RetrogeneDB ID: retro_oana_108

Retrocopy location

• Organism: Platypus (Ornithorhynchus anatinus)
• Coordinates: Ultra272:10592282..10592832(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSOANG00000007394
• Aliases: None
• Description: None

Sequence

>retro_oana_108
TGCCCACATGGTGGCTTCGCAAAGGACAAGGAACATCCAAGAAATCTGATCCCAAAACTCTGCAGGCAGTTGTATCTCTT
GGGCTGGGTCGCTGGGACTGGAGGAGGAATTAGCCTGAAGCACGGCAATGGAATCTACCTCCCTGCATCAGGACTGCAGG
AAGGATGAATTGAGCCTGAAAATATGTTTGTTGGTGATATCAATGCGTAAGGTATCAGTGACCCTCTATTATACAAGAAT
CTAAGGAGAAGTCGATGGACGTCTCTCTTTATGAATGCTTATAACCGTAAGAGGAGCTGGAACAGTGATTTACAGTCAGC
CTAAGGCTGTTGTCATGACTACCCTTCCCTTTCCAGGGTATGAGTTTAAGATTATGCATTGAGAGATGATAAAAGGAATC
AGAAAATAAACCTCAGGAGGGTGTTACAGGTACAAGGATAGATTAGTGGTCCCCGTTGCTGAGAACATGCCGGAAGAGAA
GGATTTAAAAGAATGAATGTCCCACGTAATGAATCAATACCTGGATTTCTGTGCCGTAATAGCCAGGCAA

Alignment

ORF - retro_oana_108 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.85 %
• Parental protein coverage: 75.31 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  CPRVASVQDKEHPRNLIPELCKQFYHLGWVTGTGGGISLKYGNEIYIAPSGVQKERIQPEDMFVCDINEQ
          CP......DKEHPRNLIP.LC.Q.Y.LGWV.GTGGGISLK.GN.IY...SG.Q...I.PE.MFV.DIN..
Retrocopy CPHGGFAKDKEHPRNLIPKLCRQLYLLGWVAGTGGGISLKHGNGIYLPASGLQEG*IEPENMFVGDINA*

Parental  DISGPPSYKNLKKSQCTPLFMNAY-TIRGAGAVIHSHSKAAVMATLIFPGHEFKITHQEMIKGIRKCTSG
          .IS.P..YKNL..S..T.LFMNAY.T.RGAG.VI.S..KA.VM.TL.FPG.EFKI.H.EMIKGIRK.TSG
Retrocopy GISDPLLYKNLRRSRWTSLFMNAY>TVRGAGTVIYSQPKAVVMTTLPFPGYEFKIMH*EMIKGIRK*TSG

Parental  GCYRYYDTLVVPIVENTPEEKDLKERMAQAMNQYPDSCAVLVRR
          GCYRY.D.LVVP..EN.PEEKDLKE.M...MNQY.D.CAV..R.
Retrocopy GCYRYKDRLVVPVAENMPEEKDLKE*MSHVMNQYLDFCAVIARQ

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	23.31 RPM
SRP007412_cerebellum	0.00 RPM	14.47 RPM
SRP007412_heart	0.00 RPM	11.78 RPM
SRP007412_kidney	0.00 RPM	21.61 RPM
SRP007412_liver	0.00 RPM	10.85 RPM
SRP007412_testis	0.00 RPM	13.88 RPM

ChIP-Seq

Ornithorhynchus anatinus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_oana_108 retrocopy.

TSS

Ornithorhynchus anatinus was not studied using FANTOM5 data.

Lab

retro_oana_108 was not experimentally validated.

Homology

Retrocopy orthology:

Ornithorhynchus anatinus 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 8 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Echinops telfairi	ENSETEG00000016758	1 retrocopy	retro_etel_220,
Homo sapiens	ENSG00000149089	1 retrocopy	retro_hsap_4208,
Gorilla gorilla	ENSGGOG00000022940	2 retrocopies	retro_ggor_2818, retro_ggor_2873,
Ornithorhynchus anatinus	ENSOANG00000007394	6 retrocopies	retro_oana_108 , retro_oana_109, retro_oana_121, retro_oana_63, retro_oana_85, retro_oana_96,
Pongo abelii	ENSPPYG00000003361	1 retrocopy	retro_pabe_3442,
Pan troglodytes	ENSPTRG00000003499	1 retrocopy	retro_ptro_2856,
Sarcophilus harrisii	ENSSHAG00000011523	1 retrocopy	retro_shar_574,
Ictidomys tridecemlineatus	ENSSTOG00000004390	1 retrocopy	retro_itri_1029,