RetrogeneDB ID: retro_oana_120

Retrocopy location

• Organism: Platypus (Ornithorhynchus anatinus)
• Coordinates: Ultra474:728971..729528(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TSN
• Ensembl ID: ENSOANG00000003457
• Aliases: None
• Description: translin [Source:HGNC Symbol;Acc:12379]

Sequence

>retro_oana_120
ACTCTGCTGCAAGGAATTCATGAGGATGATGGATTTCAGGATATTCCAAGAAAAATTCCTGAAAGTTCAAGAACATCTTG
GCATAGAATGAGCACAGTTAACACGCCTGAACCCCAAGTTTCCCATGGAGCAGTACCTCAGATTTTGTGAACATTGGCAG
TTCATGTTACAGCACTTGATCTTCCCTGCAGCATTCGTTGTGTAGTTGGAGTCAGAAACTTTGGTGACTCGAGAAGCTGT
CACGGAAATACGTGGCACTGAGCCCAGTCAAAAGGCCTTCACCTGGATATTGAGGATTATCTCTTTGGAGTTTTAATTAT
TGCCAATGAACTCTCCTGGCTGTCAATCACAATGTCACATCTGGGGATTATGCCAATCTCCTCCACATCGCCACTTTCAT
TATCGAGCCAGATTCCAGCGTCCTCCTCCTCCTTAACCTAAAAATGATTCATCTGAGGAATTACAATAATGGACTGAAAT
ATGAAGTCAAGAAGATGAAAGAAGTGGTCTATGGCTGAGGACTCAATAAGGAAGCAGCAGTTGCTTGTGCAGAGAAA

Alignment

ORF - retro_oana_120 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.69 %
• Parental protein coverage: 91.3 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  TLLQGVHQGSGFQDIPKKC-LKAREHFGTVRTQLTSLKTKFPVEQYYRFHEHWRFVLQRLVFLAAFVVYL
          TLLQG.H...GFQDIP.K..LK..EH.G....QLT.L..KFP.EQY.RF.EHW.F.LQ.L.F.AAFVV.L
Retrocopy TLLQGIHEDDGFQDIPRKI>LKVQEHLGIE*AQLTRLNPKFPMEQYLRFCEHWQFMLQHLIFPAAFVV*L

Parental  ESETLVSREAVTEILGIEPERERGF-HLDIEDYLSGVLILASELSRLSV-NSVTAGDYSRPLHISTFINE
          ESETLV.REAVTEI.G.EP.....F.HLDIEDYL.GVLI.A.ELS.LS....VT.GDY...LHI.TFI.E
Retrocopy ESETLVTREAVTEIRGTEPS-QKAF<HLDIEDYLFGVLIIANELSWLSI<HNVTSGDYANLLHIATFIIE

Parental  LDSG-FRLLNLKNDSLRKRYDGLKYDVKKVEEVVYDLSIRGFNKEAAAACAEK
          .DS....LLNLK...LR....GLKY.VKK..EVVY.......NKEAA.ACAEK
Retrocopy PDSSVLLLLNLKMIHLRNYNNGLKYEVKKMKEVVYG*GL---NKEAAVACAEK

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	88.40 RPM
SRP007412_cerebellum	0.00 RPM	76.07 RPM
SRP007412_heart	0.00 RPM	66.59 RPM
SRP007412_kidney	0.00 RPM	129.99 RPM
SRP007412_liver	0.00 RPM	38.69 RPM
SRP007412_testis	0.00 RPM	81.36 RPM

ChIP-Seq

Ornithorhynchus anatinus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_oana_120 retrocopy.

TSS

Ornithorhynchus anatinus was not studied using FANTOM5 data.

Lab

retro_oana_120 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 14 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000006059	1 retrocopy	retro_btau_1598,
Dasypus novemcinctus	ENSDNOG00000025740	2 retrocopies	retro_dnov_1581, retro_dnov_907,
Felis catus	ENSFCAG00000027149	1 retrocopy	retro_fcat_1577,
Homo sapiens	ENSG00000211460	1 retrocopy	retro_hsap_3760,
Gorilla gorilla	ENSGGOG00000002216	2 retrocopies	retro_ggor_2528, retro_ggor_2610,
Myotis lucifugus	ENSMLUG00000012656	1 retrocopy	retro_mluc_1420,
Macaca mulatta	ENSMMUG00000021119	1 retrocopy	retro_mmul_1718,
Monodelphis domestica	ENSMODG00000000147	1 retrocopy	retro_mdom_1896,
Nomascus leucogenys	ENSNLEG00000001202	1 retrocopy	retro_nleu_170,
Ornithorhynchus anatinus	ENSOANG00000003457	1 retrocopy	retro_oana_120 ,
Oryctolagus cuniculus	ENSOCUG00000023529	1 retrocopy	retro_ocun_271,
Otolemur garnettii	ENSOGAG00000030436	3 retrocopies	retro_ogar_1221, retro_ogar_2875, retro_ogar_3426,
Pan troglodytes	ENSPTRG00000012420	1 retrocopy	retro_ptro_2551,
Tarsius syrichta	ENSTSYG00000004395	1 retrocopy	retro_tsyr_1593,