RetrogeneDB ID: retro_mdom_134

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 3:434116787..434119106(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMODG00000009043
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000012160
• Aliases: None
• Description: None

Sequence

>retro_mdom_134
ATCAAACAAATAACATCTTGGGGGGAAAAAATGGAAGCTTCCTATCAAGTTTTAGAACAGTTATATAAGGAGGTACTTCT
TGAAGCTACACTTGAAAATGATAGCCAGGAATATGCATTTCATCTCAATCTATCATTTTCAGCCCAAGATTTATCCACAT
CAAATTTCCTAAAGTGGCCAAGTGTTCATCATGGTGACCAGGCTAATTCTGTTAACGTGGATACCTTTCCCACTCCAACA
GCATCAATAAATTTAAAAATGAATTTTCAAGTTAATAACCCCAGAGATATAATGCTACTTCAACTAACAGTAATCAAGAT
GATGATAACCAAAATATTATCCACAAAAATGGAATTCAGTATAAAAGAGAAGTACAGTGATATAATTGAAATTCTTTTAA
AGCCTTATGAACTGGAATCCAAATTAATCAGCACATTCCATGGTTCTGATAAGTTATTGTCTCATATGGCTGCAAAGTGT
CTTGCCTCAATATTATATTTACAACTAAGAGAAAAAGCTATAATAAATAAAACATGGACGGCTTTTTGTTTAAAAACTCT
TTCTGACTATCCTGAAAGTAATGCAATTTCATATTGTCTCTGGACTCTTACAGCCGTGATAAAAGAAATATTGAAAGCTA
CATGTTTACAAAAAACAGAAATATTGAAGCAGTTTTTGACATCTTTTGATTCTCCTTTTGAAGTCTTTTACTATTCAGTT
TTTTCTCAGTATTTTGAAAACTGTCAAGATTCTTTACTAAATCCCCGAATTACAAATTTCTTGATTTGTTTTTTGGAATT
TCTTGAAATTCTAATAGCCTCCCGAATTTACCTGAAGTTACATTTTACTTGCCAGAGGATTTTTTATTTGAACATATCTT
GTGCTTTGGATATTATTACCTGGCCTATTCACTCTTTAGTCAAAAAGAAGTTTATCATACTTATTAAAAGATGTCTACTA
CATAAAGTGGGTGAGGATGCCCTAAAAACTTCATTTCCCACTTCAGTTATACAAGATCCTTATTTAGATATGGACATGTT
AGCTTTGGGCAATGCTTTTTTGCAAGCTGTGAATTTGGGATGGTTGAAGCAATTAACTATAAGTAGAAAACCCAGCCATT
TTGGAGGCAGTGAAGTTCAACCTGGAAATAAAAGTCTTCTTGTCCCTGATCTCATTATGCTCAGAGCATCAAGTTTGGTT
TTACTGAAATCTTTAGAAATCAAGGCGCATAATTGTACATCAGCAATTGAAATAAAAGTTGAATTACAGAAATTCATGTC
TGAGTTGCTGGCCATCTTGAAACACCATCTTCAGTCTTCCTTAAAACTGAATCATCACTGTGAATGGCTGTCTAAAATCT
TCATAGAACAAGATGATGACATGCTAGAGGCTGCAAAAGCATCATTAGGCATTTACCAAAAGCTGACTAGAGCATGGAAT
GAAGCTGCTAAGGGCACGACCCAAGAAAAAGAAACTTGGGACCATCAGACACATGAAAATGGCCTTAATCCTCACTGTAT
TTTCTTATTTCTCTTAAAAAATATTGATTTTGATGCAACAGTTCTCCTTGACTTTTTAATTTCATCAGAAACCTGCTTTC
TTGAATACTTTGTTAGGTATTTAAAACTGCTCCAAGTAGAAAGGAACCATTTTTTAAAAGTTTGTAAGTTCTTTGATGTA
GCAGAATTAAGAGATGATATGCATATTTCTAGTACTTTCACTTCATATATTGAAAAAAGACACAGCAATGAAGCTCCTCA
CCAGCCTCTTTTTTGTGGTACAAATTATGCTCTTTTGCCCTTGACTTCTGATCCTACTTCTTCTGGAACAAATATTGAAC
AAAGAGACAACCAGACAATGAAGTCTAAGCAACCTAACTTACTGATATGCACTGATAACACATCTTCACTGGGAGCCTTT
CAACGCCTGGTTGATTATGACAGCTCAGAGGAGTCTGAAGAGGAGTCAGTGGAAGAAGAATGTTTATCAAGCATTAAACA
GACTCCTTTGAACCATCAAGCCAATATGAAGATAAGGGAAACTGTTAATATGACTGAAGAAAAGAACCAGAATATCTTAG
ATTTTAATGCCAGATTACTAGATCCAAAAAAGTCTTCTACTTTGTCATCTTTAGGTTGTGAAGCTACCCTAAATAATACT
GCTTCCCAAACTGTAATATCTTCTAAAACACTTAAATGCTTGAAAGAGCTAGAAGAGGCAATTTCCCGTTTGCAGAGGAG
ACATCTCTTTCCATACAATCCTTCGGCATTATTGAAATTGTTAAAACACACTGAAATGATAAATAAGACTGTGAACCTG

