RetrogeneDB ID:

retro_ocun_1886

Retrocopy
location
Organism:Rabbit (Oryctolagus cuniculus)
Coordinates:X:53025862..53027253(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSOCUG00000024906
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:AHCY
Ensembl ID:ENSOCUG00000008592
Aliases:None
Description:adenosylhomocysteinase [Source:HGNC Symbol;Acc:343]


Retrocopy-Parental alignment summary:






>retro_ocun_1886
TCCTGCCCAGCGCCGCCAGCCCAGTGCCTGATTTCTGCTCTAGGCCTGATCCCCTTTTCGCTCGTGTCCATCACCGCGTG
CAGCAATGCCGCCAGAATGTCTGACAAACTGCCCTACAAAGTCGCGGACATTGGCCTGGCTGCGTGGGGACGCAAGGCCC
TGGACATCGCCGAGAACGAGATGCCTGGCCTGATGCGCATGCGGGAGATGTACACGGCCTCCAAGCCACTGAAGGGCGCC
CGCATTGCCGGCTGCCTGCACATGACCGTGGAGACTGCCGTCCTCATTGAGACCCTTGTTGCCCTGGGCGCCAAGGTGCA
GTGGTCCAGCTGCAACATCTTTTCCACCCAGACCACACAGCGGTTGCCATTGCCAAGGCCGGCATTCCAGTGTATGCCTG
GAAGGGCGAAACAGACGAGGAGTACCTGTGGTGCATTGAGCAGACGCTCTACTTTAAGGACGGGCCCCTCAACATGATCC
TGGACGATGGCGGTGACCTCACCAACCTCATACACACCAAGTACCCACAGCTCCTGTCAGGCATCAGGGGCATCTCTGAG
GAGACCATGAGTGGGGTCTACAACCTCTACAAGATGATGGCCAATGGGGTCCTGAAGGTGCCTGCAATCAATGTCAGTGA
CTCCGTCACCAAGAGCAAATTTGACAACCTCTATGGCTGCCGGGAGTCCCTCATCGATGGCATCAAGCGGGCTACAGATG
TGATGATCACAGGCAAGGTGGTGGTGGTTGCAGGCTATGGCGACGTGGGCAGGGGCTGTGCCCAGGCCCTGAGGGGTTTT
GGGGCCCGTGTCATCATCACTGAGATCGACCCCATCAACGCACTGCAGGCTGCCATGGAGGGCTACGAGGTGACCTCCAT
GGATGAAGCCTGCAAGGAGGGCAACATCTTTGTCACTACCACAGGCTGTGTGGACATCATCCTTGGGCGGCACTTTGAGC
AGATGAAGGATGATGCCATCGTGTGTAACATGGGACACTTCAACGTGGAGATTGACGTCAAGTGGCTCAATGAGAATGCA
GTGGAGAAGGTGAACGTCAAGCCCCAGGTGGACCGCTATTGGCTGAAGAATGGGCGCCACATCATCCTGCTTGCCGAGGG
CCGGCTGGTCAATCTGGGCTGTGCCATGGGCCACCCCAGCTTCATGATGAGCAACTCCTTCACAAACCAGGTGCTGGCGC
AGATTGAGCTGTGGACCCACCCTGACAAGTATGCTGTAGGTGTTCACTTCCTGCCCAAGAAGCTGGACGAGGCAGTGGCT
GAAGCCCACCTGAGCAAGCTGAAAGTGAAGCTGACCAAGCTGACTGAGAAGCAGGCCCAGTACCTGGGCATGTCCCGTGA
TGGCCCTTTCAAGCCTGATCACTACCGCTAC

ORF - retro_ocun_1886 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 92.47 %
Parental protein coverage: 86.57 %
Number of stop codons detected: 0
Number of frameshifts detected: 1


Retrocopy - Parental Gene Alignment:

