RetrogeneDB ID: retro_oana_1

Retrocopy location

• Organism: Platypus (Ornithorhynchus anatinus)
• Coordinates: Ultra12:1975818..1976844(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOANG00000003172
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSOANG00000003398
• Aliases: None
• Description: None

Sequence

>retro_oana_1
TCCACTAAGCAGGCACGCTGCGCCCCGTTTCTCCCGCTGCTCCTGTGTCTGGGGGCTGCTCTCCTGCCAGCGGGCCGGAC
TAGGTCGCACTCGCTGCGCTATTTCACCACCGGAGTGAGCCGGCCCGGCCCCGGGGTGTCCGAGTTCACGTCTGTGGGCT
ACGTGGACGACGTGCAGTTCGTCAGGTTCGACGGCGATGGGAGACGGGGTCGGGCAGAGCCACGGACCCCGTGGATCCGG
GACAACGAAGGACGGGAATATTGGGACCAGGAGACAAAGATCTTCAGGAGCGGGGCGCAGAATTTCCACGTGGGCCTGCA
GAACATCATGGGCTACTACAACCAGAGCGAGGAGAGGTCTCATACCGTTCAGGGGCTGTATGGCTGCCAGCTGCGGGAGG
ACAACACCCCCGGCGAAGGGTTCATGCAGTTTGGCTACGACGGGCGGGACTACATCGCTCTGGACAAGGCCACACTGAGC
TGGATGGTGGCGGACGCCGGGGCCCTCAACACTAAGAGCAAGTGGGAGGCCGACGGAACCATCGCCGAGCGAGACAAAGC
CTATCTGGAGGACGAGTGCATTGAGTGGCTCCGGAGATACATGGGCTTCGGGGGGCCCTGCCTCACTCGGGCAGATCCCC
CCAAGGTGGACGTGATCCGTCACCCCGGCCCCGACGGGGAGGACGTCAGCCTGCGGTGCCGGGCCTTCGGCTTCTACCCG
GCGGACATCAAGTTCATGTGGAGGCGGGAAGGGGAAGACGTGAGCCTGCAAATGGAGCTGGTGGACACGCGGCCCAGCGG
AGATGGCAACTTCCAGAAATGGGCATCGGTCAGCGTGCCCCGGGGAGAGGAGCTGAAATACGTCTGCATCGTGGAGCACG
AGGGCCTGGCCCAGCCCCTCGCCGTAAAGTGGGTTCCAGATACATCCCTGTCCAATAAGGCCACTGTGGGGGTTGTGATC
GTCATCCTGCTCATCCTCGTGGCCGTGGTTGGGTTTGTCATCTGGAAGAGGTCAGGTCCCAGAGGA

Alignment

ORF - retro_oana_1 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.98 %
• Parental protein coverage: 97.76 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SHTFQWMYGCQLREDDTPGQGFVQLGYDGRDYVALDKATLSWTAADAGALNTKRKWEVDRTEAERWKAYL
          SHT.Q..YGCQLRED.TPG.GF.Q.GYDGRDY.ALDKATLSW..ADAGALNTK.KWE.D.T.AER.KAYL
Retrocopy SHTVQGLYGCQLREDNTPGEGFMQFGYDGRDYIALDKATLSWMVADAGALNTKSKWEADGTIAERDKAYL

Parental  EGRCIDGLRRYLGFGGPSLTRADPPEVEVTRHTGPDGEDVSLRCRALGFYPADIKFKWEREGKDMSQEME
          E..CI..LRRY.GFGGP.LTRADPP.V.V.RH.GPDGEDVSLRCRA.GFYPADIKF.W.REG.D.S..ME
Retrocopy EDECIEWLRRYMGFGGPCLTRADPPKVDVIRHPGPDGEDVSLRCRAFGFYPADIKFMWRREGEDVSLQME

Parental  FVGTRPSGDGNFQKWASVNVPRGEEQKYVCVVEHEGLAQPLAVKWVPDPSPPIAAIVGAVVVILLVTAAV
          .V.TRPSGDGNFQKWASV.VPRGEE.KYVC.VEHEGLAQPLAVKWVPD.S....A.VG.V.VILL...AV
Retrocopy LVDTRPSGDGNFQKWASVSVPRGEELKYVCIVEHEGLAQPLAVKWVPDTSLSNKATVGVVIVILLILVAV

Parental  VGFVIWKR
          VGFVIWKR
Retrocopy VGFVIWKR

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	6.98 RPM	77.80 RPM
SRP007412_cerebellum	20.69 RPM	161.79 RPM
SRP007412_heart	36.13 RPM	482.11 RPM
SRP007412_kidney	11.25 RPM	108.67 RPM
SRP007412_liver	14.46 RPM	148.81 RPM
SRP007412_testis	12.69 RPM	70.09 RPM

ChIP-Seq

Ornithorhynchus anatinus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_oana_1 retrocopy.

TSS

Ornithorhynchus anatinus was not studied using FANTOM5 data.

Lab

retro_oana_1 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 4 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Loxodonta africana	ENSLAFG00000029181	1 retrocopy	retro_lafr_1203,
Macropus eugenii	ENSMEUG00000003479	2 retrocopies	retro_meug_2042, retro_meug_570,
Mus musculus	ENSMUSG00000067201	1 retrocopy	retro_mmus_2265,
Ornithorhynchus anatinus	ENSOANG00000003398	1 retrocopy	retro_oana_1 ,