RetrogeneDB ID:

retro_ocun_2

Retrocopy
location
Organism:Rabbit (Oryctolagus cuniculus)
Coordinates:15:70924777..70926427(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSOCUG00000025309
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:GK
Ensembl ID:ENSOCUG00000013023
Aliases:None
Description:glycerol kinase [Source:HGNC Symbol;Acc:4289]


Retrocopy-Parental alignment summary:






>retro_ocun_2
ATGGCAGCCCCGAGGAAAGCAGTTGTGGGGCCGTTGGTGGGGGCGGTGGTCCAGGGTACCAACTCCACTCGCTTTCTGGT
TTTCAATTCAAAAACAGCGGAACTACTTAGTCATCATCAGGTGGAATTAACACAGGAGTTCCCAAAAGAAGGATGGGTAG
AACAAGACCCTAAGGAAATTCTTCAGTCTGTGTATGAGTGCATAGCGAGAACGTGTGAGAAGCTTGGTGAACTGAATATT
GATATTTCCAACGTAAAAGCTATTGGTGTCAGCAATCAAAGGGAAACCACTGTCATCTGGGACAAGCTAACTGGAGAGCC
TCTCTACAATGCCATAGTGTGGCTTGATCTAAGAACCCAGGCTACGGTTGAGACGCTGAGTAAAAAAGTCCCGGGAAATA
ATAACTTTGTCAAGTCAAAGACAGGCCTTCCGCTCAGCACTTACTTCAGCGCTGTGAAAATTCGTTGGTTGCTTGACAAT
GTGAGACAAGTTCAAAAGGCCGTTGAAGAAGGTAGAGCTCTTTTTGGGACCATTGATTCGTGGCTTATCTGGAGTTTGAC
AGGAGGAGTCAACGGAGGTGTCCATTGTACGGATGTAACAAATGCAAGTAGGACAATGCTTTTCAACATCCACTCTTTGG
AATGGGACAAAGAGCTCTGTGACTTTTTTGAAGTTCCAATGAACATTCTTCCAAATGTCTGGAGTTCTTCTGAGATCTAT
GGTCTAATGAAAGTTGGAGCCTTGGAAGGTGTGCCAATATCTGGGTGTCTGGGGGACCAGTCTGCTGCTTTAGTAGGACA
AATGTGCTTCCAGGAAGGACAAGCAAAAAACACATACGGAACAGGCTGTTTCTTACTGTGTAATACAGGTCACAAGTGTG
TATTTTCTGAACATGGCCTCCTGACCACAGTCGCTTACAAACTAGGCAGAGACAAACCAGTTTACTATGCCTTGGAAGGT
TCTGTTGCCATAGCTGGGGCTGTTGTTCGTTGGCTGAGAGACAATCTTGGAATTATACAGACCTCAGAAGAAGTTGAAAA
ACTTGCTCAAGAAGTTGGTACTTCTTATGGCTGCTATTTTGTCCCTGCCTTTTCAGGGTTATATGCACCGTACTGGGACC
CAAGTGCAAGAGGCATAATCTGTGGTCTCACTCAGTTTACCAATAAAAATCATATTGCTTTTGCTGCACTGGAGGCTGTT
TGTTTCCAGACCCGAGAGATTTTGGATGCCATGAACCGTGACTGTAGAATTCCACTCAGTCATTTGCAAGTAGATGGAGG
AATGACCAACAACAAAATTCTCATGCAACTACAAGCAGACATCCTGTGTATTCCAATAGTAAAGTCATCCATGCCCGAAA
CCACTGCACTTGGAGCTGCCATGGCAGCAGGGGCTGCAGAAGGAGTAGGTGTTTGGAGCCTTGACCCTGAGGATTTGTCA
GCTGTCATGATGGAACAGTTCGAACCTCAGATCCAGGCCACAGAAAGTGAAGTACGTTATTCTACATGGAAGAAGGCTGT
GATGAAGTCAATGGCTTGGGTTACAAGTCCTGAGGACCCTACTATCTTCTCTAGTCTGCCCTTGGGGTTTTTTATAGTGA
GTAGCATGATAATGTTAATTGGAGCAAGATATATCTCAGGTATACCATAA

ORF - retro_ocun_2 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 90.38 %
Parental protein coverage: 100.0 %
Number of stop codons detected: 0
Number of frameshifts detected: 0


Retrocopy - Parental Gene Alignment:

