RetrogeneDB ID:

retro_ocun_1092

Retrocopy
location
Organism:Rabbit (Oryctolagus cuniculus)
Coordinates:2:43135255..43136402(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSOCUG00000024237
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:PSAT1
Ensembl ID:ENSOCUG00000007765
Aliases:None
Description:phosphoserine aminotransferase 1 (PSAT1), mRNA [Source:RefSeq mRNA;Acc:NM_001082271]


Retrocopy-Parental alignment summary:






>retro_ocun_1092
GGGAGGGGGAAGGCAGCCAGCGCTGGGCGCACACTTGGCGCGGCGCGGCCGGGGACACCCGCTGGACACACTGTGGCTCC
TCAGTAGCTGACTCACCGCCCGCACCGCGGCGCCATGGATTCTCTGAGGCCGATTGTCAACTTCAGGTCGGGCCCGCCAA
GCTTCGTGCCCGGTATTGTTAGAGATACAGGAAGAATTACTGGACTACAAAAGACTTGGCATTAGTGCCCTTGAAATGAG
TCATAGGTTCTCAGATTTTGCCAAGATTGTTCACAACACAGAGAATCATGTGGGGGAATTGTTAGCAGTTCCAGACAAAT
ACAAGGTGATTTTTCTGCAAGGAGGTGGCCTTGGCCAGTTCAGTGCTGTCCCCTTAAACCTGACTGGCCTGAAACCCGGA
AGGTGTGCTGACTATGTGGTGACAGGGCTTTGGCCAGCAAAGGCTGCAGAAGAAGCTAAGAAGTTTGGGACTGTGACTAT
CATCCACCCTAAACTGTGGAGTTACACAAAAATCCCAGGTCCAAGCATCTGGAACCTTAATCCAGATGCCTCCTACGTGT
ACTATTGCACAAATGAGACAGTGCACGGCGTGGAGTTTGACTTCGTGCCTGATGTCAAGGGAGCCATTCTGGTTTGTGAC
ATGACCACAAACTTCCTCTCCAGGCCAGCAGATGTTTCCAAGTTTGGTGTGATTTTTGCTGGTGCCCAAAAGAACGTGGG
CTCTGCAGGAGCCACGGTGGTGATTGTCCGCGATGACCTGCTGGGGTTCGCCCTCCGAGACTGCCCCTCTGTCCTGGAGT
ACACAGTGCAGGCCACAAGCAACTCCTTGTACAACACGCCCCGTGTTTTAGCCTCTGTGTCGTGAGCTTGGTCCTGGAGC
AGATTAAGAACAGTGGTGGGGCAGCTGCCACAAAGAAACTCAGCACCATCAAGTCTCAAAAGATTTATGAAATTATCAAT
AACTAGCAAGGATTCTACCTCTGCCTGGTGGAGCCCCGAAATGGAAGCATGATGAATATTCCATCCCATATCGGCAACAC
CAGGGGGGACGAAGCTTTAGAAAAAATGATTCCTCAATAAAGCTCTGGAGCTCCATATGATCTCCCTGAAAGCACCCAGG
TCCATAGGAGGCATCTGGGTCTCTCTA

ORF - retro_ocun_1092 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 77.12 %
Parental protein coverage: 79.88 %
Number of stop codons detected: 2
Number of frameshifts detected: 4


Retrocopy - Parental Gene Alignment:

