RetrogeneDB ID: retro_mdom_1680

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 6:171196698..171197029(-)
• Located in intron of: None

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_1680
AAGAGTGCCACCTCCCAGGCCACCAGAATGTTTGTGCTGTACCCCATGTCTTGGGCAAACAACTTTGCAGTAAAAGGAAA
GCGGAAGACCTTAAATGCTGGTGATGTACTGTCAGCCATGGAAGAGATGGAATTTCAACAAGTCATTTCTCCTTTGATAT
AAGTACTATAGATGTGAACAGAAAATTAACAAGGCAGCTTCAGAGCAAAAGAAGACAGAGAAAAACAAACAGATGGATTC
TGAAGAGTAAGACAAGATCAAGAAAGATGATAATGATGAGGATGATGAAAGGATGAAAGAGGAGGAACAGAATGATGAAG
AAGCTGACAAT

Alignment

ORF - retro_mdom_1680 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 52.59 %
• Parental protein coverage: 77.4 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  RSAISRAASVFVLYATSCANNFAMKGKRKTLNAGDVLSAMEEMEFQRFISPLKEALDAYRREQKGKKEAS
          .SA.S.A...FVLY..S.ANNFA.KGKRKTLNAGDVLSAMEEMEFQ..ISPL...L........G...A.
Retrocopy KSATSQATRMFVLYPMSWANNFAVKGKRKTLNAGDVLSAMEEMEFQQVISPLI*VL*M*TEN*QGSFRAK

Parental  EQKKKDKDK--RIDSEEQ-DKSREDDNDEDDERMEEEEQNDEEVDN
          E...K..D...R.......D...EDD........EEE.QNDEE.DN
Retrocopy EDREKQTDGF*RVRQDQE>DDNDEDD----ERMKEEE-QNDEEADN

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_1680 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1680 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,