RetrogeneDB ID: retro_mdom_289

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 2:258485675..258486383(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMODG00000023693
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000008669
• Aliases: None
• Description: None

Sequence

>retro_mdom_289
ATGTCATGCTATGGAAGATATGGAGGAGAGACCAAAGTATATGTTGGCAACCTGGAAACCGGTGCTGGTAAAGGAGAATT
AGAAAGAGCCTTTAGTTATTATGGTCCCTTAAGAACTGTATGGATTGCCAGAAATCCTCCAGGATTTGCCTTTGTGGAGT
TTGAAGATCCAAGAGATGCAGAAGATGCAGTCCAGGGTCTGGATGGAAAAGTGATTTGTGGCTCCCGAGTTAGAGTTGAA
TTGTCAACAGGCCTGCCTCGAAGATCCCGCTATGATAGACCACCTGCACGCTGCCCGTTCGATCCTAATGATAGATGTTA
CGAGTGTGGGGAGAAAGGTCATTATGCTTATGATTGTCATCGCTATAGCCGGCGAAGGAGAAGCAGATCACGATCTAGAT
CTCACTCAAGATCCCGAGGAAGGAGATATTCTCGCTCACGAAGCAGGAGCCGTGGAAGGAGATCAAGATCTGCATCTCCT
CGAAGACCTAGATCTGCATCTCTGCGTAGATCTAGATCTGCTTCAATTCAGTCTCGATCAGGTTCTTTAAAAAGATCGAG
ATCATCCCGTTCAAGATCCCGATCCAGGTCCAGGTCTCTTTCAAGACCTAGAAGCAGCCAATCAAAGTCCAGATCACCAT
CTCCAAAGAGAAGCCACTCACCTTCTGGAAGTCCTCGCAGGAGTGCAAGTCCTGAAAGAATGGACTAA

Alignment

ORF - retro_mdom_289 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.49 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSRYGRYGGETKVYVGNLGTGAGKGELERAFSYYGPLRTVWIARNPPGFAFVEFEDPRDAEDAVRGLDGK
          MS.YGRYGGETKVYVGNL.TGAGKGELERAFSYYGPLRTVWIARNPPGFAFVEFEDPRDAEDAV.GLDGK
Retrocopy MSCYGRYGGETKVYVGNLETGAGKGELERAFSYYGPLRTVWIARNPPGFAFVEFEDPRDAEDAVQGLDGK

Parental  VICGSRVRVELSTGMPRRSRYDRPPARRPFDPNDRCYECGEKGHYAYDCHRYSRRRRSRSRSRSHSRSRG
          VICGSRVRVELSTG.PRRSRYDRPPAR.PFDPNDRCYECGEKGHYAYDCHRYSRRRRSRSRSRSHSRSRG
Retrocopy VICGSRVRVELSTGLPRRSRYDRPPARCPFDPNDRCYECGEKGHYAYDCHRYSRRRRSRSRSRSHSRSRG

Parental  RRYSRSRSRSRGRRSRSASPRRSRSASLRRSRSASIRSRSGSLKRSRYFQSSRSRSRSRSLSRPRSSRSK
          RRYSRSRSRSRGRRSRSASPRR.RSASLRRSRSASI.SRSGSLKRSR....SRSRSRSRSLSRPRSS.SK
Retrocopy RRYSRSRSRSRGRRSRSASPRRPRSASLRRSRSASIQSRSGSLKRSR-SSRSRSRSRSRSLSRPRSSQSK

Parental  SRSPSPKRSRSPSGSPRRSASPERMD
          SRSPSPKRS.SPSGSPRRSASPERMD
Retrocopy SRSPSPKRSHSPSGSPRRSASPERMD

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	97.03 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	139.07 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_289 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_289 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 12 parental genes, and 25 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000015988	1 retrocopy	retro_amel_1025,
Canis familiaris	ENSCAFG00000029620	1 retrocopy	retro_cfam_652,
Dasypus novemcinctus	ENSDNOG00000007821	2 retrocopies	retro_dnov_317, retro_dnov_829,
Macropus eugenii	ENSMEUG00000016459	1 retrocopy	retro_meug_1048,
Myotis lucifugus	ENSMLUG00000009536	2 retrocopies	retro_mluc_2005, retro_mluc_972,
Monodelphis domestica	ENSMODG00000003107	1 retrocopy	retro_mdom_697,
Monodelphis domestica	ENSMODG00000008669	1 retrocopy	retro_mdom_289 ,
Monodelphis domestica	ENSMODG00000011362	1 retrocopy	retro_mdom_934,
Mus musculus	ENSMUSG00000024097	1 retrocopy	retro_mmus_3288,
Otolemur garnettii	ENSOGAG00000010169	2 retrocopies	retro_ogar_3467, retro_ogar_3481,
Rattus norvegicus	ENSRNOG00000027360	11 retrocopies	retro_rnor_1535, retro_rnor_1977, retro_rnor_1984, retro_rnor_2419, retro_rnor_2420, retro_rnor_2421, retro_rnor_2495, retro_rnor_2501, retro_rnor_2502, retro_rnor_2503, retro_rnor_478,
Sarcophilus harrisii	ENSSHAG00000015970	1 retrocopy	retro_shar_72,