ParentalGRRKAASAGRTLGAARPR-GTHWTRRGSSVADSPPAPQRHAMDSPRQIVNFGPGPAKLPHSVLLEIQKEL
GR.KAASAGRTLGAARP...T.WT..GSSVADSPPAP.RH...........G..PAKL.........K..
RetrocopyGRGKAASAGRTLGAARPG<DTRWTHCGSSVADSPPAPRRHGFSEADCQLQVG--PAKLRARYC*RYRKNY
ParentalLDYKGLGI-SVLEMSHRSSDFAKIVNNTENLVRELLAVPDNYKVIFLQGGGCGQFSAVPLNLIGLKPGRC
...K.L...S.LEMSHR.SDFAKIV.NTEN.V.ELLAVPD.YKVIFLQGGG.GQFSAVPLNL.GLKPGRC
RetrocopyWTTKDLAL<SALEMSHRFSDFAKIVHNTENHVGELLAVPDKYKVIFLQGGGLGQFSAVPLNLTGLKPGRC
ParentalADYVVTGAWSAKAAEEAKKFGTVNIVHPKLGSYTKIPDPSTWNLNPDASYVYYCANETVHGVEFDFVPDV
ADYVVTG.W.AKAAEEAKKFGTV.I.HPKL.SYTKIP.PS.WNLNPDASYVYYC.NETVHGVEFDFVPDV
RetrocopyADYVVTGLWPAKAAEEAKKFGTVTIIHPKLWSYTKIPGPSIWNLNPDASYVYYCTNETVHGVEFDFVPDV
ParentalKGAILVCDMSSNFLSRPVDVSKFGVIFAGAQKNVGAAGVTVVIVRDDLLGFALRECPSVLEYKVQATSSS
KGAILVCDM..NFLSRP.DVSKFGVIFAGAQKNVG.AG.TVVIVRDDLLGFALR.CPSVLEY.VQATS.S
RetrocopyKGAILVCDMTTNFLSRPADVSKFGVIFAGAQKNVGSAGATVVIVRDDLLGFALRDCPSVLEYTVQATSNS
ParentalLYNTP-PCFSIYVMGLVLEWIKNNGGAAAMKKLSTIKSQMIYEIIDNSQGFYVCPVEPRNRSMMNIPFRI
LYNTP.PCFS..V..LVLE.IKN.GGAAA.KKLSTIKSQ.IYEII.N.QGFY.C.VEPRN.SMMNIP..I
RetrocopyLYNTP<PCFSLCVVSLVLEQIKNSGGAAATKKLSTIKSQKIYEIINN*QGFYLCLVEPRNGSMMNIPSHI
ParentalGNAKGDEALEKR-FLDKALELHMISLKGHRSVGGVRVSL
GN..GDEALEK..FL.KALELHMISLK..RS.GG..VSL
RetrocopyGNTRGDEALEKM>FLNKALELHMISLKAPRSIGGIWVSL

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 133 .34 RPM
SRP017611_kidney 0 .00 RPM 309 .34 RPM
SRP017611_liver 0 .08 RPM 120 .31 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_1092 retrocopy.

TSS - click to see more details

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab - click to see more details

retro_ocun_1092 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ocun_1092 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 18 parental genes, and 28 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000068981 retrocopy
retro_amel_375,
Bos taurus ENSBTAG000000139601 retrocopy
retro_btau_1658,
Canis familiaris ENSCAFG000000015701 retrocopy
retro_cfam_269,
Choloepus hoffmanni ENSCHOG000000038171 retrocopy
retro_chof_2702,
Callithrix jacchus ENSCJAG000000033191 retrocopy
retro_cjac_1203,
Echinops telfairi ENSETEG000000041581 retrocopy
retro_etel_99,
Homo sapiens ENSG000001350693 retrocopies
retro_hsap_2267, retro_hsap_4054, retro_hsap_412,
Gorilla gorilla ENSGGOG000000154801 retrocopy
retro_ggor_407,
Loxodonta africana ENSLAFG000000179172 retrocopies
retro_lafr_1249, retro_lafr_660,
Macaca mulatta ENSMMUG000000118682 retrocopies
retro_mmul_1029, retro_mmul_2341,
Mustela putorius furoENSMPUG000000125661 retrocopy
retro_mputfur_808,
Nomascus leucogenys ENSNLEG000000029893 retrocopies
retro_nleu_1010, retro_nleu_1288, retro_nleu_2805,
Oryctolagus cuniculus ENSOCUG00000007765 1 retrocopy
retro_ocun_1092 ,
Pongo abelii ENSPPYG000000193133 retrocopies
retro_pabe_1950, retro_pabe_308, retro_pabe_3328,
Pan troglodytes ENSPTRG000000210452 retrocopies
retro_ptro_1606, retro_ptro_316,
Rattus norvegicus ENSRNOG000000139711 retrocopy
retro_rnor_1663,
Tupaia belangeri ENSTBEG000000129461 retrocopy
retro_tbel_1577,
Tarsius syrichta ENSTSYG000000000932 retrocopies
retro_tsyr_1073, retro_tsyr_1212,


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