RetrogeneDB ID: retro_ocun_914

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 17:48653138..48653512(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000024246
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: FOXS1
• Ensembl ID: ENSOCUG00000021480
• Aliases: None
• Description: forkhead box S1 [Source:HGNC Symbol;Acc:3735]

Sequence

>retro_ocun_914
GCAGAGCCCGAGAAGCGGCTCACGCTCAACGGCATCTACGAGTTCATCATGAAGAACTTCCCCTACTACCGCGAGAACAA
GCAGGGCTGGCAGAACTCCATCCGCCACAACCTGTCCCTCAACAAGTGCTTCGTGAAGGTGCCGCGCCACTACGACGACC
CGGGCAAGGGCAACTACTGGATGCTGGACCCGTCGAGCGACGACGTGTTCATCGGCGGCACCACGGGCAAGCTGCGGCGC
CGCTCCACCACGTCGCGGGCCAAGCTGGCCTTCAAGCGCGGGGCGCGCCTCACCTCCACCGGCCTCACCTTCATGGACCG
CGCCGGCTCCCTCTACTGGCCCATGTCGCCCTTCCTGTCCCTGCACCACCCCCG

Alignment

ORF - retro_ocun_914 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 50.78 %
• Parental protein coverage: 83.44 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  SSPGQRATLSGIYRYIMGRFAFYRHNRPGWQNSIRHNLSLNECFVKVPRDDRKPGKGSYWTLDPDCHDMF
          ..P..R.TL.GIY..IM..F..YR.N..GWQNSIRHNLSLN.CFVKVPR....PGKG.YW.LDP...D.F
Retrocopy AEPEKRLTLNGIYEFIMKNFPYYRENKQGWQNSIRHNLSLNKCFVKVPRHYDDPGKGNYWMLDPSSDDVF

Parental  EHGSFLRRRRRFTRRPAAEGTKSPAKLSR-KAAPRSWPQPPPAPGGPADGNAP-RPPP
          ..G.....RRR.T...A....K..A.L....A.P.SW..P.P...GP.....P..PPP
Retrocopy IGGTTGKLRRRSTTSRAKLAFKRGARLTS>PASP-SWTAPAPST-GPCRPSCP>APPP

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	7.06 RPM	1.38 RPM
SRP017611_kidney	0.00 RPM	1.32 RPM
SRP017611_liver	0.00 RPM	0.08 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_914 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_914 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_914 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Oryctolagus cuniculus	ENSOCUG00000021480	1 retrocopy	retro_ocun_914 ,