAGG
CTTACCATCTGCATCCACATCAAAAGCATCGGCAATCTCTGATGAAGAGATTGAACGGCAACTTAAAGCGTTGGGCGTAG
AT

Alignment

ORF - retro_mdom_605 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.13 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MASLFKKKTVDDVIKEQNRELRGTQRAIMRDRAALEKQEKQLELEIKKMAKIGNKEACRVLAKQLVQLRK
          MASLFKKKTVDDVIKEQN.ELRGTQRAIMRDRAALEKQEKQLELEIKKMAKIGNKEACRVLAKQLVQLRK
Retrocopy MASLFKKKTVDDVIKEQN*ELRGTQRAIMRDRAALEKQEKQLELEIKKMAKIGNKEACRVLAKQLVQLRK

Parental  QKTRTFAVSSKVTSMSTQTKVMNSQMKMAGAMSTTAKTMQAVNKKMDPQKTLQTMQNFQKENMKMEMTEE
          QKTR.FAVSSKVTSMSTQTKVMNSQMKMAGAMSTTAKTMQAVNKKMDPQKTLQTMQNFQKENMKMEMTEE
Retrocopy QKTRIFAVSSKVTSMSTQTKVMNSQMKMAGAMSTTAKTMQAVNKKMDPQKTLQTMQNFQKENMKMEMTEE

Parental  MINDTLDDIFDGSDDEEESQDIVNQVLDEIGIEISGKMAKAPSAARGLPSASTSKASTISDEEIERQLKA
          MINDTLDDIFDGSDDEEESQDIVNQVLDE.GIEISGKMAKAPSAARGLPSASTSKAS.ISDEEIERQLKA
Retrocopy MINDTLDDIFDGSDDEEESQDIVNQVLDETGIEISGKMAKAPSAARGLPSASTSKASAISDEEIERQLKA

Parental  LGVD
          LGVD
Retrocopy LGVD

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	0.24 RPM	0.00 RPM
SRP007412_cerebellum	0.33 RPM	0.00 RPM
SRP007412_heart	0.00 RPM	0.00 RPM
SRP007412_kidney	1.32 RPM	0.00 RPM
SRP007412_liver	0.00 RPM	0.00 RPM
SRP007412_testis	0.20 RPM	0.00 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_605 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_605 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 5 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000006615	2 retrocopies	retro_chof_2662, retro_chof_309,
Macropus eugenii	ENSMEUG00000012195	1 retrocopy	retro_meug_106,
Myotis lucifugus	ENSMLUG00000009052	1 retrocopy	retro_mluc_1557,
Monodelphis domestica	ENSMODG00000016939	2 retrocopies	retro_mdom_522, retro_mdom_605 ,
Ictidomys tridecemlineatus	ENSSTOG00000011456	1 retrocopy	retro_itri_1036,