RetrogeneDB ID:

retro_cfam_881

Retrocopy
location
Organism:Dog (Canis familiaris)
Coordinates:2:23304..24990(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:SLC29A1
Ensembl ID:ENSCAFG00000001981
Aliases:SLC29A1, ENT1
Description:Canis lupus familiaris solute carrier family 29 (nucleoside transporters), member 1 (SLC29A1), nuclear gene encoding mitochondrial protein, mRNA. [Source:RefSeq mRNA;Acc:NM_001003367]


Retrocopy-Parental alignment summary:






>retro_cfam_881
GGCTCTTTCACTGTGTGTGCAGACCATGGTGAGCCCATTGCCCAGGGTACCAAAGTGATCCTCCATCTTAAAGAAGACCA
AAAAGAATATTTAGAGGAGAGGTGTGTCAAAGAAGTGGTGAAGAATCACTCACAGTTCATAGGTTATCCCATCACCCTTT
ATTTGGAGAAGGAATGAGAGAAAGAAATTAGTGATGATGAGGCAGAAGAGGAGAAAGGGGAGAAGGAGGAAGAAGATAAA
GATGATGAGGAGAAACCCAAGATTGAAGATGTGGGTTCAGATGAGGAGGATGATAGTGGGAATGACAAGAGAAAGAAGAC
AAAGAAGATTGAGGAAAAATACACTGATCAAGAATAACTGAACAAGACCAAGCCCATTTGGACCAGAAATCCTGAAGACA
CCACCCAGGAGGAATATGGAGAGTTTTACAAGAGCCTTACTAATGACTGGGAAGATCACCTGGCGGTCAAGCACTTCTCT
GTAGAAGGTCAGTTGGAATTCAGGGCGTTGCTCTTCATCCCTTGTTGGGATCCTTTTGACCTCTTTGAGAACAAGAAGGA
AAAGAACAACTTCAAACTCTATGTCCACCATGGGTTCATCATGGACAGCTGTGATGAATTGATATCAGAGTATCTCAACT
TCATCCGTGGTGTGGTTGACTCCGAGGACCTGCCCCTGAACATCTCCTGAGAAATGCTCCAGCAGAGCAAAATCTTGAAG
GTCATTTGCAAAAATATTGTGAAGAAATGCCTTGAGCTCTTCTCTGAATTGGCAGAAGACAAGGAGAACTATAAGAAATT
CTATGAGGCATTCTCTGAAAACCTAAAGCTTGGAATCCATGAAGATTCCACTAACCGGTGCCGCCTTTCTGAGCTGCTGT
GTTACCACACTTTCCAGTCTGGAGATGAGATTACTTCTCTTTCAGAGTATGTGTCCCATATGAAGGAGACTCAGAAGTCC
ATCTATTACATCACTGGTGAGAGCAAAGAGCAGGTTGCCAACTCCGCTTTTGTGGAGCGAGTGCAGAAACGAGGCTTCGA
GGTACTGTATATGATAGAGCCTATCGACGAGTACTGTGTGCAGCAGCTCAAGGAGTTTGATGGGAAGAGTATTGTCTCAG
TTACCAAGGAGGGCCTGGAGTTGCCTGAGGATGAAGAGGGGAAGAAGAAAATGGAGGAGAGTAAGGCCAAGTTTGAGAAT
CTCTGCAAACTCTGAAGGAAATCTTGGATAAGAAGGTTGAAAAGGTGACCATCTCCAACACGCTGGTGGCTTCACCCTGC
TGTATTGTGACTAGCACCCTATGGCTGGACTGCCAACATGGAGCGGATCATGAAAGCCCAGGCACTCCAGGACAACTCTA
CAATGGGTTATATGATGGCCAAAAAGCACCTGGAGATCAGCCCTGACCACCCCATTGTGGAGATGCTGTGGCAGAAGGCA
GAGGCAGACAAGAATGATAAGGCTGTCAAGGACCTGGTGGTGCTGCTGTTTGAAACAGTTCTGCTCTCCTCCAGCTTCTC
ACTGGAGGATCCCCAGACTCACTCCAACCGTATTTACCATATGATCAAGCTAGGCCTGGGCATTGATGAAGATGAAGTGA
CAGCAGAGGAACCCAGTGCTGCTGTTCCTGATGAGATCCCTCTGCTTGAGGGTGATGAGGATGCCTCTCACATGGAAGAA
GTCAAT

ORF - retro_cfam_881 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 90.78 %
Parental protein coverage: 77.62 %
Number of stop codons detected: 3
Number of frameshifts detected: 2


Retrocopy - Parental Gene Alignment:

