RetrogeneDB ID:

retro_cfam_1441

Retrocopy
location
Organism:Dog (Canis familiaris)
Coordinates:31:1174962..1175620(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:RPE
Ensembl ID:ENSCAFG00000013811
Aliases:None
Description:ribulose-5-phosphate-3-epimerase [Source:HGNC Symbol;Acc:10293]


Retrocopy-Parental alignment summary:






>retro_cfam_1441
ATGGCATCTGGCTGCAAGATTGGCCTGTCCATCCTTAACAGCGATTTGGACAATTTAGGGGCTCAGTGCCTCCGGATCCT
GGACTCTGGGGGCCGATTACTTGCACTTGGATGTAACAGACGGGCCTTTTGTTCCCAACATCACCTTTGGACACCCTGTG
GCAGAAAGCCTCTGAAAGTAGCGAGGCCAGGACCCTTTCTTTGATAATGCACATGATGATATCCAGACCAGAACAGCAGG
TAAAACCAATGGCTGTAGCAGGAGCCAATGGATACACCTTTCATCTTGAGGCAACAAAAACCCAGGGGCTTTGATTAAAG
ACATTCGGGAGAATGGGATGAAGCTTGGCCTTGCCATCAAACCAGGAACTACAGTTGATTATTTGGCACCGTGGGCTAAT
CAGATAGATATGGCCTTGGTTATGACAGTGGAACCTGGGTTTGGAGGGCAGAAATTCATGGAAGATATGATGCTGAGGGT
TAATTGGTTGAGAATGCAATTCCCATCTTTGGGCATAGAAGTCGATGGTGGAGTAGGTCCTGACACTATCCATAAGTGTG
CAGAGGCAGGAGCTAACATGATTGTGTCTGGCAGTGCCATTATGAGGAGGGATGACCCCAGATCTGTGATCAACCTGTTA
AGAAATGTTTGCTCAGAA

ORF - retro_cfam_1441 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 88.29 %
Parental protein coverage: 96.05 %
Number of stop codons detected: 2
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalMASGCRIGPSILNSDLANLGAECLRMLDSG-ADYLHLDVMDGHFVPNITFGHPVVESLRKQLGQDPFFD-
MASGC.IG.SILNSDL.NLGA.CLR.LDSG.ADYLHLDV.DG.FVPNITFGHPV.ESL.K..GQDPFFD.
RetrocopyMASGCKIGLSILNSDLDNLGAQCLRILDSG>ADYLHLDVTDGPFVPNITFGHPVAESL*K*RGQDPFFD>
ParentalMHMMVSRPEQWVKPMAVAGANQYTFHLEATE-NPGALIKDIRENGMKVGLAIKPGTTVEYLAPWANQIDM
MHMM.SRPEQ.VKPMAVAGAN.YTFHLEAT..NPGALIKDIRENGMK.GLAIKPGTTV.YLAPWANQIDM
RetrocopyMHMMISRPEQQVKPMAVAGANGYTFHLEATK<NPGALIKDIRENGMKLGLAIKPGTTVDYLAPWANQIDM
ParentalALVMTVEPGFGGQKFMEDMMPKVHWLRTQFPSLDIEVDGGVGPDTIHKCAEAGANMIVSGSAIMRSDDPR
ALVMTVEPGFGGQKFMEDMM..V.WLR.QFPSL.IEVDGGVGPDTIHKCAEAGANMIVSGSAIMR.DDPR
RetrocopyALVMTVEPGFGGQKFMEDMMLRVNWLRMQFPSLGIEVDGGVGPDTIHKCAEAGANMIVSGSAIMRRDDPR
ParentalSVINLLRNVCSE
SVINLLRNVCSE
RetrocopySVINLLRNVCSE

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
SRP012049_cerebellum 0 .00 RPM 8 .57 RPM
SRP017611_brain 0 .00 RPM 7 .86 RPM
SRP017611_kidney 0 .00 RPM 12 .68 RPM
SRP017611_liver 0 .00 RPM 6 .67 RPM

ChIP-Seq - click to see more details

Canis familiaris was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_cfam_1441 retrocopy.

TSS - click to see more details

Canis familiaris was not studied using FANTOM5 data.

Lab - click to see more details

retro_cfam_1441 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cfam_1441 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 24 parental genes, and 61 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000049653 retrocopies
retro_amel_1327, retro_amel_1363, retro_amel_827,
Bos taurus ENSBTAG000000478062 retrocopies
retro_btau_343, retro_btau_815,
Canis familiaris ENSCAFG00000013811 3 retrocopies
retro_cfam_1441 , retro_cfam_1596, retro_cfam_1623,
Choloepus hoffmanni ENSCHOG000000011105 retrocopies
retro_chof_1534, retro_chof_2386, retro_chof_392, retro_chof_492, retro_chof_574,
Callithrix jacchus ENSCJAG000000108222 retrocopies
retro_cjac_1199, retro_cjac_1560,
Dasypus novemcinctus ENSDNOG000000031931 retrocopy
retro_dnov_789,
Equus caballus ENSECAG000000000023 retrocopies
retro_ecab_245, retro_ecab_446, retro_ecab_562,
Homo sapiens ENSG000001977135 retrocopies
retro_hsap_133, retro_hsap_2553, retro_hsap_2620, retro_hsap_3330, retro_hsap_620,
Latimeria chalumnae ENSLACG000000028001 retrocopy
retro_lcha_21,
Loxodonta africana ENSLAFG000000141272 retrocopies
retro_lafr_675, retro_lafr_729,
Microcebus murinus ENSMICG000000099534 retrocopies
retro_mmur_1380, retro_mmur_268, retro_mmur_393, retro_mmur_713,
Macaca mulatta ENSMMUG000000105132 retrocopies
retro_mmul_366, retro_mmul_618,
Monodelphis domestica ENSMODG000000158276 retrocopies
retro_mdom_1181, retro_mdom_1676, retro_mdom_449, retro_mdom_490, retro_mdom_505, retro_mdom_667,
Mustela putorius furoENSMPUG000000079482 retrocopies
retro_mputfur_1066, retro_mputfur_1280,
Nomascus leucogenys ENSNLEG000000071723 retrocopies
retro_nleu_2263, retro_nleu_448, retro_nleu_638,
Oryctolagus cuniculus ENSOCUG000000169951 retrocopy
retro_ocun_768,
Otolemur garnettii ENSOGAG000000027781 retrocopy
retro_ogar_2673,
Pongo abelii ENSPPYG000000131324 retrocopies
retro_pabe_1052, retro_pabe_1878, retro_pabe_2340, retro_pabe_555,
Pteropus vampyrus ENSPVAG000000144522 retrocopies
retro_pvam_217, retro_pvam_636,
Sus scrofa ENSSSCG000000161521 retrocopy
retro_sscr_825,
Ictidomys tridecemlineatus ENSSTOG000000103221 retrocopy
retro_itri_1750,
Tarsius syrichta ENSTSYG000000033045 retrocopies
retro_tsyr_113, retro_tsyr_1153, retro_tsyr_1663, retro_tsyr_2129, retro_tsyr_546,
Tursiops truncatus ENSTTRG000000009081 retrocopy
retro_ttru_158,
Vicugna pacos ENSVPAG000000115851 retrocopy
retro_vpac_91,


Copyright © RetrogeneDB 2014-2017