RetrogeneDB ID: retro_mdom_522

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 1:142901235..142901873(-)
• Located in intron of: ENSMODG00000011740

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_522
ATAGCCTCTCTTTTCAAGAAGACGATGGTAAATGACATAATAAAGAAGCAGAATTGAGAGTTACAAGGTACACAGAGGGC
TATAATGAGAGTTCAAGCAGCATTAGAAAAACAGGAAAAACAGCTCGAATTAGAAATTAAGAAAATGGCCAAGAATGGTA
ACAAAGAAGCCTGCAGAGTTTTAGCTAAACAGCTTGTGCAACTGAGGAAACAGAAAACTAGAACTTTTGCTGCTAGTTCA
AAGTCATTTCTATGTCTACACAAACTAAAGTAATCAACTCTCAGATGAAGATGGCTGGAGCCATGTTCACTACTGCAAAA
CAGTGCAGCAGTTTACAAGAAGAGGAATCCACAAAAGACATTACAAATAATGCAAAATTTCCAGAAGGAAAAACATGAAA
ATGGAAATGACTGAAGAAATGATCAATGATACACTGGATGACATTTTTGATGGATCTGATGATGAAGAAAAACCAGGATA
TTGTGAACCAGGTGCTTGATGAAATTGGAATTGAAATCTCTGGAAAGATGGCCAAAGCACCATCAGCTGCCCGAGGCTTA
CCATCTGCATCCACATCAAATGCATCTAGTATCTCTGATGAAGAGATTGGATGGCCACTTAAAGCATTGGACGTAGAT

Alignment

ORF - retro_mdom_522 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.93 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  MASLFKKKTVDDVIKEQNRELRGTQRAIMRDRAALEKQEKQLELEIKKMAKIGNKEACRVLAKQLVQLRK
          .ASLFKK..V.D.IK.QN.EL.GTQRAIMR..AALEKQEKQLELEIKKMAK.GNKEACRVLAKQLVQLRK
Retrocopy IASLFKKTMVNDIIKKQN*ELQGTQRAIMRVQAALEKQEKQLELEIKKMAKNGNKEACRVLAKQLVQLRK

Parental  QKTRTFAVSSK-VTSMSTQTKVMNSQMKMAGAMSTTAK-TMQ-AVNKKMDPQKTLQTMQNFQKE-NMKME
          QKTRTFA.SSK.V.SMSTQTKV.NSQMKMAGAM.TTAK.T.Q.AV.KK..PQKTLQ.MQNFQKE.NMKME
Retrocopy QKTRTFAASSK<VISMSTQTKVINSQMKMAGAMFTTAK<TVQ<AVYKKRNPQKTLQIMQNFQKE>NMKME

Parental  MTEEMINDTLDDIFDGSDDEEE-SQDIVNQVLDEIGIEISGKMAKAPSAARGLPSASTSKASTISDEEIE
          MTEEMINDTLDDIFDGSDD.EE..QDIVNQVLDEIGIEISGKMAKAPSAARGLPSASTS.AS.ISDEEI.
Retrocopy MTEEMINDTLDDIFDGSDD-EE>NQDIVNQVLDEIGIEISGKMAKAPSAARGLPSASTSNASSISDEEIG

Parental  RQLKALGVD
          ..LKAL.VD
Retrocopy WPLKALDVD

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	0.20 RPM	0.00 RPM
SRP007412_kidney	2.63 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_522 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_522 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,