RetrogeneDB ID: retro_mdom_316

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 1:106220409..106220697(+)
• Located in intron of: ENSMODG00000010798

Retrocopy information

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

Parental gene information

• Parental gene symbol: AP3S2
• Ensembl ID: ENSMODG00000019522
• Aliases: None
• Description: adaptor-related protein complex 3, sigma 2 subunit [Source:HGNC Symbol;Acc:571]

Sequence

>retro_mdom_316
ATCAAAGGAAACCTCATATTCAACAGCAAAGGGAAATTTTAACCCTCCAAATTTTGACAGTCCAATAGTAAAAATATACA
AGTCATCAGGGAAACTTTCCATTTGGTGTCTAAATGAGATGAAAATATTTGTAATTTCCTAGGAGGAGGCCTGCTAATAG
GTACCTCTGAGAAACTGATTTAAAGACATTATGCTAAACTGTATCTTGTCTTTTGTGTGCATTCTTCAGAAAGTGAACTT
GGCATTTTAGACCTAATACAAATATTCATGGAAACATTAGACAAGTGT

Alignment

ORF - retro_mdom_316 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.65 %
• Parental protein coverage: 51.3 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  IQAILVFNNHGKPRLVRFYQRFPEEIQQQIVRETFHLVLKRDDNICNFLEGGSLIGGSDYKLIYRHYATL
          I...L.FN..GK.....F.Q.....IQ....RETFHLV.K.D.NICNFL.GG.LIG.S..KLI.RHYA.L
Retrocopy IKGNLIFNSKGKF*PSKF*QSNSKNIQ--VIRETFHLVSK*DENICNFLGGGLLIGTSE-KLI*RHYAKL

Parental  YFVFCVDSSESELGILDLIQVFVETLDKC
          Y.VFCV.SSESELGILDLIQ.F.ETLDKC
Retrocopy YLVFCVHSSESELGILDLIQIFMETLDKC

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	0.12 RPM	398.12 RPM
SRP007412_cerebellum	0.00 RPM	364.00 RPM
SRP007412_heart	0.00 RPM	96.49 RPM
SRP007412_kidney	0.00 RPM	227.81 RPM
SRP007412_liver	0.00 RPM	151.55 RPM
SRP007412_testis	0.00 RPM	53.63 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_316 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_316 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 13 parental genes, and 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000001407	1 retrocopy	retro_btau_436,
Choloepus hoffmanni	ENSCHOG00000003359	4 retrocopies	retro_chof_1775, retro_chof_194, retro_chof_434, retro_chof_88,
Dipodomys ordii	ENSDORG00000004247	1 retrocopy	retro_dord_115,
Equus caballus	ENSECAG00000024044	1 retrocopy	retro_ecab_549,
Felis catus	ENSFCAG00000028122	1 retrocopy	retro_fcat_311,
Macropus eugenii	ENSMEUG00000003421	1 retrocopy	retro_meug_2032,
Monodelphis domestica	ENSMODG00000019522	1 retrocopy	retro_mdom_316 ,
Nomascus leucogenys	ENSNLEG00000011780	2 retrocopies	retro_nleu_1380, retro_nleu_1555,
Otolemur garnettii	ENSOGAG00000030982	1 retrocopy	retro_ogar_1737,
Rattus norvegicus	ENSRNOG00000043141	1 retrocopy	retro_rnor_931,
Sus scrofa	ENSSSCG00000030174	7 retrocopies	retro_sscr_1109, retro_sscr_199, retro_sscr_268, retro_sscr_339, retro_sscr_620, retro_sscr_721, retro_sscr_753,
Tursiops truncatus	ENSTTRG00000015554	2 retrocopies	retro_ttru_1233, retro_ttru_1361,
Vicugna pacos	ENSVPAG00000008668	1 retrocopy	retro_vpac_54,