RetrogeneDB ID: retro_mdom_1511

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 5:75726292..75726847(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: C6orf136
• Ensembl ID: ENSMODG00000015898
• Aliases: None
• Description: chromosome 6 open reading frame 136 [Source:HGNC Symbol;Acc:21301]

Sequence

>retro_mdom_1511
GTGTCTCTTCCTTCTGGGAAGGGGGAGGATGGACCAGGGCTAGGATTGCACAGAGGCAGCCTGGAGGAGCTTAGAAGCCT
CTCTGAAGAATTGCCTTGCCCCTATCCTGGGACTCTGATGTCATTCCAGGTCCCTAAAAGTCCTCACCCTGCTCCTGCCA
CTCCCTCAGAGACCCACAGCATGGAGGAAAATCTAGCCATCATGAATGAGAAACTGAGGCAGGAGCTCCCTAGCCTGTCT
CTTCCCTCCCACAATTACAACCTCTACTCATCTGATGTGGAATTCATCAGAGAGATTCTGCACATTTGAAGCAAAGGCCA
CACATGATATATTCTATCATTGACCCTCTGCCAATTCTTGGCCAGGGATTATTCTGCTCAGGTGCAGCTGGAAGTCCTTA
GGGTAAGCCAACATCCTGAAGACTGCATACTGCAGGCACACTGGTGGCTTGAGGGTTTGCCTACCCATCTCCTCTTCCTG
CACTTCCACCACCAGGACAAGGATGAACTTTACCAGACATAGGATGCATATTCTATTTTCTACCTAAACTCCAAA

Alignment

ORF - retro_mdom_1511 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.27 %
• Parental protein coverage: 58.18 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VGLPSEKGEDGQGPGLHGGCLDGLRSLFEELPCPHPGAVIPFRAPGSPHPSPATPSGNPNMEEHLAVMHE
          V.LPS.KGEDG.G.GLH.G.L..LRSL.EELPCP.PG....F..P.SPHP.PATPS....MEE.LA.M.E
Retrocopy VSLPSGKGEDGPGLGLHRGSLEELRSLSEELPCPYPGTLMSFQVPKSPHPAPATPSETHSMEENLAIMNE

Parental  KLRQELPNLFLRSHDYNLYSSDVEFINEILNIRTKGRTWYILSLTLCRFLAWNYFAQLQLEVLRLSQHPE
          KLRQELP.L.L.SH.YNLYSSDVEFI.EIL.I..KG.T.YILSLTLC.FLA..Y.AQ.QLEVLR.SQHPE
Retrocopy KLRQELPSLSLPSHNYNLYSSDVEFIREILHI*SKGHT*YILSLTLCQFLARDYSAQVQLEVLRVSQHPE

Parental  DWTLQARWRLVGLPTHLLFLRFYRRDKDDLYRTYDAYSTFYLNSE
          D..LQA.W.L.GLPTHLLFL.F...DKD.LY.T.DAYS.FYLNS.
Retrocopy DCILQAHWWLEGLPTHLLFLHFHHQDKDELYQT*DAYSIFYLNSK

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_1511 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1511 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
Felis catus	ENSFCAG00000007692	1 retrocopy	retro_fcat_1622,
Monodelphis domestica	ENSMODG00000015898	1 retrocopy	retro_mdom_1511 ,