RetrogeneDB ID: retro_oana_5

Retrocopy location

• Organism: Platypus (Ornithorhynchus anatinus)
• Coordinates: Contig13525:8931..9609(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOANG00000001673
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSOANG00000010404
• Aliases: None
• Description: None

Sequence

>retro_oana_5
ATGACCTCAGCATCCAGGCCCACCTTTGAACCTGCGCGTGGTGGGAGAGGTAAAGGAGAGGGAGACCTGAGTCTTCTCTC
CAAGCAGTACTCAAGTAGAGATCTTCCTTCTCACACAAAGATCAAATACAGAAAGACAACCCAGGATGCTCCCGAAGAGG
TCTGTCACCGAGATTTCAGAAAGGAACTGGCAGAGCGAGAGAGAGTTGCTGCAAGGGTGAAAAATGGAGATCGTCCAAAT
TGGGCAAACTCATCCCCTGTGTCGAAAAAGCCTCGGTTGGCTCAAATCTCTGTGGCAAACCTCGATGCAGATGACCCTCT
CACAGACGAGGATGAGGAAGATGAGGAAAGTGAGGATGACGACACAGCGGCCCTTCTGGCTGAACTGGAGAAGATCAAAA
AGGAAAGGGCTGAAGAAGAGGCCCGCAAGGAGCGAGAGGAAAGGGCGGAAAAGGAGAGGATTAGATCGGAGAATGTTCTA
AATGGAAATCCTCTATTGAAATTCACTGGCCTGGCCCAGCCTCAGTCGAACTTTAAAGTAAAGAGAAGGTGGGATGATGA
TGTCATCTTTAAGAACTGTGCTAAAGAGGTTAAAGGCTCCAAAAGGGACAAAAAATTTGTCAATGATACTTTGCGATCTG
AATTTCACACTAAGTTTATGGAGAAGTATTTCAGGTAG

Alignment

ORF - retro_oana_5 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.7 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MTTAARPTFEPARGGRGKGEGDLSQLSKQYSSRDLPSHTKIKYRQTTQDAPEEVRNRDFRRELEERERVA
          MT.A.RPTFEPARGGRGKGEGDLS.LSKQYSSRDLPSHTKIKYR.TTQDAPEEV..RDFR.EL.ERERVA
Retrocopy MTSASRPTFEPARGGRGKGEGDLSLLSKQYSSRDLPSHTKIKYRKTTQDAPEEVCHRDFRKELAERERVA

Parental  AREKTRDRPTREHTTSSVSKKPRLDQIPAANLDADDPLTDEDDEDEDLDEESDDDDTAALLAELEKIKKE
          AR.K..DRP......S.VSKKPRL.QI..ANLDADDPLTDED.E....DEES.DDDTAALLAELEKIKKE
Retrocopy ARVKNGDRPNWANS-SPVSKKPRLAQISVANLDADDPLTDEDEE----DEESEDDDTAALLAELEKIKKE

Parental  RAEEQARKEQEQKAEEERIRMENILSGNPLLNLTGPAQPQANFKVKRRWDDDVVFKNCAKGVDELKKDKR
          RAEE.ARKE.E..AE.ERIR.EN.L.GNPLL..TG.AQPQ.NFKVKRRWDDDV.FKNCAK.V...K.DK.
Retrocopy RAEEEARKEREERAEKERIRSENVLNGNPLLKFTGLAQPQSNFKVKRRWDDDVIFKNCAKEVKGSKRDKK

Parental  FVNDTLRSEFHKKFMEKYIK
          FVNDTLRSEFH.KFMEKY..
Retrocopy FVNDTLRSEFHTKFMEKYFR

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	23.58 RPM
SRP007412_cerebellum	0.00 RPM	23.97 RPM
SRP007412_heart	0.00 RPM	21.70 RPM
SRP007412_kidney	0.00 RPM	14.21 RPM
SRP007412_liver	0.00 RPM	7.68 RPM
SRP007412_testis	0.00 RPM	19.93 RPM

ChIP-Seq

Ornithorhynchus anatinus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_oana_5 retrocopy.

TSS

Ornithorhynchus anatinus was not studied using FANTOM5 data.

Lab

retro_oana_5 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 16 parental genes, and 34 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000011392	1 retrocopy	retro_amel_1913,
Bos taurus	ENSBTAG00000007913	1 retrocopy	retro_btau_703,
Canis familiaris	ENSCAFG00000004134	6 retrocopies	retro_cfam_1329, retro_cfam_2123, retro_cfam_503, retro_cfam_537, retro_cfam_61, retro_cfam_805,
Callithrix jacchus	ENSCJAG00000004188	1 retrocopy	retro_cjac_2802,
Cavia porcellus	ENSCPOG00000006249	1 retrocopy	retro_cpor_708,
Dipodomys ordii	ENSDORG00000011075	1 retrocopy	retro_dord_313,
Echinops telfairi	ENSETEG00000006649	1 retrocopy	retro_etel_647,
Felis catus	ENSFCAG00000007826	1 retrocopy	retro_fcat_1416,
Myotis lucifugus	ENSMLUG00000002032	3 retrocopies	retro_mluc_102, retro_mluc_2143, retro_mluc_2478,
Mus musculus	ENSMUSG00000004096	2 retrocopies	retro_mmus_2482, retro_mmus_593,
Ornithorhynchus anatinus	ENSOANG00000010404	1 retrocopy	retro_oana_5 ,
Oryctolagus cuniculus	ENSOCUG00000001629	4 retrocopies	retro_ocun_1037, retro_ocun_1605, retro_ocun_679, retro_ocun_743,
Otolemur garnettii	ENSOGAG00000001686	2 retrocopies	retro_ogar_2476, retro_ogar_456,
Rattus norvegicus	ENSRNOG00000008490	3 retrocopies	retro_rnor_2452, retro_rnor_251, retro_rnor_476,
Sarcophilus harrisii	ENSSHAG00000016534	5 retrocopies	retro_shar_26, retro_shar_333, retro_shar_447, retro_shar_596, retro_shar_768,
Tarsius syrichta	ENSTSYG00000000407	1 retrocopy	retro_tsyr_1585,