RetrogeneDB ID: retro_mdom_239

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 5:66994103..66995348(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMODG00000028257
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000018500
• Aliases: None
• Description: None

Sequence

>retro_mdom_239
ATGGTGGCTCATGATGAGATTGGAAGTTTTCTGCCTATTAAAAGGACTATTCGTGTCCTCGATGTTAATAATCAGTCCTT
TAGAGAACAAGAGGAGCCAAGCAACAAAAGAGTTCGATCTCTGGCTCGAGTCTCATCTTTGGCAAATTTAATCTCTCCTG
TGAGAAATGGAGCAGTCAAACGTTTTGGTCAAACGATACAGTCATTTACACTTCGTGGTGACAACAGATCTCCTGCTTGT
GCCCAGAAATCATTTAACAGGGCTACTGTCCCAACTCCTTCTAAAAGAAGAAACAGTGTACGATGGTCAGAGATGTTAGA
TATCAACATGAAAGAATCTTTAACCACCAAAGAAATCAAACGTCAAGAGGCAATATATGAAATGCTCCGAGGAGAACAGG
ATTTAATTGAGGATCTTAAGCCTGCCAGAAAGGCCTACCATGATCCTATGTTGAAGTTATCTATCATGTCTGAGGAAGAA
CTCACACATATATTTGGAGATTTAGATGCTTACATACCTCTGCATGAAGATCTGTTGGCAAGATTAGGAGAAGCAACAAA
GCCAGATGGGACAGTGGAGCAAATTGGTCATATTCTTGTGAACTGGTTGCCAGGTTTAAATGCTTATAGAGGCTACTGCA
GTAACCAGCTTGCAGCTAACGCTCTTCTTGATCAGAAAAAACAAGATGCAAGAGTTCAAGATTTCCTTCAGCGTTGTCTT
GAGTCTCCTTTCAGTAGGAAATTAGACCTCTGGAGTTTCCTGGACATTCCTCGAAGTCGCCTAGTTAAATATCCCTTGTT
GTTAAAAGAAATTCTCAGACATACACCCAAAGACCACACTGATATAAAACCTCTAGAAGAAGCTCTATTGGTAATACAAG
GAGTACTCTCTGATATCAACTTGAAGAAAGGAGAATCAGAATGCCAATATTATATTGATAAACTGGAATATCTGGATGAC
AAACAGAAGGATCCTAGGATTGAAGCTAGCAAGGTGTTGCTTTGCCATGGAGAACTGAAGAATAAAAATGGACATAAACT
CTATATTTTCTTGTTTCAAGACATCCTTGTCTTGACTCGTCCTGTTATACGCAATGAACGCCACTCCTATCAAGTATACC
GTCAGCCTATTCCTGTCAAGGAGCTGGTGTTAGAGGACCTGCAGGATGGTGATGTGAGAATGGGAGGTTCCTTTAGAGGT
GCTTTTAGCAACTCAGACAAAGGTAAAGAAAAAAGTTTTAGATAA

Alignment

ORF - retro_mdom_239 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.7 %
• Parental protein coverage: 62.46 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KRREKDDDVVSLSSLDLKEPSNKRVRSLARVSSLANLISPVRNGAVKRFECKLRSFTLRGDNRSPACAQK
          KR.....DV...S.....EPSNKRVRSLARVSSLANLISPVRNGAVKRF.....SFTLRGDNRSPACAQK
Retrocopy KRTIRVLDVNNQSFREQEEPSNKRVRSLARVSSLANLISPVRNGAVKRFGQTIQSFTLRGDNRSPACAQK

Parental  SFNRATVPTPSKRRNSVRWSEMLDINMKESLTTKEIKRQEAIYEMLRGEQDLIEDLKLARKAYHDPMLKL
          SFNRATVPTPSKRRNSVRWSEMLDINMKESLTTKEIKRQEAIYEMLRGEQDLIEDLK.ARKAYHDPMLKL
Retrocopy SFNRATVPTPSKRRNSVRWSEMLDINMKESLTTKEIKRQEAIYEMLRGEQDLIEDLKPARKAYHDPMLKL

Parental  SIMSEEELTHIFGDLDAYIPLHEDLLARLGEATKPDGTVEQIGHILVNWLPGLNAYRGYCSNQLAAKALL
          SIMSEEELTHIFGDLDAYIPLHEDLLARLGEATKPDGTVEQIGHILVNWLPGLNAYRGYCSNQLAA.ALL
Retrocopy SIMSEEELTHIFGDLDAYIPLHEDLLARLGEATKPDGTVEQIGHILVNWLPGLNAYRGYCSNQLAANALL

Parental  DQKKQDARVQDFLQRCLESPFSRKLDLWSFLDIPRSRLVKYPLLLKEILRHTPKDHTDIKPLEEALLVIQ
          DQKKQDARVQDFLQRCLESPFSRKLDLWSFLDIPRSRLVKYPLLLKEILRHTPKDHTDIKPLEEALLVIQ
Retrocopy DQKKQDARVQDFLQRCLESPFSRKLDLWSFLDIPRSRLVKYPLLLKEILRHTPKDHTDIKPLEEALLVIQ

Parental  GVLSDINLKKGESECQYYIDKLEYLDDKQKDPRIEASKVLLCHGELKNKNGHKLYIFLFQDILVLTRPVI
          GVLSDINLKKGESECQYYIDKLEYLDDKQKDPRIEASKVLLCHGELKNKNGHKLYIFLFQDILVLTRPVI
Retrocopy GVLSDINLKKGESECQYYIDKLEYLDDKQKDPRIEASKVLLCHGELKNKNGHKLYIFLFQDILVLTRPVI

Parental  RNERHSYQVYRQPIPVKELVLEDLQDGDVRMGGSFRGAFSNSDKAK
          RNERHSYQVYRQPIPVKELVLEDLQDGDVRMGGSFRGAFSNSDK.K
Retrocopy RNERHSYQVYRQPIPVKELVLEDLQDGDVRMGGSFRGAFSNSDKGK

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_239 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_239 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 3 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000010007	1 retrocopy	retro_chof_1896,
Monodelphis domestica	ENSMODG00000018500	2 retrocopies	retro_mdom_21, retro_mdom_239 ,
Mus musculus	ENSMUSG00000021215	1 retrocopy	retro_mmus_1144,