RetrogeneDB ID: retro_mdom_734

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 2:258708520..258709243(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PDCL3
• Ensembl ID: ENSMODG00000001489
• Aliases: None
• Description: phosducin-like 3 [Source:HGNC Symbol;Acc:28860]

Sequence

>retro_mdom_734
ATGCAGGATCCCAATGCAAACACTGAGTGGAATGACATCTTGCGCAAGAAGGGGATATTCCCCCTAAAAGAAAGTTTGAA
AGAGCTGGAAAAGAAGAGGGAAGAGGAGGAAGAGAATCACATCCTTCAGCAATCAATAGTGAAAACATATAAACATATAA
CTTTGGAAGAACTAGAAGAAAATGAAGATGAATTTAATGAGGAAGATGAGCGTGCTATTGAAATGTACAGGAAACAAAGG
CTTGCAGAATGGAAAGTGACTCAATTAAAGAACAAATTTGGAGAAGTGTTAGAGATATCAGGCAAAGATTATGTTCAAGA
AGTTACCAAAGCTGGCAAAGACTTGTGGGTAATTTTGCACTTTTACAAACCAGGAATCCCTCTCTGTACACTTATAAACC
AGCACTTTAGTGGACTTGCAAGGAAGTTTCCTGATGTGAAATTTATCAAAGCTATCTCAAAGACTTGCATACCCAACAAT
CCTGATAGGAATCTGCCCACAATATTTGTCTACCTTGTGGGTGATATCTAAGCCCAGTTTATTGGTCCTTTAGTATTTGG
TGGCATGAATCTGAAAAGGGATGAAATGGAGTGGAAACTTTCTGAATCTGGAGATATCAAAACTGATCTGGAGGAAAACC
CAAAGAAACAGATTGAAGATAAATTGATGTCCTCAGTCAGGTGCTCTCTCCCAACAAAGAAAGAAAGTGATTCAGAGGAT
GAC

Alignment

ORF - retro_mdom_734 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.78 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MQDPNADTEWNDILRKKGILPPKESLKELEKKREEEEENHILQQSVVKTYEDMTLEELEENEDEFNEEDE
          MQDPNA.TEWNDILRKKGI.P.KESLKELEKKREEEEENHILQQS.VKTY...TLEELEENEDEFNEEDE
Retrocopy MQDPNANTEWNDILRKKGIFPLKESLKELEKKREEEEENHILQQSIVKTYKHITLEELEENEDEFNEEDE

Parental  RAIEMYRKQRLAEWKATQLKNKFGEVLEISGKDYVQEVTKAGKDLWVILHLYKPGIPLCTLINQHFSGLA
          RAIEMYRKQRLAEWK.TQLKNKFGEVLEISGKDYVQEVTKAGKDLWVILH.YKPGIPLCTLINQHFSGLA
Retrocopy RAIEMYRKQRLAEWKVTQLKNKFGEVLEISGKDYVQEVTKAGKDLWVILHFYKPGIPLCTLINQHFSGLA

Parental  RKFPDVKFIKAISTTCIPNYPDRNLPTIFVYLEGDIKAQFIGPLVFGGMNLKRDELEWKLSESGAIKTDL
          RKFPDVKFIKAIS.TCIPN.PDRNLPTIFVYL.GDI.AQFIGPLVFGGMNLKRDE.EWKLSESG.IKTDL
Retrocopy RKFPDVKFIKAISKTCIPNNPDRNLPTIFVYLVGDI*AQFIGPLVFGGMNLKRDEMEWKLSESGDIKTDL

Parental  EENPKKQIEDKLMSSVRCSLPTKKESDSEDD
          EENPKKQIEDKLMSSVRCSLPTKKESDSEDD
Retrocopy EENPKKQIEDKLMSSVRCSLPTKKESDSEDD

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_734 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_734 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 15 parental genes, and 34 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000002226	1 retrocopy	retro_cfam_1740,
Callithrix jacchus	ENSCJAG00000010160	3 retrocopies	retro_cjac_1486, retro_cjac_1599, retro_cjac_2055,
Dipodomys ordii	ENSDORG00000012397	1 retrocopy	retro_dord_702,
Erinaceus europaeus	ENSEEUG00000000224	1 retrocopy	retro_eeur_506,
Homo sapiens	ENSG00000115539	7 retrocopies	retro_hsap_1132, retro_hsap_151, retro_hsap_2684, retro_hsap_2757, retro_hsap_3535, retro_hsap_3961, retro_hsap_4102,
Microcebus murinus	ENSMICG00000000657	1 retrocopy	retro_mmur_899,
Myotis lucifugus	ENSMLUG00000016446	1 retrocopy	retro_mluc_1443,
Monodelphis domestica	ENSMODG00000001489	1 retrocopy	retro_mdom_734 ,
Monodelphis domestica	ENSMODG00000020680	2 retrocopies	retro_mdom_1048, retro_mdom_993,
Mus musculus	ENSMUSG00000026078	1 retrocopy	retro_mmus_2284,
Nomascus leucogenys	ENSNLEG00000014393	8 retrocopies	retro_nleu_1499, retro_nleu_1575, retro_nleu_2741, retro_nleu_2891, retro_nleu_538, retro_nleu_571, retro_nleu_778, retro_nleu_926,
Oryctolagus cuniculus	ENSOCUG00000001469	2 retrocopies	retro_ocun_1035, retro_ocun_920,
Otolemur garnettii	ENSOGAG00000015138	2 retrocopies	retro_ogar_1147, retro_ogar_2959,
Ochotona princeps	ENSOPRG00000011600	2 retrocopies	retro_opri_1070, retro_opri_289,
Tursiops truncatus	ENSTTRG00000006242	1 retrocopy	retro_ttru_1184,