RetrogeneDB ID:

retro_cfam_2143

Retrocopy
location
Organism:Dog (Canis familiaris)
Coordinates:X:32579031..32580232(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:GLUL
Ensembl ID:ENSCAFG00000013102
Aliases:None
Description:Canis lupus familiaris glutamate-ammonia ligase (GLUL), mRNA. [Source:RefSeq mRNA;Acc:NM_001002965]


Retrocopy-Parental alignment summary:






>retro_cfam_2143
CCCGGCCTCCTCTCCTCACCGCACCTCGCTCTCGCAGCCTGCCTGCCCTGCTGCTTGCGACCCACCCAGAACAACTTCCA
CCATGGCCACCTCTGCGAGTTCCCACTTGAACAAAGGCATCAAGCAGGTGTACATGTCCCTGCCTCAGGGCGAGAAAGTG
CAAGCTATGTATATTTGGATTGACGGGACTGGAGAAGGATTACGTTGCAAGACCCGGACCTTGGACAGTGAGCCCAAGGG
TGTTGAAGAGTTGCCTGAATGGAATTTTGATGGCTCTAGCACCTTTCAATCTGAAGGCTCCAACAGTGACATGTATCTTG
TCCCTGCTGCCATGTTTCGTGACCCTTTCTGCAAAGACCCCAACAAGCTGGTATTCTGTGAAGTCTTCAAATACAACAGA
AAGCCTGCAGAAACCAATTTAAGGCATACCTGTAAACGGATAATGGACATGGTGAGCAACCAGCACCCCTGGTTTGGAAT
GGAGCAGGAATATACTCTCATGGGCACAGATGGGCACCCTTTTGGTTGGCCTTCCAATGGCTTCCCTGGGCCCCAAGGTC
CGTACTACTGTGGTGTGGGAGTGGACAAAGCCTATGGCAGGGATATCGTGGAGGCTCACTACCGGTCCTGCTTGTACGCT
GGCATCAGGATTGCTGGGACAAACGCTGAGGTCATGCCTGCCCAGTGGGAATTCCAGATAGGACCCTGTGAAGGAATCAA
CATGGGAGATCATCTCTGGGTGGCCCGTTTCATCTTGCATCATGTATGTGAAGACTTCAGAGTGATAGCAACCTTTGATC
TTAAGCCCATTCCCGGAAACTGGAATGGTGCAGGCTGCCACACCAACTTCAGCACCAAGGCCATGCGAGAGGAGAATGGT
CTAAAGTACATTGAGGAGTCCATTGAGAAACTGAGCAAGTGGCACCAGTACCACATCTGAGCCTACGATCCCAAGGGAGG
CCTGGATAATGCCTGGCGCCTAACTGGATTCCATGAGACATCCAACATCAATGACTTTTCTGCCGGCGTGGCCAACCATG
GTGCTAGCATCCGCATTCCCCGGACTGTCGGCCAGGAGAAGAAGGGTTACTTTGAAGACCGTCACCCTTCTGCCAACTGC
GACCCCTTTTCGGTGACAGAAGCCCTCATCTGCACATGTCTTCTCAACGAAACTGGCAATGAACACTTCCAGTACAAAAA
C

ORF - retro_cfam_2143 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 91.83 %
Parental protein coverage: 99.75 %
Number of stop codons detected: 1
Number of frameshifts detected: 1


Retrocopy - Parental Gene Alignment:

ParentalPPLLAAPR-SRGPPALLPATRPVLLCRTTSTMATSASSHLNKGIKQVYMSLPQGEKVQAMYIWIDGTGEG
P.LL..P..S...PA...A..P....RTTSTMATSASSHLNKGIKQVYMSLPQGEKVQAMYIWIDGTGEG
RetrocopyPGLLSSPH>SLSQPACPAACDPP---RTTSTMATSASSHLNKGIKQVYMSLPQGEKVQAMYIWIDGTGEG
ParentalLRCKTRTLDSEPKGVEELPEWNFDGSSTFQSEGSNSDMYLVPAAMFRDPFRKDPNKLVFCEVFKYNRKPA
LRCKTRTLDSEPKGVEELPEWNFDGSSTFQSEGSNSDMYLVPAAMFRDPF.KDPNKLVFCEVFKYNRKPA
RetrocopyLRCKTRTLDSEPKGVEELPEWNFDGSSTFQSEGSNSDMYLVPAAMFRDPFCKDPNKLVFCEVFKYNRKPA
ParentalETNLRHTCKRIMDMVSNQHPWFGMEQEYTLMGTDGHPFGWPSNGFPGPQGPYYCGVGADKAYGRDIVEAH
ETNLRHTCKRIMDMVSNQHPWFGMEQEYTLMGTDGHPFGWPSNGFPGPQGPYYCGVG.DKAYGRDIVEAH
RetrocopyETNLRHTCKRIMDMVSNQHPWFGMEQEYTLMGTDGHPFGWPSNGFPGPQGPYYCGVGVDKAYGRDIVEAH
ParentalYRACLYAGIKIAGTNAEVMPAQWEFQIGPCEGIDMGDHLWVARFILHRVCEDFGVIATFDPKPIPGNWNG
YR.CLYAGI.IAGTNAEVMPAQWEFQIGPCEGI.MGDHLWVARFILH.VCEDF.VIATFD.KPIPGNWNG
RetrocopyYRSCLYAGIRIAGTNAEVMPAQWEFQIGPCEGINMGDHLWVARFILHHVCEDFRVIATFDLKPIPGNWNG
ParentalAGCHTNFSTKAMREENGLKYIEESIEKLSKRHQYHIRAYDPKGGLDNARRLTGFHETSNINDFSAGVANR
AGCHTNFSTKAMREENGLKYIEESIEKLSK.HQYHI.AYDPKGGLDNA.RLTGFHETSNINDFSAGVAN.
RetrocopyAGCHTNFSTKAMREENGLKYIEESIEKLSKWHQYHI*AYDPKGGLDNAWRLTGFHETSNINDFSAGVANH
ParentalGASIRIPRTVGQEKKGYFEDRRPSANCDPFSVTEALIRTCLLNETGDEPFQYKN
GASIRIPRTVGQEKKGYFEDR.PSANCDPFSVTEALI.TCLLNETG.E.FQYKN
RetrocopyGASIRIPRTVGQEKKGYFEDRHPSANCDPFSVTEALICTCLLNETGNEHFQYKN