ParentalMAATKKAILGPLVGAVDQGTSSTRFLVFNSKTAELLSHHQVEIKQEFPKEGWVEQDPKEILQSVYECIEK
MAA..KA..GPLVGAV.QGT.STRFLVFNSKTAELLSHHQVE..QEFPKEGWVEQDPKEILQSVYECI..
RetrocopyMAAPRKAVVGPLVGAVVQGTNSTRFLVFNSKTAELLSHHQVELTQEFPKEGWVEQDPKEILQSVYECIAR
ParentalTCEKLGQLNIDISNIKAIGVSNQRETTVVWDKLTGEPLYNAVVWLDLRTQSTVENLSKRIPGNNNFVKSK
TCEKLG.LNIDISN.KAIGVSNQRETTV.WDKLTGEPLYNA.VWLDLRTQ.TVE.LSK..PGNNNFVKSK
RetrocopyTCEKLGELNIDISNVKAIGVSNQRETTVIWDKLTGEPLYNAIVWLDLRTQATVETLSKKVPGNNNFVKSK
ParentalTGLPLSTYFSAVKLRWLLDNVRKVQKAVEENRALFGTIDSWLIWSLTGGVNGGVHCTDVTNASRTMLFNI
TGLPLSTYFSAVK.RWLLDNVR.VQKAVEE.RALFGTIDSWLIWSLTGGVNGGVHCTDVTNASRTMLFNI
RetrocopyTGLPLSTYFSAVKIRWLLDNVRQVQKAVEEGRALFGTIDSWLIWSLTGGVNGGVHCTDVTNASRTMLFNI
ParentalHSLEWDKELCEFFEIPMEILPNVRSSSEIYGLMKAGALEGVPISGCLGDQSAALVGQMCFQDGQAKNTYG
HSLEWDKELC.FFE.PM.ILPNV.SSSEIYGLMK.GALEGVPISGCLGDQSAALVGQMCFQ.GQAKNTYG
RetrocopyHSLEWDKELCDFFEVPMNILPNVWSSSEIYGLMKVGALEGVPISGCLGDQSAALVGQMCFQEGQAKNTYG
ParentalTGCFLLCNTGHKCVFSEHGLLTTVAYKLGRDKPVYYALEGSVAIAGAVIRWLRDNLGIIKSSEEIEKLAK
TGCFLLCNTGHKCVFSEHGLLTTVAYKLGRDKPVYYALEGSVAIAGAV.RWLRDNLGII..SEE.EKLA.
RetrocopyTGCFLLCNTGHKCVFSEHGLLTTVAYKLGRDKPVYYALEGSVAIAGAVVRWLRDNLGIIQTSEEVEKLAQ
ParentalEVGTSYGCYFVPAFSGLYAPYWEPSARGIICGLTQFTNKCHIAFAALEAVCFQTREILDAMNRDCGIPLS
EVGTSYGCYFVPAFSGLYAPYW.PSARGIICGLTQFTNK.HIAFAALEAVCFQTREILDAMNRDC.IPLS
RetrocopyEVGTSYGCYFVPAFSGLYAPYWDPSARGIICGLTQFTNKNHIAFAALEAVCFQTREILDAMNRDCRIPLS
ParentalHLQVDGGMTSNKILMQLQADILYIPVVKPSMPETTALGAAMAAGAAEGVGVWSLEPEDLSAVTMERFEPQ
HLQVDGGMT.NKILMQLQADIL.IP.VK.SMPETTALGAAMAAGAAEGVGVWSL.PEDLSAV.ME.FEPQ
RetrocopyHLQVDGGMTNNKILMQLQADILCIPIVKSSMPETTALGAAMAAGAAEGVGVWSLDPEDLSAVMMEQFEPQ
ParentalINAEESEIRYSTWKKAVMKSMGWVTTQSPESGDPSIFCSLPLGFFIVSSMVMLIGARYISG
I.A.ESE.RYSTWKKAVMKSM.WVT..SPE..DP.IF.SLPLGFFIVSSM.MLIGARYISG
RetrocopyIQATESEVRYSTWKKAVMKSMAWVT--SPE--DPTIFSSLPLGFFIVSSMIMLIGARYISG

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 0 .00 RPM 9 .49 RPM
SRP017611_kidney 0 .00 RPM 97 .91 RPM
SRP017611_liver 0 .00 RPM 21 .50 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_2 retrocopy.

TSS - click to see more details

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab - click to see more details

retro_ocun_2 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ocun_2 has 1 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Equus caballus retro_ecab_9
Parental genes homology:
Parental genes homology involve 20 parental genes, and 33 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000091611 retrocopy
retro_amel_45,
Canis familiaris ENSCAFG000000137131 retrocopy
retro_cfam_19,
Callithrix jacchus ENSCJAG000000076333 retrocopies
retro_cjac_125, retro_cjac_3161, retro_cjac_4035,
Cavia porcellus ENSCPOG000000032612 retrocopies
retro_cpor_11, retro_cpor_20,
Equus caballus ENSECAG000000035991 retrocopy
retro_ecab_9,
Echinops telfairi ENSETEG000000082792 retrocopies
retro_etel_2000, retro_etel_247,
Felis catus ENSFCAG000000042641 retrocopy
retro_fcat_140,
Homo sapiens ENSG000001988144 retrocopies
retro_hsap_3087, retro_hsap_3120, retro_hsap_4885, retro_hsap_70,
Loxodonta africana ENSLAFG000000076321 retrocopy
retro_lafr_30,
Myotis lucifugus ENSMLUG000000010462 retrocopies
retro_mluc_151, retro_mluc_853,
Monodelphis domestica ENSMODG000000024171 retrocopy
retro_mdom_234,
Mus musculus ENSMUSG000000250592 retrocopies
retro_mmus_119, retro_mmus_97,
Nomascus leucogenys ENSNLEG000000101022 retrocopies
retro_nleu_1650, retro_nleu_771,
Oryctolagus cuniculus ENSOCUG00000013023 2 retrocopies
retro_ocun_2 , retro_ocun_81,
Pteropus vampyrus ENSPVAG000000124601 retrocopy
retro_pvam_1417,
Rattus norvegicus ENSRNOG000000341162 retrocopies
retro_rnor_114, retro_rnor_34,
Sarcophilus harrisii ENSSHAG000000064701 retrocopy
retro_shar_35,
Sus scrofa ENSSSCG000000122022 retrocopies
retro_sscr_479, retro_sscr_59,
Ictidomys tridecemlineatus ENSSTOG000000087321 retrocopy
retro_itri_1436,
Tarsius syrichta ENSTSYG000000082491 retrocopy
retro_tsyr_29,


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