RetrogeneDB ID: retro_mdom_791

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 2:509313045..509313826(+)
• Located in intron of: ENSMODG00000006694

Retrocopy information

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

Parental gene information

• Parental gene symbol: KRR1
• Ensembl ID: ENSMODG00000020451
• Aliases: None
• Description: KRR1, small subunit (SSU) processome component, homolog (yeast) [Source:HGNC Symbol;Acc:5176]

Sequence

>retro_mdom_791
GCTTCTTTTCCACTTACATGGCCTAGGAAAGGGGCCATAGAAGCGGAAAATGGTTTTCGGAACCAGAAGTGGGGGAACCA
TGGTGTGGATGAATCAGAACTCCTCACTGTTCCTGATGGATGGAAAGAACCCCCATTTACAAAAGATGACAACCCCAGAG
GACTGTTAGAGGAAAACAGTTCTGCAACTTTGTTTCCCAAATACAGAGAAGCTTACCTGAAGGAATGTTGGCCTTTGGTG
CAGAAAGTGTTGCATGAACATCACCTAAATGCAACTCTGGACCTAATTGAGGGTATTATAACTGTTTGCGCAACTAAGAA
GACTTTTCATCCTTAGATTATCATCAAGGCCAGGAACTTAATAAATCTTTTAGGAAGAAGTATCCCATTTGAACAGGCAA
TAAGAATTCTTGAAGATAATACTGCTTGTGACATTATTAAGATTGGCTCTATAGTAAGAAACAAAGAGAGATCTGTAAAA
CGAAGACAAAGGCTTATTGGGCCAAAAGGATCTACTCTGAAGGCATTAGAACTGTTAACAAACTGTTGTTACATTATGGT
TCAGGGGAACACTGTTTCAGCTCTTGGGCCACTTAATAGTTTAAAAGAAGTTAAAAAAGTATTCCTGGATACAATAAAAG
ATCTTCATCCAATCTATAACATCAAAACACTTGATGATTAACCAAGAGCTCTCAAAGGATGCTGAATTAACATCACAAAA
TTGGGAAAGGTTTTTGCCACAGTTCAAACACAAAAATTTGAATAAACACAAGGAACCAAAG

Alignment

ORF - retro_mdom_791 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.44 %
• Parental protein coverage: 67.62 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  ASSPPARLGKGAIEAENGFRNQKRGNRGVDESELLTVPDGWKEPPFTKDDNPRGLLEESSFATLFPKYRE
          AS.P.....KGAIEAENGFRNQK.GN.GVDESELLTVPDGWKEPPFTKDDNPRGLLEE.S.ATLFPKYRE
Retrocopy ASFPLTWPRKGAIEAENGFRNQKWGNHGVDESELLTVPDGWKEPPFTKDDNPRGLLEENSSATLFPKYRE

Parental  AYLKECWPLVQKALHEHHINATLDLIEGSMTVCTTKKTFDPYIIIRARDLIKLLARSVPFEQAIRILEDN
          AYLKECWPLVQK.LHEHH.NATLDLIEG..TVC.TKKTF.P.III.AR.LI.LL.RS.PFEQAIRILEDN
Retrocopy AYLKECWPLVQKVLHEHHLNATLDLIEGIITVCATKKTFHP*IIIKARNLINLLGRSIPFEQAIRILEDN

Parental  NACDIIKIGSLVRNKERFVKRRQRLIGPKGSTLKALELLTN-CYIMVQGNTVSALGPFNGLKEVRKVVLD
          .ACDIIKIGS.VRNKER.VKRRQRLIGPKGSTLKALELLTN.CYIMVQGNTVSALGP.N.LKEV.KV.LD
Retrocopy TACDIIKIGSIVRNKERSVKRRQRLIGPKGSTLKALELLTNCCYIMVQGNTVSALGPLNSLKEVKKVFLD

Parental  TMKNIHPIYNIKT-LMIKRELSKDAELRSQNWERFLPQFKHKNLNKRKEPK
          T.K..HPIYNIKT.LMI..ELSKDAEL.SQNWERFLPQFKHKNLNK.KEPK
Retrocopy TIKDLHPIYNIKT>LMINQELSKDAELTSQNWERFLPQFKHKNLNKHKEPK

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_791 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_791 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 5 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006437	1 retrocopy	retro_amel_1292,
Canis familiaris	ENSCAFG00000005665	1 retrocopy	retro_cfam_1091,
Choloepus hoffmanni	ENSCHOG00000009636	5 retrocopies	retro_chof_1030, retro_chof_1826, retro_chof_2438, retro_chof_2452, retro_chof_365,
Monodelphis domestica	ENSMODG00000020451	1 retrocopy	retro_mdom_791 ,
Tupaia belangeri	ENSTBEG00000008145	5 retrocopies	retro_tbel_1056, retro_tbel_2060, retro_tbel_2911, retro_tbel_2915, retro_tbel_3679,