RetrogeneDB ID: retro_ocun_1703

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: GL018788:822782..824015(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RALGPS2
• Ensembl ID: ENSOCUG00000005161
• Aliases: None
• Description: Ral GEF with PH domain and SH3 binding motif 2 [Source:HGNC Symbol;Acc:30279]

Sequence

>retro_ocun_1703
ATGGCCCTCATGAATGGGCAGGCAAGCAGCGTCAGCCTTGCAGCCACGGCTTCCGAGAACAGTAGAAGCTCTGAATCATT
AAGTGACAAAGGTTCCGAATTGAAGAAAAGCTTTGATGCTATGGTACTTGATGTTCTTAAGGTTACACCAGAAGAGTATG
TGGGTCAGATAACACTAATGGATGTTCCAGTATTTAAAGCTATTCAACCAGATGAGCTTTCAAGTTGTGGATGGAATAAA
AAAGAAAAATACAGTTCTGTGCCAAATGCTGTTGCTTTCACAAGAAGATTTAATCATGTGAACTTTTGGGTTGTTAGAGA
GATTCTTCATGCTCAGACATTAAAAATTAGAGCAGAAGTTTTGAGTCACTATATGAAAACTGCTAAGAAACTGTATGAGC
TGAATAACCTTCATGCACTTATGGCAATGGTTTCTGGCTTACAGAGCGCCCCAATTTTCAGGTTGACTAAGACATGGGCA
TTACTAAGTAAAAAAGACAAAACTACCTTTGAAAAATTAGAGTATGTGGTGAGTAAAGAGGATAACTGCAAAAGACTCTG
AGACTATGTAAGTAGCTTAAAGATGACACCCTATTTAGGCATCTATCTGTCAGATTTAACATACATTGATTCAGCGTACC
CATCAACTGGCAGCATTCTAGAAATCGAGCAAAGATCAAATTTAATGAATAACATTCTTAGGATAATTTCTGATTTACAG
CAGTCCTGTGAATATGATATTCCCTTGTTGCCTCATGTTAAAAAACATCTGAACTCTGTTCAGTATATAAAACTGCAAAA
GTTTGTGGAAGATAATAATTACAAGCTTTCATTAAAGATAGAACCAGGGACAAGCACACCACGTTCTGCTGCCTCCAGGG
AAGATTTAGTAGGTCCTGAAGTGGGGGCATCACCACAGAGTGGGAGGAAGAGTGTGGCCACTGAAGGAGCCTTGCCACCA
CAGACACCCCCATCCCCATGGAATCTGATTCCATGTGGACATAGGAAGTGCCATAGCTTGGATTATAATTTCATTCATAA
AATGAACACAGCAGAGTTTAAGAGTGCAACATTCCCAAATGCAGGGCCAAGACATCTGTTAGATGATAGCATCATGAAAT
CCCATGCACCATCTCAAGGCCAAGTTGAAAGTTCTACTCTTTCTAGTGGAATATCAAAAGGTAGCAATGATGGTTCTGAA
CTAAGTGAAGAGACCTCATGGCTTGCTTTTGAA

Alignment

ORF - retro_ocun_1703 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.33 %
• Parental protein coverage: 71.18 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MALMNGQASSVSLAATASEKSSSSESLSDKGSELKKSFDAVVFDVLKVTPEEYAGQITLMDVPVFKAIQP
          MALMNGQASSVSLAATASE.S.SSESLSDKGSELKKSFDA.V.DVLKVTPEEY.GQITLMDVPVFKAIQP
Retrocopy MALMNGQASSVSLAATASENSRSSESLSDKGSELKKSFDAMVLDVLKVTPEEYVGQITLMDVPVFKAIQP

Parental  DELSSCGWNKKEKYSSAPNAVAFTRRFNHVSFWVVREILHAQTLKIRAEVLSHYIKTAKKLYELNNLHAL
          DELSSCGWNKKEKYSS.PNAVAFTRRFNHV.FWVVREILHAQTLKIRAEVLSHY.KTAKKLYELNNLHAL
Retrocopy DELSSCGWNKKEKYSSVPNAVAFTRRFNHVNFWVVREILHAQTLKIRAEVLSHYMKTAKKLYELNNLHAL

Parental  MAVVSGLQSAPIFRLTKTWALLSRKDKTTFEKLEYVMSKEDNYKRLRDYISSLKMTPCIPYLGIYLSDLT
          MA.VSGLQSAPIFRLTKTWALLS.KDKTTFEKLEYV.SKEDN.KRL.DY.SSLKMTP...YLGIYLSDLT
Retrocopy MAMVSGLQSAPIFRLTKTWALLSKKDKTTFEKLEYVVSKEDNCKRL*DYVSSLKMTP---YLGIYLSDLT

Parental  YIDSAYPSTGSILENEQRSNLMNNILRIISDLQQSCEYDIPLLPHVQKYLNSVQYIEELQKFVEDDNYKL
          YIDSAYPSTGSILE.EQRSNLMNNILRIISDLQQSCEYDIPLLPHV.K.LNSVQYI..LQKFVED.NYKL
Retrocopy YIDSAYPSTGSILEIEQRSNLMNNILRIISDLQQSCEYDIPLLPHVKKHLNSVQYI-KLQKFVEDNNYKL

Parental  SLKIEPGTSTPRSAASREDLVGPEVGASPQSGRKSVAAEGALLPQTPPSPRNLIPHGHRKCHSLGYNFIH
          SLKIEPGTSTPRSAASREDLVGPEVGASPQSGRKSVA.EGAL.PQTPPSP.NLIP.GHRKCHSL.YNFIH
Retrocopy SLKIEPGTSTPRSAASREDLVGPEVGASPQSGRKSVATEGALPPQTPPSPWNLIPCGHRKCHSLDYNFIH

Parental  KMNTAEFKSATFPNAGPRHLLDDSVMEPHAPSRGQAESSTLSSGISIGSSDGSELSEETSWPAFE
          KMNTAEFKSATFPNAGPRHLLDDS.M..HAPS.GQ.ESSTLSSGIS.GS.DGSELSEETSW.AFE
Retrocopy KMNTAEFKSATFPNAGPRHLLDDSIMKSHAPSQGQVESSTLSSGISKGSNDGSELSEETSWLAFE

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	0.33 RPM	11.76 RPM
SRP017611_kidney	0.20 RPM	4.87 RPM
SRP017611_liver	0.08 RPM	18.88 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1703 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1703 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1703 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	ENSOCUG00000005161	1 retrocopy	retro_ocun_1703 ,