RetrogeneDB ID: retro_mdom_1465

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 5:180404980..180405292(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: POLR2I
• Ensembl ID: ENSMODG00000014172
• Aliases: None
• Description: polymerase (RNA) II (DNA directed) polypeptide I, 14.5kDa [Source:HGNC Symbol;Acc:9196]

Sequence

>retro_mdom_1465
ATGGAGCCCACTCAGACAGTAGAGCCAGGCTTTTGGGGATCCACTTCTTCTTCCAGCAACGCAACAACGTTCTCTACCCC
AAGAAGGACAAGGACCATCACATCCTTCTCTAGGCATGTCACAACTGTTACTACAAATACGAAGAAGACAATGGCTACAT
CTTTGTGAACAATATGAACCATAAGGTGGATGAGTTGAATCAGATCCTTATAGACATATAGCAGGAACCCACTCTTCCAA
GGACAGAAAAATCACCCATAATAAAAGTGTGATCATACAGAGACAGTATGCTTCTAGTTCTACAGTGCCCAG

Alignment

ORF - retro_mdom_1465 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.6 %
• Parental protein coverage: 82.4 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MEPDGTYEPGF-VGIRFC-QECNNMLYPKEDKENRILLYACRNCDYQQEADNSCIYVNKITHEVDELTQI
          MEP..T.EPGF..GI.F..Q..NN.LYPK.DK...ILL.AC.NC.Y..E.DN..I.VN...H.VDEL.QI
Retrocopy MEPTQTVEPGF<LGIHFFFQQRNNVLYPKKDKDHHILL*ACHNCYYKYEEDNGYIFVNNMNHKVDELNQI

Parental  IADVSQDPTLPRTE-DHPCQKCGHKEAVFFQSHSAR
          ..D..Q.PTLPRTE..HP..KC.H.E.V.F...SA.
Retrocopy LIDI*QEPTLPRTE>NHP**KCDHTETVCF*FYSAQ

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_1465 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1465 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 9 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000006601	1 retrocopy	retro_cfam_1400,
Callithrix jacchus	ENSCJAG00000009671	1 retrocopy	retro_cjac_2777,
Dipodomys ordii	ENSDORG00000001852	2 retrocopies	retro_dord_264, retro_dord_555,
Monodelphis domestica	ENSMODG00000014172	1 retrocopy	retro_mdom_1465 ,
Mus musculus	ENSMUSG00000019738	1 retrocopy	retro_mmus_2287,
Oryctolagus cuniculus	ENSOCUG00000013044	2 retrocopies	retro_ocun_103, retro_ocun_1603,
Otolemur garnettii	ENSOGAG00000024254	1 retrocopy	retro_ogar_386,
Ochotona princeps	ENSOPRG00000001789	2 retrocopies	retro_opri_350, retro_opri_837,
Tursiops truncatus	ENSTTRG00000003919	1 retrocopy	retro_ttru_223,