RetrogeneDB ID:

retro_ocun_43

Retrocopy
location
Organism:Rabbit (Oryctolagus cuniculus)
Coordinates:1:144761960..144762536(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSOCUG00000017602
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:RAC2
Ensembl ID:ENSOCUG00000016115
Aliases:None
Description:ras-related C3 botulinum toxin substrate 2 (rho family, small GTP binding protein Rac2) [Source:HGNC Symbol;Acc:9802]


Retrocopy-Parental alignment summary:






>retro_ocun_43
ATGCAGAGCATCAAGTGTGTGGTGGTGGGTGATGGAGCAGTGGGCAAGACGTGCCTGCTCATCTGCTACACAACCAATGC
CTTCCCCAAAGAGTACATCCCCACGGTGTTCGACAATTACAGTGCCCAGAGCGCAGTGGATGGGCGCACAGTGAACCTGA
ACCTGTGGGACACTGCGGGCCAGGAGGAGTACGACCGCCTCCGCACACTCTCCTATCCTCAGACCAACGTCTTCGTCATC
TGTTTCTCCATTGCCAGCCCGCCCTCCTACGAGAATGTGCGGCACAAATGGCACCCGGAAGTGTGCCACCACTGCCCCGA
CGTGCCCATCCTCCTGGTGGGCACCAAGAAGGACCTGAGAGCCCAGCCTGACACCCTACGGCGCCTCAAGGAGCAGGGCC
AGGCGCCCATCACACCGCAGCAGGGCCAGGCACTGGCCAAGCAGATCCACGCTGTGCGCTACCTCGAGTGCTCGGCCCTG
CAGCAGGACGGCGTCAAGGAAGTGTTTGCCGAGGCTGTCCGGGCTGTGCTCAACCCCACACCGATCAAGCGTGGGCGGTC
CTGTGTCCTCTTGTGA

ORF - retro_ocun_43 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 70.83 %
Parental protein coverage: 100.0 %
Number of stop codons detected: 0
Number of frameshifts detected: 0


Retrocopy - Parental Gene Alignment:

ParentalMQAIKCVVVGDGAVGKTCLLISYTTNAFPGEYIPTVFDNYSANVMVDSKPVNLGLWDTAGQEDYDRLRPL
MQ.IKCVVVGDGAVGKTCLLI.YTTNAFP.EYIPTVFDNYSA...VD...VNL.LWDTAGQE.YDRLR.L
RetrocopyMQSIKCVVVGDGAVGKTCLLICYTTNAFPKEYIPTVFDNYSAQSAVDGRTVNLNLWDTAGQEEYDRLRTL
ParentalSYPQTDVFLICFSLVSPASYENVRAKWYPEVRHHCPSTPIILVGTKLDLRDDKDTIEKLKEKKLAPITYP
SYPQT.VF.ICFS..SP.SYENVR.KW.PEV.HHCP..PI.LVGTK.DLR...DT...LKE...APIT..
RetrocopySYPQTNVFVICFSIASPPSYENVRHKWHPEVCHHCPDVPILLVGTKKDLRAQPDTLRRLKEQGQAPITPQ
ParentalQGLALAKEIDSVKYLECSALTQRGLKTVFDEAIRAVLCPQPTRQQKRPCSIL
QG.ALAK.I..V.YLECSAL.Q.G.K.VF.EA.RAVL.P.P.....R.C..L
RetrocopyQGQALAKQIHAVRYLECSALQQDGVKEVFAEAVRAVLNPTPIK-RGRSCVLL

Legend:
*Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide






RNA-Seq - click to see more details

(Hint: click retrocopy or parental gene accession number on the plot's legend, to show / hide expression level values)

Expression validation based on RNA-Seq data:
Library Retrocopy expression Parental gene expression
SRP017611_brain 12 .69 RPM 2 .21 RPM
SRP017611_kidney 15 .51 RPM 2 .33 RPM
SRP017611_liver 9 .09 RPM 4 .01 RPM

ChIP-Seq - click to see more details

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_ocun_43 retrocopy.

TSS - click to see more details

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab - click to see more details

retro_ocun_43 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ocun_43 has 6 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_28
Gorilla gorilla retro_ggor_188
Pongo abelii retro_pabe_21
Macaca mulatta retro_mmul_210
Mus musculus retro_mmus_234
Rattus norvegicus retro_rnor_230
Parental genes homology:
Parental genes homology involve 23 parental genes, and 56 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000098892 retrocopies
retro_amel_1691, retro_amel_647,
Callithrix jacchus ENSCJAG000000021444 retrocopies
retro_cjac_1158, retro_cjac_1954, retro_cjac_2917, retro_cjac_847,
Equus caballus ENSECAG000000225702 retrocopies
retro_ecab_619, retro_ecab_705,
Erinaceus europaeus ENSEEUG000000095091 retrocopy
retro_eeur_20,
Felis catus ENSFCAG000000257762 retrocopies
retro_fcat_1064, retro_fcat_826,
Gorilla gorilla ENSGGOG000000106122 retrocopies
retro_ggor_1403, retro_ggor_188,
Loxodonta africana ENSLAFG000000130121 retrocopy
retro_lafr_117,
Macropus eugenii ENSMEUG000000122952 retrocopies
retro_meug_252, retro_meug_552,
Microcebus murinus ENSMICG000000177754 retrocopies
retro_mmur_1104, retro_mmur_1557, retro_mmur_20, retro_mmur_600,
Myotis lucifugus ENSMLUG000000126682 retrocopies
retro_mluc_326, retro_mluc_860,
Macaca mulatta ENSMMUG000000188542 retrocopies
retro_mmul_1346, retro_mmul_210,
Mustela putorius furoENSMPUG000000126822 retrocopies
retro_mputfur_872, retro_mputfur_911,
Nomascus leucogenys ENSNLEG000000147597 retrocopies
retro_nleu_1215, retro_nleu_1330, retro_nleu_2094, retro_nleu_2355, retro_nleu_689, retro_nleu_724, retro_nleu_87,
Oryctolagus cuniculus ENSOCUG000000099561 retrocopy
retro_ocun_305,
Oryctolagus cuniculus ENSOCUG000000099861 retrocopy
retro_ocun_60,
Oryctolagus cuniculus ENSOCUG00000016115 1 retrocopy
retro_ocun_43 ,
Otolemur garnettii ENSOGAG000000041381 retrocopy
retro_ogar_2977,
Pongo abelii ENSPPYG000000117913 retrocopies
retro_pabe_1591, retro_pabe_21, retro_pabe_3818,
Pteropus vampyrus ENSPVAG000000022812 retrocopies
retro_pvam_21, retro_pvam_609,
Sarcophilus harrisii ENSSHAG000000148521 retrocopy
retro_shar_763,
Sus scrofa ENSSSCG000000219444 retrocopies
retro_sscr_40, retro_sscr_565, retro_sscr_582, retro_sscr_882,
Ictidomys tridecemlineatus ENSSTOG000000237661 retrocopy
retro_itri_510,
Tursiops truncatus ENSTTRG000000010998 retrocopies
retro_ttru_1029, retro_ttru_1065, retro_ttru_1188, retro_ttru_1599, retro_ttru_1904, retro_ttru_318, retro_ttru_379, retro_ttru_825,


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