RetrogeneDB ID: retro_ocun_422

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 10:21213085..21213383(+)
• Located in intron of: ENSOCUG00000015861

Retrocopy information

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

Parental gene information

• Parental gene symbol: SNCA
• Ensembl ID: ENSOCUG00000023825
• Aliases: None
• Description: synuclein, alpha (non A4 component of amyloid precursor) [Source:HGNC Symbol;Acc:11138]

Sequence

>retro_ocun_422
GAAGCAACAGCAAAAGTAAGATCCAAAACCAAGAACGAGTGGTTCAGGGTTTAGCAACAGTGGCTGAAAAGACCAAAGAG
CACATGACAAATGTTGGATGGGTGGTGACAGATGTAACAGCAGCATCCTAGAAGACAATGACAGAAGCAAGGAGCATTGC
AGGCATCACTGGTTTTGTTGAAAAAGATAGGCTGGGCAAGAATGAAGACGGAGTCCTCTAGGATGGAACTCTGCTAATAC
ACCTGTGCATCCTGACCGTGAGGCTTCTGAAACGCCTTCTGAGGAAGGAAATCAAGAC

Alignment

ORF - retro_ocun_422 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.28 %
• Parental protein coverage: 72.14 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  EGVLYVGSKTK-EGVVHGVTTVAEKTKEQVTNVGEAVVTGVTAVAQKTVEGAGSIAAATGFVKKDQQGKS
          E....V.SKTK.E.VV.G..TVAEKTKE..TNVG..VVT.VTA...KT...A.SIA..TGFV.KD..GK.
Retrocopy EATAKVRSKTK<ERVVQGLATVAEKTKEHMTNVG-WVVTDVTAAS*KTMTEARSIAGITGFVEKDRLGKN

Parental  EEGAPQEGIL-EAMPMDPDSEAYEMPSEEGYQD
          E.G....G.L....P..PD.EA.E.PSEEG.QD
Retrocopy EDGVL*DGTL<ANTPVHPDREASETPSEEGNQD

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
SRP017611_brain	0.00 RPM	182.62 RPM
SRP017611_kidney	0.00 RPM	8.51 RPM
SRP017611_liver	0.00 RPM	1.46 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_422 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_422 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_422 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000007186	1 retrocopy	retro_chof_92,
Felis catus	ENSFCAG00000011488	1 retrocopy	retro_fcat_452,
Microcebus murinus	ENSMICG00000005634	1 retrocopy	retro_mmur_272,
Oryctolagus cuniculus	ENSOCUG00000023825	1 retrocopy	retro_ocun_422 ,