RetrogeneDB ID: retro_mdom_167

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: Un:73657860..73658916(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMODG00000022599
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000018535
• Aliases: None
• Description: None

Sequence

>retro_mdom_167
ACTATGTCCCACCAGACTGGCATCCAAGCAAGTGATGAAGTCAAAGGTATCTTTGCCAAAGCAAGAAACGGGAAATACAG
ACTTCTAAAGATTTCAATTGAGGATGAACAACTTGTAGTTGGATCTTCTAGTCAGCCTGCAGAGACTTGGGATAAAGATT
ATGATACTTTCATTCTACCACTATTAGAAGAGAAGCAACCATGCTACATATTGTACAGGTTAGATTCTCAGAATGCACAA
GGATATGAGTGGATCTTCATTGCATGGTCACCAGACTATTCTCACGTTCGTCAAAAAATGTTGTATGCAGCAACCAGAGC
AACTCTGAAAAAGGAGTTTGGAGGTGGTCATATTAAAGATGAAATATTTGGGACAGTGAAGGAAGATGTTTCATTGAATG
GATATAGAAAATATTTGATATCTCAGTCCTCCCCAGCTCCACTGACTGCAGCTGAGGAAGAATTACGGCAAATTAAAATT
AATGAGGTCCAAACTGATGTTGGTGTGGACACTAAGCATCAAACACTACAAGGAGTAGCATTCCCTATTGCTGGAGAAGC
TCTTCAAGCTTTGGAAAAATTGAATAATAGACAGCTCAACTATGTACAGTTGGAAATAGATATAAAAAATGAAGTTATTA
TTTTGGCCAACACAACAAATACAGAGCTAAAAGACTTGCCAAAAAGGATTCCAAAGGACTCGGCACGTTATCATTTCTTT
CTGTATAAACATTCCCATGAAGGAGACTATTTGGAGTCTATAGTTTTTATTTACTCAATGCCTGGGTACACATGCAGCAT
AAAGGAACGGATGCTTTATTCTAGCTGCAAAAGTACTCTGCTAGAAATTGTAGAAAGAAAACTACAGATGGATATAATTA
GAAAGATTGAAATAGATAATGGAGATGAATTAACTGCAGACTTCCTTTATGAAGAAGTACATCCAAAACAACATGCACAT
AAGCAGAGTTTTGCTAAACCAAAAGGTCCTGCAGGAAAAAGAGGAATTAGAAGACTAATTAGGGGTCCAGCTGAAACTGA
AGCTACTACTGAGTGA

Alignment

ORF - retro_mdom_167 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 100. %
• Parental protein coverage: 93.35 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  TMSHQTGIQASDEVKGIFAKARNGKYRLLKISIEDEQLVVGSSSQPAETWDKDYDTFILPLLEEKQPCYI
          TMSHQTGIQASDEVKGIFAKARNGKYRLLKISIEDEQLVVGSSSQPAETWDKDYDTFILPLLEEKQPCYI
Retrocopy TMSHQTGIQASDEVKGIFAKARNGKYRLLKISIEDEQLVVGSSSQPAETWDKDYDTFILPLLEEKQPCYI

Parental  LYRLDSQNAQGYEWIFIAWSPDYSHVRQKMLYAATRATLKKEFGGGHIKDEIFGTVKEDVSLNGYRKYLI
          LYRLDSQNAQGYEWIFIAWSPDYSHVRQKMLYAATRATLKKEFGGGHIKDEIFGTVKEDVSLNGYRKYLI
Retrocopy LYRLDSQNAQGYEWIFIAWSPDYSHVRQKMLYAATRATLKKEFGGGHIKDEIFGTVKEDVSLNGYRKYLI

Parental  SQSSPAPLTAAEEELRQIKINEVQTDVGVDTKHQTLQGVAFPIAGEALQALEKLNNRQLNYVQLEIDIKN
          SQSSPAPLTAAEEELRQIKINEVQTDVGVDTKHQTLQGVAFPIAGEALQALEKLNNRQLNYVQLEIDIKN
Retrocopy SQSSPAPLTAAEEELRQIKINEVQTDVGVDTKHQTLQGVAFPIAGEALQALEKLNNRQLNYVQLEIDIKN

Parental  EVIILANTTNTELKDLPKRIPKDSARYHFFLYKHSHEGDYLESIVFIYSMPGYTCSIKERMLYSSCKSTL
          EVIILANTTNTELKDLPKRIPKDSARYHFFLYKHSHEGDYLESIVFIYSMPGYTCSIKERMLYSSCKSTL
Retrocopy EVIILANTTNTELKDLPKRIPKDSARYHFFLYKHSHEGDYLESIVFIYSMPGYTCSIKERMLYSSCKSTL

Parental  LEIVERKLQMDIIRKIEIDNGDELTADFLYEEVHPKQHAHKQSFAKPKGPAGKRGIRRLIRGPAETEATT
          LEIVERKLQMDIIRKIEIDNGDELTADFLYEEVHPKQHAHKQSFAKPKGPAGKRGIRRLIRGPAETEATT
Retrocopy LEIVERKLQMDIIRKIEIDNGDELTADFLYEEVHPKQHAHKQSFAKPKGPAGKRGIRRLIRGPAETEATT

Parental  E
          E
Retrocopy E

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_167 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_167 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 10 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017332	1 retrocopy	retro_amel_1224,
Choloepus hoffmanni	ENSCHOG00000008386	5 retrocopies	retro_chof_1525, retro_chof_2013, retro_chof_2569, retro_chof_391, retro_chof_509,
Homo sapiens	ENSG00000151239	2 retrocopies	retro_hsap_1819, retro_hsap_4916,
Monodelphis domestica	ENSMODG00000018535	1 retrocopy	retro_mdom_167 ,
Mustela putorius furo	ENSMPUG00000000364	1 retrocopy	retro_mputfur_1629,
Mus musculus	ENSMUSG00000022451	1 retrocopy	retro_mmus_2961,
Nomascus leucogenys	ENSNLEG00000017931	1 retrocopy	retro_nleu_2877,
Otolemur garnettii	ENSOGAG00000007525	1 retrocopy	retro_ogar_1058,
Pan troglodytes	ENSPTRG00000004846	1 retrocopy	retro_ptro_3279,
Rattus norvegicus	ENSRNOG00000022507	1 retrocopy	retro_rnor_2176,