RetrogeneDB ID: retro_mdom_1179

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 3:378478113..378478915(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: C1orf51
• Ensembl ID: ENSMODG00000018781
• Aliases: None
• Description: chromosome 1 open reading frame 51 [Source:HGNC Symbol;Acc:25200]

Sequence

>retro_mdom_1179
AAGTGTAAAGAGCTCCAATGATTCATTTGCCCCCTTAAAGACCTGTTGAATGGGCTGAAGACAGGCCTCTATGAGAGAGG
ATTAAGCAGTTTTCAACAAAGTGTGGCAATGGACAGGAACTGTCATGTAGTAGGGGTCCTACAGAAGACTGAGATAGGTG
AGCATTATCTAGGGACCTTGCTACAATTAGAGACTATGTTGAAGACCTGGTTCCCTCATATTGCCTCTCAAAGGGCACTC
CAGGGGATGGAAAGCACAAGCTTCTCTCGAAGTATTTGCTATCAGTCAGGCATACCCAACTGGTCCCTCAGCTGATCTTG
CTAGAAAGGAGGTGAATCAGATTCAGTTAAGACATATAGATCCAGGAAAAAGAGAAGTTGCATTCTCAAGAACAAGAGTT
GCCCCAACTCCTCCCTGAATGGTCAGTCATGAACTTGACATGGATCCACACAACCCCTATTTACAATCCACCTTTCAGTT
CCTTTGGCTCAGCAGCCTTCAGTCATGGTCTTTTGGGTCCTGGGGCAAGCTTGGGTTTAACCTCTTCCTTCAACATTGAA
CACAATATTTTGCATGTTTATCACCCATCACTTCTGTCCCCTATTCTGCAGTGTCTTCTGTTGTCTGTGATGGTCCAAAG
AACATCTCTGAAGAAGAACCTCATTGCTACAGTTTTCCAGTTTCTCTAGCATCTACTCCACTGACCTCAAAGAGGAGCCA
TTCTCTGTCCTGACCCTGTTTACCCACTGTGACCAGAAAGAACACAACTAGAATGGATGAAAAACAGGCCCTTCATTTCT
GC

Alignment

ORF - retro_mdom_1179 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.62 %
• Parental protein coverage: 68.72 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  KCKELQGFIRPLTDLLNGLKMGRYERGLSSFQQSVAMDRIQRIVGVLQKPEMGERYLGTLLQVEGMLKTW
          KCKELQ.FI.PL.DLLNGLK.G.YERGLSSFQQSVAMDR....VGVLQK.E.GE.YLGTLLQ.E.MLKTW
Retrocopy KCKELQ*FICPLKDLLNGLKTGLYERGLSSFQQSVAMDRNCHVVGVLQKTEIGEHYLGTLLQLETMLKTW

Parental  FPHVASQRA-TPGDGKHRLLSKRLAS-SQANPTGPSADLARKNLNQIQLRHLDQGK-EKLHSQEQELPQL
          FPH.ASQRA.TPGDGKH.LLSK.L.S.SQA.PTGPSADLARK..NQIQLRH.D.GK.EKLHSQEQELPQL
Retrocopy FPHIASQRA<TPGDGKHKLLSKYLLS<SQAYPTGPSADLARKEVNQIQLRHIDPGK>EKLHSQEQELPQL

Parental  LPEWPAMNLTWIHTTPICNPPLSSLGSAAFSHGLLGPGASFG-FILFLQHGAQSFARSAPTTPVPYSAVS
          LPEW..MNLTWIHTTPI.NPP.SS.GSAAFSHGLLGPGAS.G.F.LFLQH..Q.FA...P.T.VPYSAVS
Retrocopy LPEWSVMNLTWIHTTPIYNPPFSSFGSAAFSHGLLGPGASLG<FNLFLQH*TQYFACLSPITSVPYSAVS

Parental  SVVCDGPKNISEEEPRCYSLPVSLSSTPLTSERSHSLSSPCLPTVTREKTPRMDEKQALHFC
          SVVCDGPKNISEEEP.CYS.PVSL.STPLTS.RSHSLS.PCLPTVTR..T.RMDEKQALHFC
Retrocopy SVVCDGPKNISEEEPHCYSFPVSLASTPLTSKRSHSLS*PCLPTVTRKNTTRMDEKQALHFC

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_1179 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1179 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 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000008999	1 retrocopy	retro_chof_2196,
Monodelphis domestica	ENSMODG00000018781	1 retrocopy	retro_mdom_1179 ,
Mus musculus	ENSMUSG00000038550	1 retrocopy	retro_mmus_685,