RetrogeneDB ID: retro_mdom_988

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 3:130297872..130299010(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMODG00000004180
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: POLR3D
• Ensembl ID: ENSMODG00000009491
• Aliases: None
• Description: polymerase (RNA) III (DNA directed) polypeptide D, 44kDa [Source:HGNC Symbol;Acc:1080]

Sequence

>retro_mdom_988
CCTTCACTGCCCGGGGCCCTGGGTCTGATCGGCATTGGCCCCCGGCCCCCCTTACCCCAGGATGCCTCCCTTCTATCCAT
TCCAGGGACCTCACCCTGGGGGGGTCAAGAAGAAAACATTCACTCCTAACATCATTAGCCGGAAGATCAAGGGAAGAGCC
AAAGGAAGAAATATTGGTCAAGAAAGAGAAGCGAGAGAGGGATTGAGATCTACGAGATGGGCATGGTCGGGGAAGGGGTC
AGCCAGAAGTGATCCAGTCTCACTCTATCTTTGAGCAAGGACCAGCTGAAATGATGAAGAAAAAAGGCAACTGGGATAAG
ACAGTGGATGTGTCAGACTTTGGCCCATCTCATATTATCAACATCAAAAGGAGAAAAGGGAAACAGATGAGGAAACTAAA
CAAATTCTTTGCATGCTGGAGAAGGATGATTTCATAGATGATCCAGGGCTCAAGAATAATACTCGAAACAAGCCTGTGCA
GCTTCCTCTGGCGCACTCGGGGTGGCTTTTAAAAGAAGAGAGTGAAGAAGCTGATGTCAAGCCCTGGATAGGAAAAACCA
AAGAAGAAAGCATGGAGGTGGATATACCAGCCCTGAAAGTGAAAGAAGAACCACAAGATGAGGATGAGACCAGGGCAGCT
GCTCCCCCCAAGCCTGGCCAAGTGGTGCCTGGACTTCCTCAAGATGTGTCTGTGGCAGACTTACTCAGGGAACTGAGCTT
TGCCAAGGAGGAAGAGCTGTTGTTTCTACAGTTGCCTGACACACTCCCTGGTCAACTCAGGACATCAAACCCATCAAGAC
AGAGGTTCAAGGAGAGGATGGGCAGATGGTGCTTGTGAAGCCAGAGAAAGACTGGGAAGCTAAACTGGCAGAGAACCTAT
GTACCTTGAGTGACCTGACAGAGGGTCAGGTGGGAAAACTGCTTATCCAAAAATCAGGAAAGGTGCAACTACTTCTGGGC
AAAGTGACGCTTGATGTAACAGTGGGTACTTCCTGCTCCTTTTTTGCAGGAGCTGGTGTCTGTGAGTATTGGAGACAGCA
GAACAGGCGATTTGACAGTTTTGGGCCATGTAAAACACAAGCTCATGTGTTCCCCTGATTTTGAATCCCTATTGGATCAC
AAACAGCGGTAGAGTCAG

Alignment

ORF - retro_mdom_988 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.86 %
• Parental protein coverage: 99.48 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  PSLPGARGLIG-RRPAAPLTPGRLPSIRSRDLTLGG-VKKKTFTPNIISRKIK-EEPKEEILVKKEKRER
          PSLPGA.GLIG...P.APLTPG.LPSI.SRDLTLGG.VKKKTFTPNIISRKIK.EEPKEEILVKKEKRER
Retrocopy PSLPGALGLIG<HWPPAPLTPGCLPSIHSRDLTLGG<VKKKTFTPNIISRKIK>EEPKEEILVKKEKRER

Parental  DRDRQRDGHGRGRGRPEVIQSHSIFEQGPAEMMKKKGNWDKTVDVSDFGPSHIINIK-KEKRETDEETKQ
          D.D..RDGHGRGRG.PEVIQSHSIFEQGPAEMMKKKGNWDKTVDVSDFGPSHIINIK.KEKRETDEETKQ
Retrocopy D*DL-RDGHGRGRGQPEVIQSHSIFEQGPAEMMKKKGNWDKTVDVSDFGPSHIINIK<KEKRETDEETKQ

Parental  ILRMLEKDDFIDDPGLKNDTRNKPVQLPLAHSGWLFKEESEEPDVKPWIGRTKEESMEVDIPALKVKEEP
          IL.MLEKDDFIDDPGLKN.TRNKPVQLPLAHSGWL.KEESEE.DVKPWIG.TKEESMEVDIPALKVKEEP
Retrocopy ILCMLEKDDFIDDPGLKNNTRNKPVQLPLAHSGWLLKEESEEADVKPWIGKTKEESMEVDIPALKVKEEP

Parental  QDEDETRAAAPPKPGRVAPGLPQDVSVADLLRELSFAKEEELLFLQLPDTLPGQPPTQDIKPIKTEVQGE
          QDEDETRAAAPPKPG.V.PGLPQDVSVADLLRELSFAKEEELLFLQLPDTLPGQ..T....P........
Retrocopy QDEDETRAAAPPKPGQVVPGLPQDVSVADLLRELSFAKEEELLFLQLPDTLPGQLRTSN--PSRQRFKER

Parental  DGQMVL-VKPEKDREAKLAENLCTLSDLTEGQVGKLLIRKSGKVQLLLGKVTLDVTVGTSCS-FLQELVS
          .G...L.VKPEKD.EAKLAENLCTLSDLTEGQVGKLLI.KSGKVQLLLGKVTLDVTVGTSCS.FLQELVS
Retrocopy MGRWCL<VKPEKDWEAKLAENLCTLSDLTEGQVGKLLIQKSGKVQLLLGKVTLDVTVGTSCS>FLQELVS

Parental  VSIGDSRTGDLTVLGHVKHKLVCSPSNPYWITNSGRVSQ
          VSIGDSRTGDLTVLGHVKHKL.CSP..........R.SQ
Retrocopy VSIGDSRTGDLTVLGHVKHKLMCSPDFESLLDHKQR*SQ

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	63.77 RPM
SRP007412_cerebellum	0.00 RPM	49.62 RPM
SRP007412_heart	0.00 RPM	32.89 RPM
SRP007412_kidney	0.00 RPM	56.62 RPM
SRP007412_liver	0.00 RPM	51.36 RPM
SRP007412_testis	0.00 RPM	85.65 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_988 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_988 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.

---

Parental genes homology:

Parental genes homology involve 12 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000013488	1 retrocopy	retro_dnov_1681,
Equus caballus	ENSECAG00000025090	1 retrocopy	retro_ecab_43,
Erinaceus europaeus	ENSEEUG00000007632	2 retrocopies	retro_eeur_277, retro_eeur_705,
Homo sapiens	ENSG00000168495	1 retrocopy	retro_hsap_596,
Macropus eugenii	ENSMEUG00000000465	1 retrocopy	retro_meug_1550,
Myotis lucifugus	ENSMLUG00000002109	1 retrocopy	retro_mluc_2339,
Macaca mulatta	ENSMMUG00000023226	1 retrocopy	retro_mmul_2449,
Monodelphis domestica	ENSMODG00000009491	1 retrocopy	retro_mdom_988 ,
Nomascus leucogenys	ENSNLEG00000015502	1 retrocopy	retro_nleu_2218,
Pongo abelii	ENSPPYG00000018419	1 retrocopy	retro_pabe_594,
Pan troglodytes	ENSPTRG00000020056	1 retrocopy	retro_ptro_439,
Tursiops truncatus	ENSTTRG00000012745	1 retrocopy	retro_ttru_1189,