RetrogeneDB ID: retro_oana_11

Retrocopy location

• Organism: Platypus (Ornithorhynchus anatinus)
• Coordinates: 1:39961422..39962078(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FSCN1
• Ensembl ID: ENSOANG00000030243
• Aliases: None
• Description: fascin homolog 1, actin-bundling protein (Strongylocentrotus purpuratus) [Source:HGNC Symbol;Acc:11148]

Sequence

>retro_oana_11
AGGAACGTCTCCACCCGCCAGGGAATGGACCTCGCTGAAAATCAGGATGCAGAGAGTGACCAAAAGACCTTCCAACTGGA
GATCAATAGGGACACCAAGAAGTGTGCTTTCCCGATCTCCATGGACAAGTACTGGACCCTCACTCCCATAGTGGTGTGCA
GTCAACTGCTTCAGTCAAGAATTCCAGTTGCTACTTTGATATCAAGTGGCTCGACAGGAGGATCACCCTGAGAGCTGTCA
ACGGCAAGTACGTGACAGCCAAGAAGAATGATCAGCTGGCCACCTCAGTGGAAACTGTGGGTGAAACCAAACACTTTTTG
ATGAAGCTGATCAACCAGCCCATCATCATCCTGTGTGGAGAGCTTGGTTTCATTGGCTGCCGGAAAGTAATGGGGACCAA
GGACTCCAACTGGTTTTCTTATGACATGTTTCAACTGGAATTTGATGATGGCACCAATAATAAAGATTTCACTGGGAAGT
ACTGGATGGTTGGATGGTTGACCAGAAGCAGCGATACCCCTGTGGACTTCTGCTTCAAGTTCTGCAACTGCAACAAAATG
GCCATCAAAACCAATGGCCAGTACCTGAAAGGCATCCACGCCGGGGTCCTGAAAGCTTCTGCCGACTCCACTGCCTCTTC
CACACTCTGGGAGTAC

Alignment

ORF - retro_oana_11 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.79 %
• Parental protein coverage: 77.97 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  RSVSPQTGMDLSANQDEESDQETFQLEINRDTKKCAFRTSTGKYWTLTP-SGGIQSTASVKNSSCYFDIE
          R.VS...GMDL..NQD.ESDQ.TFQLEINRDTKKCAF..S..KYWTLTP...G.QSTASVKNSSCYFDI.
Retrocopy RNVSTRQGMDLAENQDAESDQKTFQLEINRDTKKCAFPISMDKYWTLTP<HSGVQSTASVKNSSCYFDIK

Parental  WLDRRITLKAANGKYVTAKKNGQLAASVETVGETEHFLMKLINRPIIVLRGEHGFIGCRKVTGTLDSNRS
          WLDRRITL.A.NGKYVTAKKN.QLA.SVETVGET.HFLMKLIN.PII.L.GE.GFIGCRKV.GT.DSN..
Retrocopy WLDRRITLRAVNGKYVTAKKNDQLATSVETVGETKHFLMKLINQPIIILCGELGFIGCRKVMGTKDSNWF

Parental  SYDVFQLEFNDGAYNIKDSTGKYWMVGNESSVTSSSDTPVDFFFEFCDYNKVAIKTNGRYLKGDHAGVLK
          SYD.FQLEF.DG..N.KD.TGKYWMVG.....T.SSDTPVDF.F.FC..NK.AIKTNG.YLKG.HAGVLK
Retrocopy SYDMFQLEFDDGTNN-KDFTGKYWMVG---WLTRSSDTPVDFCFKFCNCNKMAIKTNGQYLKGIHAGVLK

Parental  ASADSIDPSTLWEY
          ASADS...STLWEY
Retrocopy ASADSTASSTLWEY

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	153.75 RPM
SRP007412_cerebellum	0.00 RPM	90.40 RPM
SRP007412_heart	0.00 RPM	3.28 RPM
SRP007412_kidney	0.00 RPM	4.44 RPM
SRP007412_liver	0.00 RPM	0.27 RPM
SRP007412_testis	0.00 RPM	8.42 RPM

ChIP-Seq

Ornithorhynchus anatinus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_oana_11 retrocopy.

TSS

Ornithorhynchus anatinus was not studied using FANTOM5 data.

Lab

retro_oana_11 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.

---

Parental genes homology:

Parental genes homology involve 4 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000075618	1 retrocopy	retro_hsap_1476,
Monodelphis domestica	ENSMODG00000001028	1 retrocopy	retro_mdom_423,
Ornithorhynchus anatinus	ENSOANG00000030243	1 retrocopy	retro_oana_11 ,
Pongo abelii	ENSPPYG00000017337	3 retrocopies	retro_pabe_1225, retro_pabe_3201, retro_pabe_3544,