RetrogeneDB ID: retro_mdom_1920

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 8:144168024..144168276(-)
• Located in intron of: ENSMODG00000016983

Retrocopy information

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

Parental gene information

• Parental gene symbol: POLE3
• Ensembl ID: ENSMODG00000004358
• Aliases: None
• Description: polymerase (DNA directed), epsilon 3, accessory subunit [Source:HGNC Symbol;Acc:13546]

Sequence

>retro_mdom_1920
ATGGAGGAAAGGCCAGAGGGCTTAAATCTTCTTAATGATGTCATCATCAGGATGGTCAAGTAGGTGCTCCCTGAAGGTGT
CAACATCTCCAAAGGGGACCAAAGTACCATATCCGAGGCCACCACTATGTTAGTGTGGTGCACCATGTCTTGTGCAAACA
TTTTTGAAGTGAAAGGAAATTGGAAGACCATATACACTGGTGATATACTGTTGGCCATGGAAGAGCAGGAATTTCAAGGA
TTCCTTTCCCCT

Alignment

ORF - retro_mdom_1920 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.14 %
• Parental protein coverage: 57.53 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAERPEDLNLPNAVITRIIKEALPDGVNISKEARSAISRAASVFVLYATSCANNFAMKGKRKTLNAGDVL
          M.ERPE.LNL.N.VI.R..K..LP.GVNISK...S.IS.A....V....SCAN.F..KG..KT...GD.L
Retrocopy MEERPEGLNLLNDVIIRMVK*VLPEGVNISKGDQSTISEATTMLVWCTMSCANIFEVKGNWKTIYTGDIL

Parental  SAMEEMEFQRFISP
          .AMEE.EFQ.F.SP
Retrocopy LAMEEQEFQGFLSP

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	107.16 RPM
SRP007412_cerebellum	0.00 RPM	49.29 RPM
SRP007412_heart	0.00 RPM	18.34 RPM
SRP007412_kidney	0.00 RPM	71.11 RPM
SRP007412_liver	0.00 RPM	31.22 RPM
SRP007412_testis	0.00 RPM	344.54 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_1920 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1920 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 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000017917	1 retrocopy	retro_cjac_4121,
Cavia porcellus	ENSCPOG00000000313	1 retrocopy	retro_cpor_355,
Dipodomys ordii	ENSDORG00000003073	2 retrocopies	retro_dord_526, retro_dord_652,
Monodelphis domestica	ENSMODG00000004358	3 retrocopies	retro_mdom_1680, retro_mdom_1920 , retro_mdom_647,
Mus musculus	ENSMUSG00000028394	2 retrocopies	retro_mmus_124, retro_mmus_555,
Pteropus vampyrus	ENSPVAG00000004717	1 retrocopy	retro_pvam_302,
Rattus norvegicus	ENSRNOG00000015392	1 retrocopy	retro_rnor_55,
Ictidomys tridecemlineatus	ENSSTOG00000027365	1 retrocopy	retro_itri_866,
Tupaia belangeri	ENSTBEG00000005211	1 retrocopy	retro_tbel_4052,