RetrogeneDB ID: retro_ocun_1004

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 19:27956974..27957398(+)
• Located in intron of: ENSOCUG00000006683

Retrocopy information

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

Parental gene information

• Parental gene symbol: SAR1B
• Ensembl ID: ENSOCUG00000008250
• Aliases: None
• Description: SAR1 homolog B (S. cerevisiae) [Source:HGNC Symbol;Acc:10535]

Sequence

>retro_ocun_1004
GACTGGATTTACAGTTGTTTCAACACCAGGCTACAGTTTTCAGGATTACATAGGACAACTGGCAAATTGGTATTTGTTGG
ATTGGATAATGTGGGAAAAACATTGCTACACATATGCTAACAGATGACAGACTTGGACAACATGTCCCAATGTTATATCC
CACTTCAGAAGAACTGACCATTGCCAGCATCACTTTTATAACTTCGGATCTGAGTAAACATATTCAAGCTCAAGGAGTGC
GGAGAAACTGCCTTCCTGTTATCAATGGCACTGTATTTCTGGAGGACTGTACAGCCCACGAGAGGCTATTGGAATCAAAA
GAAGAACTTGATTCACTAAGGACAGATGAAATCATTGTTAATGTGCTTAAAATGATTCTAGGGGATAAGATAACAGACTC
GAAACCATTAGTGAAAAGAAGTTA

Alignment

ORF - retro_ocun_1004 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.06 %
• Parental protein coverage: 71.72 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  DWIYSGFSSVLQFLGLYKKTGKLVFLGLDNAGKTTL-LHMLKDDRLGQHVPTLHPTSEELTIAGMTFTTF
          DWIYS.F...LQF.GL...TGKLVF.GLDN.GKT.L..HML.DDRLGQHVP.L.PTSEELTIA..TF.T.
Retrocopy DWIYSCFNTRLQFSGLHRTTGKLVFVGLDNVGKTLL<THMLTDDRLGQHVPMLYPTSEELTIASITFITS

Parental  DLGGHVQARRVWKNYLPAINGIVFLVDCADHERLLESKEELDSLMTDETIANVPILILGNKI-DRPEAIS
          DL..H.QA..V..N.LP.ING.VFL.DC..HERLLESKEELDSL.TDE.I.NV...ILG.KI..R.E.IS
Retrocopy DLSKHIQAQGVRRNCLPVINGTVFLEDCTAHERLLESKEELDSLRTDEIIVNVLKMILGDKI<NRLETIS

Parental  EERL
          E..L
Retrocopy EKKL

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	31.62 RPM
SRP017611_kidney	0.00 RPM	61.02 RPM
SRP017611_liver	0.00 RPM	71.68 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1004 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1004 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1004 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017849	1 retrocopy	retro_amel_1075,
Dasypus novemcinctus	ENSDNOG00000013784	3 retrocopies	retro_dnov_1584, retro_dnov_1804, retro_dnov_919,
Loxodonta africana	ENSLAFG00000001021	1 retrocopy	retro_lafr_1043,
Oryctolagus cuniculus	ENSOCUG00000004547	1 retrocopy	retro_ocun_638,
Oryctolagus cuniculus	ENSOCUG00000008250	1 retrocopy	retro_ocun_1004 ,
Pteropus vampyrus	ENSPVAG00000012433	2 retrocopies	retro_pvam_1219, retro_pvam_725,
Tursiops truncatus	ENSTTRG00000016864	2 retrocopies	retro_ttru_1225, retro_ttru_857,