RetrogeneDB ID: retro_mdom_852

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 2:206224170..206224686(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: C11orf54
• Ensembl ID: ENSMODG00000000412
• Aliases: None
• Description: chromosome 11 open reading frame 54 [Source:HGNC Symbol;Acc:30204]

Sequence

>retro_mdom_852
GTTCTATAGAATGGACTTAAAAATAATTTGCTGATGTCTAGGTCTCTGTAGCTGATCACCCTGATCTGTCTAAGGCACCA
TAATCATTTCCTGTTACAGGAATCTGTGGGAAACTGAGAACTGCAGAAGTAGATGAGGTTCCTTACCTCATGCCTCTTGT
GAATCAAGAAAAGGTTTACGATATGAATACTGTTGCAAAGCAAATTAATCTTCCTAGGGCTTTCATTCTTGGAGTAGGAG
CAGCCCCATTTCAGACTATGGGGATCAATGCTGAGTTCATGCCAATTGTCCAGACTCAAAGTGATCACAAGCCTGCTGGG
AATGGAAGCTACTTTGCCTAGATTTAACTCTGCAGATGGAGGGTGCCTGTTAGAGAAATATAGTGGGAAATACAATGGCT
TTGGATTTGCCTTACTGGCTAATCTCTTTGCTAGTGAAGGCCATCCTGGCAAGGTCAATGAGGTAAAAGCCAAAGGAAGA
ACTGGGAAGTATAATTTTGTGACTTGTATGAGACAA

Alignment

ORF - retro_mdom_852 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.86 %
• Parental protein coverage: 57.67 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  VLQNGLKNN-FADVQVSVVDCPDLSKEPYTFPVKGICGKPRIAEVGGVPYLMPLVNREKVYDMNTVAKQI
          VL.NGLKNN.FADV.VSV.D.PDLSK.P..FPV.GICGK.R.AEV..VPYLMPLVN.EKVYDMNTVAKQI
Retrocopy VL*NGLKNN<FADV*VSVADHPDLSKAP*SFPVTGICGKLRTAEVDEVPYLMPLVNQEKVYDMNTVAKQI

Parental  DLPGAFILGAGAAPFQTLGINAEFMPIVQTESDHKPAVNGSYFA-QINPADGGYLLEKYSGKYNDFGFAL
          .LP.AFILG.GAAPFQT.GINAEFMPIVQT.SDHKPA.NGSYFA...N.ADGG.LLEKYSGKYN.FGFAL
Retrocopy NLPRAFILGVGAAPFQTMGINAEFMPIVQTQSDHKPAGNGSYFA>RFNSADGGCLLEKYSGKYNGFGFAL

Parental  LANLFASEGQPGKILELVKAKGRTGKYNFVTCMRQ
          LANLFASEG.PGK..E.VKAKGRTGKYNFVTCMRQ
Retrocopy LANLFASEGHPGKVNE-VKAKGRTGKYNFVTCMRQ

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_852 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_852 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 6 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000013446	1 retrocopy	retro_chof_593,
Cavia porcellus	ENSCPOG00000014146	1 retrocopy	retro_cpor_1286,
Monodelphis domestica	ENSMODG00000000412	2 retrocopies	retro_mdom_1467, retro_mdom_852 ,
Otolemur garnettii	ENSOGAG00000002523	1 retrocopy	retro_ogar_3359,
Tupaia belangeri	ENSTBEG00000007819	1 retrocopy	retro_tbel_4251,
Tursiops truncatus	ENSTTRG00000001140	3 retrocopies	retro_ttru_244, retro_ttru_334, retro_ttru_560,