RetrogeneDB ID: retro_ocun_552

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 12:26061409..26061802(-)
• Located in intron of: ENSOCUG00000029416

Retrocopy information

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

Parental gene information

• Parental gene symbol: STX6
• Ensembl ID: ENSOCUG00000004714
• Aliases: None
• Description: syntaxin 6 [Source:HGNC Symbol;Acc:11441]

Sequence

>retro_ocun_552
GTTGCAGCAAATCCTAGGAAATTCAACCTCGATGCTGCTGAACTGAGTCTAAGAAAAGCCTTCATTACAAGCGCTCAGCA
AGTTGTCAGGGACATGAAGGATCAGATGTCAACTGTGTCTGTGCAGGCGTTAGCTAAAACTTCAAAGAATTAGGCACTTG
CTGGGACACAGTGGCAGCCAGAGTTAGAGCAGCAGAGCCCCAGATAAATACGGCGCCTGGGCAGAGAGCTGCAGTCGGCC
AACTCCCATTTCCTCAAGGATGGGCAGGCACAGCAGGATGAGCGGCTGGAGCAGGTCTCTGGCAGCATCGGGGTGAGAAG
AGTATGCCCCAGCATAGGAGGGGAGCTGGAGAGCACTCAGTCTCGGCTGGACAATGAGATGAAGAAACTTGCC

Alignment

ORF - retro_ocun_552 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.9 %
• Parental protein coverage: 68.09 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  VEANPRKFNLDATELSVRKAFITSTRQVVRDMKDQMSASSVQALAERRNRQA-LLGDSGGQSWSSRAPDK
          V.ANPRKFNLDA.ELS.RKAFITS..QVVRDMKDQMS..SVQALA......A.LLG.SG.QS.SSRAPDK
Retrocopy VAANPRKFNLDAAELSLRKAFITSAQQVVRDMKDQMSTVSVQALAKTSKN*A>LLGHSGSQS*SSRAPDK

Parental  YG-RLDRELQVANSHFIEEQQAQQQLIVEQQDEQLEL--VSGSIG-VLKSMSQRIGGELEEQA
          YG.RL.RELQ.ANSHF....QAQQ....EQ.........V..SIG..L.S...R...E....A
Retrocopy YG<RLGRELQSANSHFLKDGQAQQDERLEQVSGSIGVRRVCPSIGGELESTQSRLDNEMKKLA

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	68.27 RPM
SRP017611_kidney	0.00 RPM	26.66 RPM
SRP017611_liver	0.00 RPM	9.09 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_552 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_552 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_552 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Mustela putorius furo	ENSMPUG00000011478	1 retrocopy	retro_mputfur_905,
Oryctolagus cuniculus	ENSOCUG00000004714	1 retrocopy	retro_ocun_552 ,
Pelodiscus sinensis	ENSPSIG00000009402	1 retrocopy	retro_psin_57,