RetrogeneDB ID: retro_mdom_1930

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 8:184039313..184039731(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PEF1
• Ensembl ID: ENSMODG00000017573
• Aliases: None
• Description: penta-EF-hand domain containing 1 [Source:HGNC Symbol;Acc:30009]

Sequence

>retro_mdom_1930
CCCCAGTATGAAGGCGGGCTGCCCCCTGGTGGGAGTTATGGAGGCCCAGCTCCTGAAGGGCCTTATGGACCACCATCTGG
TGGAGGGGTCTATGGACATCCCAGCCAAGGGGGCTCCCCTCAGGAGCTTCTGAAGGACCATATGGAGGCTCTGCCCCAGG
AGGTCCCTATGGCCAGCCTAGTATGAATCCCGATCATACCCCTTTCCCAGGACCTTCTGAGCAAGGCCCATCAGTAGGCA
GGTGTAGACCCCAAGCAGACTCCTGGCTCCATTCAGTGGATTCACATACCAGTGGGTACATCTCGGTGAAGGAGCTCAAG
CAAGCTTTGGTCCACTCCAATTGGTCCACAGTGATGAGACCTGCTTATTGATGATGAATACATTTGACAAAACTAAAGCA
GGCTGCATGGACCTCTGG

Alignment

ORF - retro_mdom_1930 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.11 %
• Parental protein coverage: 51.24 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  PQYGGGLPPGGGYGGPAPGGPYGPPSGGGAYGHPS-PGGLPSVAPGGPYGGSAPGGPYGQPATNPYNTPQ
          PQY.GGLPPGG.YGGPAP.GPYGPPSGGG.YGHPS.P.GLPS.A..GPYGGSAPGGPYGQP..NP..TP.
Retrocopy PQYEGGLPPGGSYGGPAPEGPYGPPSGGGVYGHPS<PRGLPSGASEGPYGGSAPGGPYGQPSMNPDHTPF

Parental  PGPYGQGPSVGGIPPGVDPEAYSWFHSVDSDHSGYISVKELKQALVNSNWSTF-NDETCLMMINMFDKTK
          PGP..QGPSVG...P..D....SW.HSVDS..SGYISVKELKQALV.SNWST.......LMM.N.FDKTK
Retrocopy PGPSEQGPSVGRCRPQAD----SWLHSVDSHTSGYISVKELKQALVHSNWSTV<DETCLLMM-NTFDKTK

Parental  AGRIDLY
          AG..DL.
Retrocopy AGCMDLW

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_1930 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1930 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 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000006355	1 retrocopy	retro_cjac_1745,
Homo sapiens	ENSG00000162517	1 retrocopy	retro_hsap_497,
Gorilla gorilla	ENSGGOG00000015897	1 retrocopy	retro_ggor_464,
Macropus eugenii	ENSMEUG00000014458	1 retrocopy	retro_meug_375,
Microcebus murinus	ENSMICG00000001374	1 retrocopy	retro_mmur_937,
Macaca mulatta	ENSMMUG00000023397	1 retrocopy	retro_mmul_146,
Monodelphis domestica	ENSMODG00000010355	1 retrocopy	retro_mdom_782,
Monodelphis domestica	ENSMODG00000017573	1 retrocopy	retro_mdom_1930 ,
Nomascus leucogenys	ENSNLEG00000001979	1 retrocopy	retro_nleu_2422,
Oryctolagus cuniculus	ENSOCUG00000005744	1 retrocopy	retro_ocun_461,
Pongo abelii	ENSPPYG00000001611	1 retrocopy	retro_pabe_238,
Pan troglodytes	ENSPTRG00000000463	1 retrocopy	retro_ptro_375,
Rattus norvegicus	ENSRNOG00000013972	2 retrocopies	retro_rnor_1563, retro_rnor_2505,