Alignment

ORF - retro_mdom_134 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.35 %
• Parental protein coverage: 99.61 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GKKMEASYQVLEQLYKEVLLEATLENDSQEYAFHLNLSFSAQDLSTSNFLKWPSVHHGDQANSVNVDTFP
          G.KMEASYQVLEQLYKEVLLEATLENDSQEYAFHLNLSFSAQDLSTSNFLKWPSVHHGDQANSVNVDTFP
Retrocopy GEKMEASYQVLEQLYKEVLLEATLENDSQEYAFHLNLSFSAQDLSTSNFLKWPSVHHGDQANSVNVDTFP

Parental  TPTASINLKMNFQVNNPRDIMLLQLTVIKMMITKILSTKMEFSIKEKYSDIIEILLKPYELESKLISTFH
          TPTASINLKMNFQVNNPRDIMLLQLTVIKMMITKILSTKMEFSIKEKYSDIIEILLKPYELESKLISTFH
Retrocopy TPTASINLKMNFQVNNPRDIMLLQLTVIKMMITKILSTKMEFSIKEKYSDIIEILLKPYELESKLISTFH

Parental  GSDKLLSHMAAKCLASILYLQLREKAIINKTWTAFCLKTLSDYPESNAISYCLWTLTAVIKEILKATCLQ
          GSDKLLSHMAAKCLASILYLQLREKAIINKTWTAFCLKTLSDYPESNAISYCLWTLTAVIKEILKATCLQ
Retrocopy GSDKLLSHMAAKCLASILYLQLREKAIINKTWTAFCLKTLSDYPESNAISYCLWTLTAVIKEILKATCLQ

Parental  KTEILKQFLTSFDSPFEVFYYSVFSQYFENCQDSLLNPRITNFLICFLEFLEILIASRIYLKLHFTCQRI
          KTEILKQFLTSFDSPFEVFYYSVFSQYFENCQDSLLNPRITNFLICFLEFLEILIASRIYLKLHFTCQRI
Retrocopy KTEILKQFLTSFDSPFEVFYYSVFSQYFENCQDSLLNPRITNFLICFLEFLEILIASRIYLKLHFTCQRI

Parental  FYLNISCALDIITWPIHSLVKKKFIILIKRCLLHKVGEDALKTSFSTSVIQDPYLDMDMLALGNAFLQAV
          FYLNISCALDIITWPIHSLVKKKFIILIKRCLLHKVGEDALKTSF.TSVIQDPYLDMDMLALGNAFLQAV
Retrocopy FYLNISCALDIITWPIHSLVKKKFIILIKRCLLHKVGEDALKTSFPTSVIQDPYLDMDMLALGNAFLQAV

