RetrogeneDB ID: retro_mdom_1725

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 7:91181476..91181830(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: POLR2E
• Ensembl ID: ENSMODG00000005494
• Aliases: None
• Description: polymerase (RNA) II (DNA directed) polypeptide E, 25kDa [Source:HGNC Symbol;Acc:9192]

Sequence

>retro_mdom_1725
CAAATGTACTATTAGTGGATTAAAGAGAAGAATATCACCAGGGCCCTCCTCATGATGTAACAGGACATGATACCCTCTAC
TAAGCAGTCATTGATTAATATGGCTCCCAAGTATACTTTGGAGTAGTTTCTATAGCAGGACCTCCTCATTAGCATCATGG
AACATGAGCTGCTTGCAGAACATGTTGTTATGACAAAAGAGGAAGTCACCAAGATAATGGCTCAACATAAGCTTCAAGAA
AACCAGTTGCCCAGATTCAAGGCAGGAGATCCTATAGGATAATACTTTGTACAAAAACAAGAGCAATTAGTGAAGATCAA
AAGATCCAGTAATACTACAGACAGCTATATCACT

Alignment

ORF - retro_mdom_1725 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.02 %
• Parental protein coverage: 56.19 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KMYCQRMQEENITRALIVVQQGMTPSAKQSLVDMAPKYILEQFLQQELLINITEHELVPEHVVMTKEEVT
          .MY.....E.NITRAL....Q.M.PS.KQSL..MAPKY.LE.FL.Q.LLI.I.EHEL..EHVVMTKEEVT
Retrocopy QMYY*WIKEKNITRALLMM*QDMIPSTKQSLINMAPKYTLE*FL*QDLLISIMEHELLAEHVVMTKEEVT

Parental  ELLARYKLRENQLPRIQAGDPVARYFGIKRGQVVKIIRPSETAGRYIT
          ...A..KL.ENQLPR..AGDP...YF..K..Q.VKI.R.S.T...YIT
Retrocopy KIMAQHKLQENQLPRFKAGDPIG*YFVQKQEQLVKIKRSSNTTDSYIT

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_1725 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1725 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 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000099817	1 retrocopy	retro_hsap_822,
Myotis lucifugus	ENSMLUG00000013193	1 retrocopy	retro_mluc_1636,
Monodelphis domestica	ENSMODG00000005494	1 retrocopy	retro_mdom_1725 ,
Mustela putorius furo	ENSMPUG00000008953	1 retrocopy	retro_mputfur_1524,
Nomascus leucogenys	ENSNLEG00000001207	1 retrocopy	retro_nleu_255,
Pongo abelii	ENSPPYG00000009305	1 retrocopy	retro_pabe_733,