ParentalSCPAPPAQCLISALGLIPFSPVCITACSNAARMSDKLPYKVADIGLAAWGRKALDIAENEMPGLMRMREM
SCPAPPAQCLISALGLIPFS.V.ITACSNAARMSDKLPYKVADIGLAAWGRKALDIAENEMPGLMRMREM
RetrocopySCPAPPAQCLISALGLIPFSLVSITACSNAARMSDKLPYKVADIGLAAWGRKALDIAENEMPGLMRMREM
ParentalYSASKPLKGARIAGCLHMTVETAVLIETLVALGAEVQWSSCNIFSTQ-DHAAAAIAKAGIPVYAWKGETD
Y.ASKPLKGARIAGCLHMTVETAVLIETLVALGA.VQWSSCNIFSTQ.DH.A.AIAKAGIPVYAWKGETD
RetrocopyYTASKPLKGARIAGCLHMTVETAVLIETLVALGAKVQWSSCNIFSTQ<DHTAVAIAKAGIPVYAWKGETD
ParentalEEYLWCIEQTLYFKDGPLNMILDDGGDLTNLIHTKYPQLLSGIRGISEETTTGVHNLYKMMANGVLKVPA
EEYLWCIEQTLYFKDGPLNMILDDGGDLTNLIHTKYPQLLSGIRGISEET..GV.NLYKMMANGVLKVPA
RetrocopyEEYLWCIEQTLYFKDGPLNMILDDGGDLTNLIHTKYPQLLSGIRGISEETMSGVYNLYKMMANGVLKVPA
ParentalINVNDSVTKSKFDNLYGCRESLIDGIKRATDVMIAGKVAVVAGYGDVGKGCAQALRGFGARVIITEIDPI
INV.DSVTKSKFDNLYGCRESLIDGIKRATDVMI.GKV.VVAGYGDVG.GCAQALRGFGARVIITEIDPI
RetrocopyINVSDSVTKSKFDNLYGCRESLIDGIKRATDVMITGKVVVVAGYGDVGRGCAQALRGFGARVIITEIDPI
ParentalNALQAAMEGYEVTTMDEACKEGNIFVTTTGCVDIILGRHFEQMKDDAIVCNIGHFDVEIDVKWLNENAVE
NALQAAMEGYEVT.MDEACKEGNIFVTTTGCVDIILGRHFEQMKDDAIVCN.GHF.VEIDVKWLNENAVE
RetrocopyNALQAAMEGYEVTSMDEACKEGNIFVTTTGCVDIILGRHFEQMKDDAIVCNMGHFNVEIDVKWLNENAVE
ParentalKVNIKPQVDRYWLKNGRRIILLAEGRLVNLGCAMGHPSFVMSNSFTNQVLAQIELWTHPDKYAVGVHFLP
KVN.KPQVDRYWLKNGR.IILLAEGRLVNLGCAMGHPSF.MSNSFTNQVLAQIELWTHPDKYAVGVHFLP
RetrocopyKVNVKPQVDRYWLKNGRHIILLAEGRLVNLGCAMGHPSFMMSNSFTNQVLAQIELWTHPDKYAVGVHFLP
ParentalKKLDEAVAEAHLSKLNVKLTKLTEKQAQYLGMSRDGPFKPDHYRY
KKLDEAVAEAH...............AQYLGMSRDGPFKPDHYRY
RetrocopyKKLDEAVAEAHXXXXXXXXXXXXXXXAQYLGMSRDGPFKPDHYRY

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 .77 RPM 34 .55 RPM
SRP017611_kidney 0 .30 RPM 160 .75 RPM
SRP017611_liver 11 .10 RPM 741 .69 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_1886 retrocopy.

TSS - click to see more details

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab - click to see more details

retro_ocun_1886 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ocun_1886 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 18 parental genes, and 61 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000181011 retrocopy
retro_btau_1140,
Canis familiaris ENSCAFG000000075042 retrocopies
retro_cfam_1486, retro_cfam_552,
Callithrix jacchus ENSCJAG000000183037 retrocopies
retro_cjac_1028, retro_cjac_1248, retro_cjac_1806, retro_cjac_2132, retro_cjac_2839, retro_cjac_3287, retro_cjac_480,
Echinops telfairi ENSETEG000000025761 retrocopy
retro_etel_444,
Homo sapiens ENSG000001014446 retrocopies
retro_hsap_1496, retro_hsap_2325, retro_hsap_2365, retro_hsap_4213, retro_hsap_571, retro_hsap_803,
Gorilla gorilla ENSGGOG000000146945 retrocopies
retro_ggor_1148, retro_ggor_1795, retro_ggor_2822, retro_ggor_3087, retro_ggor_511,
Monodelphis domestica ENSMODG000000027531 retrocopy
retro_mdom_1974,
Mus musculus ENSMUSG000000275971 retrocopy
retro_mmus_197,
Nomascus leucogenys ENSNLEG000000100414 retrocopies
retro_nleu_1717, retro_nleu_2785, retro_nleu_40, retro_nleu_929,
Oryctolagus cuniculus ENSOCUG00000008592 1 retrocopy
retro_ocun_1886 ,
Otolemur garnettii ENSOGAG000000167873 retrocopies
retro_ogar_3223, retro_ogar_3401, retro_ogar_3402,
Pongo abelii ENSPPYG000000109359 retrocopies
retro_pabe_1247, retro_pabe_1978, retro_pabe_2108, retro_pabe_2189, retro_pabe_3446, retro_pabe_647, retro_pabe_658, retro_pabe_665, retro_pabe_718,
Pan troglodytes ENSPTRG000000134147 retrocopies
retro_ptro_1015, retro_ptro_1698, retro_ptro_1730, retro_ptro_2860, retro_ptro_3011, retro_ptro_559, retro_ptro_771,
Rattus norvegicus ENSRNOG000000177777 retrocopies
retro_rnor_1142, retro_rnor_1820, retro_rnor_1903, retro_rnor_2120, retro_rnor_569, retro_rnor_647, retro_rnor_839,
Sus scrofa ENSSSCG000000072781 retrocopy
retro_sscr_119,
Tarsius syrichta ENSTSYG000000071633 retrocopies
retro_tsyr_1178, retro_tsyr_1529, retro_tsyr_1582,
Tursiops truncatus ENSTTRG000000036321 retrocopy
retro_ttru_1666,
Xenopus tropicalis ENSXETG000000194861 retrocopy
retro_xtro_62,


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