RetrogeneDB ID:

retro_cfam_2175

Retrocopy
location
Organism:Dog (Canis familiaris)
Coordinates:X:65635879..65637098(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:SLC11A2
Ensembl ID:ENSCAFG00000007902
Aliases:None
Description:solute carrier family 11 (proton-coupled divalent metal ion transporters), member 2 [Source:HGNC Symbol;Acc:10908]


Retrocopy-Parental alignment summary:






>retro_cfam_2175
ACAACAGGATCTCTTCCACCGTCCACCAGGCATTCACAGGAACATTTCACCATCTATTTTGGTGGGATGATCACCATTCC
TGAGGAACAGTATTCTTGTTTTAGCTTCATAAACTCTGGGCTTTCACAGGACCCGACTTTCTTATGAGCACTGCCTACCT
GGATCCAGAAAACATTGAATCTTATTTGTAGTCTGGAACAGTGGCTGGATTGAAGTTGCTGTTGGTTTTTCTGTTGGCCA
CCATCATGGGGCTCCTGCTCCAGCATCATGCAGCTGGACTGGGGGTGGTGAGGGGTTTGCCTATTGCTGAAGTATGTTGC
TCTCATTATCCTAGGTACCCACGAATTAGCCTATGGTTCATGGTAGAGTTGGCTGTTTTTTTGCTCAGATATACAAGAAG
TTATTGGTTCAGTCATTGCCATCAATTTTCCGTCTATAGGAAGGGTACCTCTGTTGGGTGGAGTTCTCATGACCATTGCA
GACATTTGTATTTCTCTTTTTTTTGTACAAAAAAAAGGCTTGTGGAAACTAGAAGCATTTTTTAGGTTTTCTCATCACTA
TTATGACCCTCATATTTGGACATGAATATATTTACAGTGAAACCCAGAGTACCCAGAGCCGGGTACTCTAGGGCATATTC
CTGCACTTGTGTTTGGACTGTCATATCTCACAGATTAAGCAGGCTGTGGGCATCATGGAAATTGTCATCATGCCCCACAA
TATGTACCTGCATTCTGCCTTAGTCTGGTCCAGACATGTAAACCAAGCCAATAAGCAGGAAGTTCAAGAAGCTAGTAAGT
ACTTTTTCATTGACTCCTGAGTTGCTCTCTTTGTTCCCTTCATCATCAACATATTTGTTATCTCAGTCTTTGCTGAAGAA
TTTTTTTTTGAAAAAAACAACAACTAGGTGGTTGCAGTCTGTGGAAATAACAGCAGTTCACACATTACCCTTTCTCCTGA
TGATAACTCACAACTGGCTATGGACATCTACAAAGCAGGTGTTGTGCTAGGATGTAACTTTGGGCTTGCTGCACTCTATA
TCTGGGCAGTGGGGATCCTGGCTGTAGGACAAAGCTCCACCGTGGCAGGAATGTAGTCTGGACAGTTAGTCATGGAGAGA
TTCCTGAACCTAAAATGGTCATGTTTTTCCTGAGTGATTCTGACACCATCTTTTGCTATCATCCCCATTCTGCTTGTTGC
CATCCTCCAAGATGTAAAG

ORF - retro_cfam_2175 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 67.97 %
Parental protein coverage: 70.77 %
Number of stop codons detected: 6
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalSNSSLPQSTEHSQEPFTTYFDEKIAIPEEEYSCFSF-RKLWAFTGPGFLMSIAYLDPGNIESDLQSGAVA
...SLP.ST.HSQE.FT.YF...I.IPEE.YSCFSF..KLWAFTGP.FLMS.AYLDP.NIES.L.SG.VA
RetrocopyTTGSLPPSTRHSQEHFTIYFGGMITIPEEQYSCFSF<HKLWAFTGPDFLMSTAYLDPENIESYL*SGTVA
ParentalGFKLLWVLLLATIVGLLLQRLAARLGVVTGLHLAEVCHRQYPKVPRIILWLMVELAII-GSDMQEVIGSA
G.KLL.V.LLATI.GLLLQ..AA.LGVV.GL..AEVC...YP..PRI.LW.MVELA....SD.QEVIGS.
RetrocopyGLKLLLVFLLATIMGLLLQHHAAGLGVVRGLPIAEVCCSHYPRYPRISLWFMVELAVF>CSDIQEVIGSV
ParentalIAINLLSVGRVPLWGGVLITIADTFV-FLFLDKYGLRKLEAFF-GFLITIMALTFGYEYV--TVKPSQSQ
IAIN..S.GRVPL.GGVL.TIAD...........GL.KLEAFF.GFLITIM.L.FG.EY........QS.
RetrocopyIAINFPSIGRVPLLGGVLMTIADICISXXXVXXXGLWKLEAFF>GFLITIMTLIFGHEYIYSETQSTQSR
ParentalVLKGMFLPSCSGCHTPQIEQAVGIVGAVIMPHNMYLHSALVKSRQINRANKQEVREANKYFFIESCIALF
VL.G.FL..C..CH..QI.QAVGI...VIMPHNMYLHSALV.SR..N.ANKQEV.EA.KYFFI.S..ALF
RetrocopyVL*GIFLHLCLDCHISQIKQAVGIMEIVIMPHNMYLHSALVWSRHVNQANKQEVQEASKYFFIDS*VALF
ParentalVSFIINVFVVSVFAEAFF-EKTNDQVVAVCRNSSSPHSHLFPDDNSTLAVDIYKGGVVLGCYFGPAALYI
V.FIIN.FV.SVFAE....EK.N..VVAVC.N.SS.H..L.PDDNS.LA.DIYK.GVVLGC.FG.AALYI
RetrocopyVPFIINIFVISVFAEEXXXEKNNN*VVAVCGNNSSSHITLSPDDNSQLAMDIYKAGVVLGCNFGLAALYI
ParentalWAVGILAAGQSSTMTGTYSGQFVMEGFLNLRWSRFARVILTRSIAIIPTLLVAIFQDVE
WAVGILA.GQSST..G..SGQ.VME.FLNL.WS.F..VILT.S.AIIP.LLVAI.QDV.
RetrocopyWAVGILAVGQSSTVAGM*SGQLVMERFLNLKWSCFS*VILTPSFAIIPILLVAILQDVK

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 10 .04 RPM
SRP017611_brain 0 .00 RPM 12 .94 RPM
SRP017611_kidney 0 .00 RPM 16 .84 RPM
SRP017611_liver 0 .00 RPM 7 .83 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_2175 retrocopy.

TSS - click to see more details

Canis familiaris was not studied using FANTOM5 data.

Lab - click to see more details

retro_cfam_2175 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cfam_2175 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species Parental gene accession Retrocopies number
Canis familiaris ENSCAFG00000007902 1 retrocopy
retro_cfam_2175 ,


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