RetrogeneDB ID: retro_ocun_977

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 18:48369762..48370302(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PIGX
• Ensembl ID: ENSOCUG00000012329
• Aliases: None
• Description: phosphatidylinositol glycan anchor biosynthesis, class X [Source:HGNC Symbol;Acc:26046]

Sequence

>retro_ocun_977
TTAATTAAACAGGAAATCCCAACAGGACTTTTTGTAGATTCATATGAATTGGCTTCATTACGAGAGAGAAGCATAACAGA
GGTAGTGATGCTTTCATAAAATTTTAATATAGACGCTCCTAACTATCTGTCCAAGGCATCCTGAAGTTCTCATTTATGTG
CCAGACAAGATTCATAATATGTTGACTGTTTCCCAGCTTTTTTGCCTGTGTACCACTGCTATCATTGGCCACATAGTAAA
GATGGAGAAACCTTTATTGTGGTCAGTAACCCAGATTTGCTGATGGATTGTGACCAAGAGTTTCCAATTTTGAAATGCTG
GGCTCAGTCAGAAGTGGCAGCTCTTTGTGCTGTGGAGAATGAGGATATCTGCCAATGGCACAATATGAAGTACAAATCAG
GATATGAGAATGTGACTCTGCATGTTCCAGCAGGACTGACAGTTCATGCCTCTTTACTATGTTTTATGACTCTGTTAATT
ACAATCCTGTGTTCTGTGCTGATCCTTGTAGCTGTTTTCAAATATGGCCATTTTCCCCTC

Alignment

ORF - retro_ocun_977 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.33 %
• Parental protein coverage: 69.11 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LIKQEIPTGLFVDPYELASLQERNLIEAVMISENFDIEAPSYLSKES-AVLIYARQDSQCSDCFQALLPV
          LIKQEIPTGLFVD.YELASL.ER...E.VM.S.NF.I.AP.YLSK.S......ARQDS...DCF.A.LPV
Retrocopy LIKQEIPTGLFVDSYELASLRERSITEVVMLS*NFNIDAPNYLSKAS*SSHLCARQDS*YVDCFPAFLPV

Parental  HYRYHRPHSKDGETFVVVSNPDLLMYCNQEFPILKCWTQSEVAAPCALENEDICQWSSMKYRSVYKNVTL
          ...YH.PHSKDGETF.VVSNPDLLM.C.QEFPILKCW.QSEVAA.CA.ENEDICQW..MKY.S.Y.NVTL
Retrocopy YHCYHWPHSKDGETFIVVSNPDLLMDCDQEFPILKCWAQSEVAALCAVENEDICQWHNMKYKSGYENVTL

Parental  QVPVGLTIHTSLVCFVTLFITILCSVLILIAVFRYGHFSL
          .VP.GLT.H.SL.CF.TL.ITILCSVLIL.AVF.YGHF.L
Retrocopy HVPAGLTVHASLLCFMTLLITILCSVLILVAVFKYGHFPL

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	8.11 RPM
SRP017611_kidney	0.00 RPM	14.39 RPM
SRP017611_liver	0.00 RPM	4.47 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_977 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_977 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_977 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000003759	1 retrocopy	retro_amel_386,
Callithrix jacchus	ENSCJAG00000013676	1 retrocopy	retro_cjac_2794,
Monodelphis domestica	ENSMODG00000018455	1 retrocopy	retro_mdom_1758,
Mustela putorius furo	ENSMPUG00000003841	1 retrocopy	retro_mputfur_1090,
Mus musculus	ENSMUSG00000023791	1 retrocopy	retro_mmus_943,
Oryctolagus cuniculus	ENSOCUG00000012329	1 retrocopy	retro_ocun_977 ,
Rattus norvegicus	ENSRNOG00000033623	2 retrocopies	retro_rnor_1998, retro_rnor_2555,