Parental  NLGWLKQLTISRKPSHFGGSEVQPGNKSLLVPDLIMLRASSLVLLKSLEIKAHNCTSAIEIKVELQKFMS
          NLGWLKQLTISRKPSHFGGSEVQPGNKSLLVPDLIMLRASSLVLLKSLEIKAHNCTSAIEIKVELQKFMS
Retrocopy NLGWLKQLTISRKPSHFGGSEVQPGNKSLLVPDLIMLRASSLVLLKSLEIKAHNCTSAIEIKVELQKFMS

Parental  ELLAVLKHHLPSSLKLNHHCEWLSKIFIEQDDDMLEAAKASLGIYQKLTRAWNEAAKGTTQEKETWDHQT
          ELLA.LKHHL.SSLKLNHHCEWLSKIFIEQDDDMLEAAKASLGIYQKLTRAWNEAAKGTTQEKETWDHQT
Retrocopy ELLAILKHHLQSSLKLNHHCEWLSKIFIEQDDDMLEAAKASLGIYQKLTRAWNEAAKGTTQEKETWDHQT

Parental  HENGLNPHCIFLFLLKNIDFDATVLLDFLISSETCFLEYFVRYLKLLQVERNHFLKVCKFFDVAELRDDM
          HENGLNPHCIFLFLLKNIDFDATVLLDFLISSETCFLEYFVRYLKLLQVERNHFLKVCKFFDVAELRDDM
Retrocopy HENGLNPHCIFLFLLKNIDFDATVLLDFLISSETCFLEYFVRYLKLLQVERNHFLKVCKFFDVAELRDDM

Parental  HISSTFTSYIEKRHSNEAPHQPHFCGTNYALLPLTSDPTSSGTNIEQRDNQTMKSKQPNLLICTDNTSSL
          HISSTFTSYIEKRHSNEAPHQP.FCGTNYALLPLTSDPTSSGTNIEQRDNQTMKSKQPNLLICTDNTSSL
Retrocopy HISSTFTSYIEKRHSNEAPHQPLFCGTNYALLPLTSDPTSSGTNIEQRDNQTMKSKQPNLLICTDNTSSL

Parental  GAFQRLVDYDSSEESEEESVEEECLSSIKQTPLNHQANMKIRETVNMTEEKNQNILDFNARLLDPKKSST
          GAFQRLVDYDSSEESEEESVEEECLSSIKQTPLNHQANMKIRETVNMTEEKNQNILDFNARLLDPKKSST
Retrocopy GAFQRLVDYDSSEESEEESVEEECLSSIKQTPLNHQANMKIRETVNMTEEKNQNILDFNARLLDPKKSST

Parental  LSSLGCEATLNNTASQTVISSKTLKCLKELEEAISRLQRRHLFPYNPSALLKLLKHTEMINKTVNL
          LSSLGCEATLNNTASQTVISSKTLKCLKELEEAISRLQRRHLFPYNPSALLKLLKHTEMINKTVNL
Retrocopy LSSLGCEATLNNTASQTVISSKTLKCLKELEEAISRLQRRHLFPYNPSALLKLLKHTEMINKTVNL

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	5.60 RPM
SRP007412_cerebellum	0.00 RPM	3.92 RPM
SRP007412_heart	0.00 RPM	1.20 RPM
SRP007412_kidney	0.00 RPM	1.32 RPM
SRP007412_liver	0.00 RPM	0.00 RPM
SRP007412_testis	0.00 RPM	11.39 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_134 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_134 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000009790	1 retrocopy	retro_dnov_1742,
Monodelphis domestica	ENSMODG00000012160	1 retrocopy	retro_mdom_134 ,