ParentalGSFTVRADHGEPIGRGTKVILHLKEDQTEYLEERRVKEVVKKHSQFIGYPITLYLEKEREKEISDDEAEE
GSFTV.ADHGEPI..GTKVILHLKEDQ.EYLEER.VKEVVK.HSQFIGYPITLYLEKE.EKEISDDEAEE
RetrocopyGSFTVCADHGEPIAQGTKVILHLKEDQKEYLEERCVKEVVKNHSQFIGYPITLYLEKE*EKEISDDEAEE
ParentalEKGEKEEEDKDDEEKPKIEDVGSDEEDDSGKDKKKKTKKIKEKYIDQEELNKTKPIWTRNPDDITQEEYG
EKGEKEEEDKDDEEKPKIEDVGSDEEDDSG.DK.KKTKKI.EKY.DQE.LNKTKPIWTRNP.D.TQEEYG
RetrocopyEKGEKEEEDKDDEEKPKIEDVGSDEEDDSGNDKRKKTKKIEEKYTDQE*LNKTKPIWTRNPEDTTQEEYG
ParentalEFYKSLTNDWEDHLAVKHFSVEGQLEFRALLFIPRRAPFDLFENKKKKNNIKLYVRRVFIMDSCDELIPE
EFYKSLTNDWEDHLAVKHFSVEGQLEFRALLFIP...PFDLFENKK.KNN.KLYV...FIMDSCDELI.E
RetrocopyEFYKSLTNDWEDHLAVKHFSVEGQLEFRALLFIPCWDPFDLFENKKEKNNFKLYVHHGFIMDSCDELISE
ParentalYLNFIRGVVDSEDLPLNISREMLQQSKILKVIRKNIVKKCLELFSELAEDKENYKKFYEAFSKNLKLGIH
YLNFIRGVVDSEDLPLNIS.EMLQQSKILKVI.KNIVKKCLELFSELAEDKENYKKFYEAFS.NLKLGIH
RetrocopyYLNFIRGVVDSEDLPLNIS*EMLQQSKILKVICKNIVKKCLELFSELAEDKENYKKFYEAFSENLKLGIH
ParentalEDSTNRRRLSELLRYHTSQSGDEMTSLSEYVSRMKETQKSIYYITGESKEQVANSAFVERVRKRGFEVVY
EDSTNR.RLSELL.YHT.QSGDE.TSLSEYVS.MKETQKSIYYITGESKEQVANSAFVERV.KRGFEV.Y
RetrocopyEDSTNRCRLSELLCYHTFQSGDEITSLSEYVSHMKETQKSIYYITGESKEQVANSAFVERVQKRGFEVLY
ParentalMTEPIDEYCVQQLKEFDGKSLVSVTKEGLELPEDEEEKKKMEESKAKFENLCKL-MKEILDKKVEKVTIS
M.EPIDEYCVQQLKEFDGKS.VSVTKEGLELPEDEE.KKKMEESKAKFENLCKL..KEILDKKVEKVTIS
RetrocopyMIEPIDEYCVQQLKEFDGKSIVSVTKEGLELPEDEEGKKKMEESKAKFENLCKL<LKEILDKKVEKVTIS
ParentalNRLVSSPCCIVTST-YGWTANMERIMKAQALRDNSTMGYMMAKKHLEINPDHPIVETLRQKAEADKNDKA
N.LV.SPCCIVTST.YGWTANMERIMKAQAL.DNSTMGYMMAKKHLEI.PDHPIVE.L.QKAEADKNDKA
RetrocopyNTLVASPCCIVTST>YGWTANMERIMKAQALQDNSTMGYMMAKKHLEISPDHPIVEMLWQKAEADKNDKA
ParentalVKDLVVLLFETALLSSGFSLEDPQTHSNRIYRMIKLGLGIDEDEVAAEEPSAAVPDEIPPLEGDEDASRM
VKDLVVLLFET.LLSS.FSLEDPQTHSNRIY.MIKLGLGIDEDEV.AEEPSAAVPDEIP.LEGDEDAS.M
RetrocopyVKDLVVLLFETVLLSSSFSLEDPQTHSNRIYHMIKLGLGIDEDEVTAEEPSAAVPDEIPLLEGDEDASHM
ParentalEEVD
EEV.
RetrocopyEEVN

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 792 .27 RPM
SRP017611_brain 0 .16 RPM 591 .71 RPM
SRP017611_kidney 0 .13 RPM 601 .80 RPM
SRP017611_liver 0 .00 RPM 460 .46 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_881 retrocopy.

TSS - click to see more details

Canis familiaris was not studied using FANTOM5 data.

Lab - click to see more details

retro_cfam_881 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cfam_881 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 12 parental genes, and 26 retrocopies.

Species Parental gene accession Retrocopies number
Canis familiaris ENSCAFG00000001981 4 retrocopies
retro_cfam_1108, retro_cfam_411, retro_cfam_562, retro_cfam_881 ,
Canis familiaris ENSCAFG000000180361 retrocopy
retro_cfam_1094,
Felis catus ENSFCAG000000097641 retrocopy
retro_fcat_1177,
Gorilla gorilla ENSGGOG000000088892 retrocopies
retro_ggor_1011, retro_ggor_701,
Macropus eugenii ENSMEUG000000137351 retrocopy
retro_meug_1896,
Myotis lucifugus ENSMLUG000000052392 retrocopies
retro_mluc_1604, retro_mluc_865,
Macaca mulatta ENSMMUG000000226862 retrocopies
retro_mmul_1319, retro_mmul_1869,
Mus musculus ENSMUSG000000239443 retrocopies
retro_mmus_1916, retro_mmus_3528, retro_mmus_856,
Otolemur garnettii ENSOGAG000000119611 retrocopy
retro_ogar_2574,
Pongo abelii ENSPPYG000000166552 retrocopies
retro_pabe_2425, retro_pabe_415,
Rattus norvegicus ENSRNOG000000198346 retrocopies
retro_rnor_1561, retro_rnor_1562, retro_rnor_1787, retro_rnor_597, retro_rnor_598, retro_rnor_87,
Tupaia belangeri ENSTBEG000000148731 retrocopy
retro_tbel_1428,


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