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 2 .06 RPM 302 .06 RPM
SRP017611_brain 3 .33 RPM 907 .69 RPM
SRP017611_kidney 0 .13 RPM 27 .93 RPM
SRP017611_liver 0 .65 RPM 333 .27 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_2143 retrocopy.

TSS - click to see more details

Canis familiaris was not studied using FANTOM5 data.

Lab - click to see more details

retro_cfam_2143 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cfam_2143 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 24 parental genes, and 57 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000136314 retrocopies
retro_btau_1050, retro_btau_1474, retro_btau_336, retro_btau_824,
Canis familiaris ENSCAFG00000013102 2 retrocopies
retro_cfam_1691, retro_cfam_2143 ,
Callithrix jacchus ENSCJAG000000046541 retrocopy
retro_cjac_2837,
Dasypus novemcinctus ENSDNOG000000139484 retrocopies
retro_dnov_1386, retro_dnov_1870, retro_dnov_2393, retro_dnov_842,
Equus caballus ENSECAG000000158651 retrocopy
retro_ecab_979,
Echinops telfairi ENSETEG000000083293 retrocopies
retro_etel_143, retro_etel_189, retro_etel_1968,
Felis catus ENSFCAG000000105511 retrocopy
retro_fcat_1811,
Homo sapiens ENSG000001358214 retrocopies
retro_hsap_2364, retro_hsap_3255, retro_hsap_848, retro_hsap_935,
Gorilla gorilla ENSGGOG000000247123 retrocopies
retro_ggor_1794, retro_ggor_2216, retro_ggor_754,
Loxodonta africana ENSLAFG000000007001 retrocopy
retro_lafr_196,
Macropus eugenii ENSMEUG000000017746 retrocopies
retro_meug_1013, retro_meug_1394, retro_meug_1561, retro_meug_409, retro_meug_433, retro_meug_746,
Macaca mulatta ENSMMUG000000228842 retrocopies
retro_mmul_2047, retro_mmul_954,
Monodelphis domestica ENSMODG000000067874 retrocopies
retro_mdom_1268, retro_mdom_488, retro_mdom_823, retro_mdom_892,
Mus musculus ENSMUSG000000264733 retrocopies
retro_mmus_1730, retro_mmus_1767, retro_mmus_696,
Nomascus leucogenys ENSNLEG000000180073 retrocopies
retro_nleu_1388, retro_nleu_293, retro_nleu_416,
Pongo abelii ENSPPYG000000004401 retrocopy
retro_pabe_2698,
Pan troglodytes ENSPTRG000000017514 retrocopies
retro_ptro_2201, retro_ptro_2823, retro_ptro_589, retro_ptro_647,
Sarcophilus harrisii ENSSHAG000000001161 retrocopy
retro_shar_553,
Sus scrofa ENSSSCG000000155451 retrocopy
retro_sscr_726,
Ictidomys tridecemlineatus ENSSTOG000000145292 retrocopies
retro_itri_1083, retro_itri_743,
Tupaia belangeri ENSTBEG000000035223 retrocopies
retro_tbel_2230, retro_tbel_3079, retro_tbel_3992,
Tarsius syrichta ENSTSYG000000020661 retrocopy
retro_tsyr_385,
Tursiops truncatus ENSTTRG000000107811 retrocopy
retro_ttru_543,
Drosophila melanogaster FBgn00011451 retrocopy
retro_dmel_44,


Copyright © RetrogeneDB 2014-2017