RetrogeneDB ID: retro_mdom_2015

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: X:36593748..36594075(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: POLR2F
• Ensembl ID: ENSMODG00000019063
• Aliases: None
• Description: polymerase (RNA) II (DNA directed) polypeptide F [Source:HGNC Symbol;Acc:9193]

Sequence

>retro_mdom_2015
GATAATGAAGACAATTATAATAGTGATGACTTTGATGACATGGAGGAAGATGTTGGCCTAGAGGGCATGGAGGACCTTGA
AGAAGAGGAGCAGGAAAAGAAGGACATCTTTCCCTTTGGAAAATAACAATAGGGGTAACAGGCAAACTAGGGGCAGGGTA
CTACATGCTATATGACCAAGTATTAGTATGACCAAGTCTTGGATATTGAGGGCCTATAGATTATGACATGTACCACTGTG
ATGGTGGAACTAGAAAGAGGGCCTTACTACCTTCTCATCACCATCATAGATACCAATGCTCAGAAGACCTCCATCATCAT
CCACCAA

Alignment

ORF - retro_mdom_2015 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 50.46 %
• Parental protein coverage: 83.46 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  DNEDNYDGDDFDDVEEDEGLDDLENPEEEGQENVEILPSGERQ---QANQKRITTPYMTKYERARVLGTR
          DNEDNY..DDFDD.EED.GL...E..EEE.QE...I.P.G..Q...QAN....TT.YMTKY....VL...
Retrocopy DNEDNYNSDDFDDMEEDVGLEGMEDLEEEEQEKKDIFPFGK*Q*G*QAN*GQGTTCYMTKY*YDQVLDIE

Parental  ALQIAMCAPVMVELEGETDPLLIAMKELKARKIPIIIRR
          .L.I..C..VMVELE.....LLI......A.K..III..
Retrocopy GL*IMTCTTVMVELERGPYYLLITIIDTNAQKTSIIIHQ

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_2015 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_2015 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 7 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000010331	1 retrocopy	retro_amel_716,
Bos taurus	ENSBTAG00000004820	1 retrocopy	retro_btau_1648,
Canis familiaris	ENSCAFG00000001437	1 retrocopy	retro_cfam_596,
Myotis lucifugus	ENSMLUG00000014315	1 retrocopy	retro_mluc_199,
Monodelphis domestica	ENSMODG00000019063	2 retrocopies	retro_mdom_1276, retro_mdom_2015 ,
Mustela putorius furo	ENSMPUG00000012997	1 retrocopy	retro_mputfur_1158,
Otolemur garnettii	ENSOGAG00000025463	1 retrocopy	retro_ogar_1639,