RetrogeneDB ID: retro_ocun_1779

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: GL018888:310419..311022(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PBX3
• Ensembl ID: ENSOCUG00000012302
• Aliases: None
• Description: pre-B-cell leukemia homeobox 3 [Source:HGNC Symbol;Acc:8634]

Sequence

>retro_ocun_1779
CTGCAAGAACAAAGCCAGACCAGGCCCATCTCCCCGAAGGAGATCGAGCGGATGGTAAACACCATCTACTACAGGTTCAG
CTCCATCCAGATGCAGCTCAAGCAGGGCACGTGTGAGGCCATCATGATCCTGCATTCCTGATTTCTGGATGCGCAGCAGA
AGAGACGGAATTTCAACAACCCGGCAACGGAAATCCTGAATGAATATTTCTATTCCCATCTCAGCAACACTTACCCCAGT
GAGGAAGCCAAAGAAGAATTAGCCAAGAAGTGTGGCATCACAGTCTCCCAGGTATCAAACTGGTTTAGAAACAAGAGAAT
CCAGTACAAGAAGAACATAGGTAAATTTCAAAAGGAAGCTAATATTTATGCTGCCAAAACAGCTGTCACTGCTACCAATG
TGTCAGCCCATGGAAGCCAAGCTAACTCACCCTCAAACCCCAACTCAGCTGGTTCTTCCAGTTCTTTTAACATGTCAAAC
TCTGGAGATTTGTTCACGAACATGCAGTCACTCAATGGGGATTCTTACCAAGGGGCCCAGGTTGGAGCCAATATGCAATC
ATAGGTGGATACCCTTCGCCATGTTATCAGCCAGACAGGAGGA

Alignment

ORF - retro_ocun_1779 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.94 %
• Parental protein coverage: 56.55 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LREQSRTRPISPKEIERMVGIIHRKFSSIQMQLKQSTCEAVMILRSRFLDARRKRRNFSKQATEILNEYF
          L.EQS.TRPISPKEIERMV..I...FSSIQMQLKQ.TCEA.MIL.S.FLDA..KRRNF...ATEILNEYF
Retrocopy LQEQSQTRPISPKEIERMVNTIYYRFSSIQMQLKQGTCEAIMILHS*FLDAQQKRRNFNNPATEILNEYF

Parental  YSHLSNPYPSEEAKEELAKKCSITVSQVSNWFGNKRIRYKKNIGKFQEEANLYAAKTAVTAAHAVAAAVQ
          YSHLSN.YPSEEAKEELAKKC.ITVSQVSNWF.NKRI.YKKNIGKFQ.EAN.YAAKTAVTA....A....
Retrocopy YSHLSNTYPSEEAKEELAKKCGITVSQVSNWFRNKRIQYKKNIGKFQKEANIYAAKTAVTATNVSA---H

Parental  NNQTNSPTTPNS-GSSGSFNLPNSGDMFMNMQSLNGDSYQGSQVGANVQSQVDTLRHVINQTGG
          ..Q.NSP..PNS.GSS.SFN..NSGD.F.NMQSLNGDSYQG.QVGAN.QS.VDTLRHVI.QTGG
Retrocopy GSQANSPSNPNSAGSSSSFNMSNSGDLFTNMQSLNGDSYQGAQVGANMQS*VDTLRHVISQTGG

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	0.06 RPM	13.08 RPM
SRP017611_kidney	0.00 RPM	11.76 RPM
SRP017611_liver	0.00 RPM	5.78 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1779 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1779 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1779 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Oryctolagus cuniculus	ENSOCUG00000012302	1 retrocopy	retro_ocun_1779 ,