RetrogeneDB ID:

retro_itri_207

Retrocopy
location
Organism:Squirrel (Ictidomys tridecemlineatus)
Coordinates:JH393279.1:34518227..34520013(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:SLC34A2
Ensembl ID:ENSSTOG00000012971
Aliases:None
Description:solute carrier family 34 (type II sodium/phosphate contransporter), member 2 [Source:HGNC Symbol;Acc:11020]


Retrocopy-Parental alignment summary:






>retro_itri_207
CACAAGTCCACACCAGCCAAAGGCAAGGAGTCTGGCAAAAATGACAGCAGTGGTCCTACAGCCAAAATTGAACTTCTGCC
CTTGTACTCCACTGCGACTTTGATAGAGGAGCCCACTGATGTGGAAGACCCCTAGGACCTGCCCACACTCCAGGATACTG
GGATCAAAGTGGTCAGAGAGAGACACCAAAGGGAAGCTCTTATGTGTCTTCCAAGGGATTGGAAAATTCATTTGACTCCT
GGGGTTCCTCTACTTGTTTGTTTGCTCCTTGGATGTCCTCAGCAGTGCCTTCCAGCTGGTTGGAGGAAAAGTGGCCGGGC
AGTTCTTCAGCAACAACTCCATCATGTCCAACCTCATGGCTGGACTGGTGATCAGGGTGCTGGTGACCTTCATGGTGCAG
AGCTCCAGCACCTCCTCATCCATCATCATCAGCATGGTGGCCTCCTCATTGCTGACCGTGTGGGCAGCCATCCCCATCAT
CATGAGGGCCAACATCGGGACCTCCATCACCAACACCATTGCACTACTCATGCAGGCCGGAGACTGCAGCGAGTTTAGGA
GGGCTTTTGTAGGGGCTACCATCCATGACTTCTTCAACTGGCTGTCTGTACTGGTGCTCTTGCCCCTGGAGGTTGCCACC
CACTACCTGGAGATTCTGACCAACCTGGTGGTGGACACCTTCCACTTTCAGAATGGAGAAGATGCCCCAGCACTTCTGAA
AGTCATCACAGATCCCTTCACGAAGCTCATCATTCAGCTGGATAAAAAAGTCATCCACCAAATTGCAATGAATGACGAAT
TGGCCCAAAACAAGAGTCTGATCAAGATTTGGTGCAAAACTTTTACAAATACGACTCAGATGAATGTCGCTGTCCCCTCG
CCTGAGAACTGCACTTCCCCTTCCCTCTGTTGGACAGAGGGTATCTACACCTGGACAATCAAGAACGTGACCTACAAGGA
GAACATTGCCAAGTACCAGCACATCTTTGTGAATTTTAACCTCCCGGATCTGGCTGTGGGCATCATCATGCTGATTGTCT
CCCTGATGGTCCTCTGTGGCTGCCTGATCATGATCGTCAAGCTCCTGGGCTCTGTGCTCAAGGGACAGGTTGCCATTGTC
ATCAAGAAAACCATCAACACTGATTTCCCCTTTCCCTTTGCCTGGGTGACTGGCTACCTAGCCATCCTCGTCGGAGCGGG
CATGACCTTCATCGTCCAGAGCAGTTCAGTGTTCACGTCTGCCATGACCCCTCTGATCAGTATCGGTGTGATAACCATTG
AGAGGGCTTATCCGCTCACTCTGGGCTCCAACATCGGCACCACCACCACCGCCATCCTGGCCGCCTTAGCCAGCCCGGGC
AACACTCTCAAGAGTTCTCTCCAGCTCTCCCTGTGCCACTTTTTCTTCAACATCTCTGGCATTTTGCTGTGGTACCTGAT
CCCGTTCACCCGCCTGCCGATCTGCCTGGCCAAGGGGCTGGGCAACATCTCCGCCAAGTACCGCTGGTTTGCTGTGTTCT
ACCTGATCTTCTTCTCCTTCCTGACCCCGCTGACCGTGTTCGGCCTCTCGCTGGCCGGCTCGCCCGTGTTGGTGGGCGTG
GGGGTGCCCATCATCCTCCTGCTGCTGCTGGTGGTCTGCCTCAGGCTCCTGCAGTCCTGCTGCCCACGCATCCTGCCCAT
CAAGCTCCGCAATTGGCACTTCCTGCCCCAGTGGATGCACTCCCTGAAGCACTGGGACAACCTCATCACCTTGGCCACCA
GCTGCTGCCAGCAGCGCTGCTGTTGC

ORF - retro_itri_207 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 92.46 %
Parental protein coverage: 92.26 %
Number of stop codons detected: 2
Number of frameshifts detected: 1


Retrocopy - Parental Gene Alignment:

ParentalHQSTPAKGQETGKTDDGSGPAAKIELLPSYSTATLIEEPTDVEDPWDLPALQDTGIK-WSERDAKGKLLC
H.STPAKG.E.GK..D.SGP.AKIELLP.YSTATLIEEPTDVEDP.DLP.LQDTGIK.WSERD.KGKLLC
RetrocopyHKSTPAKGKESGK-NDSSGPTAKIELLPLYSTATLIEEPTDVEDP*DLPTLQDTGIK>WSERDTKGKLLC
ParentalVFQGIGKFILLLGFLYLFVCSLDVLSSAFQLVGGKVAGQFFSNNSIMSNPVAGLVIGVLVTVMVQSSSTS
VFQGIGKFI.LLGFLYLFVCSLDVLSSAFQLVGGKVAGQFFSNNSIMSN..AGLVI.VLVT.MVQSSSTS
RetrocopyVFQGIGKFI*LLGFLYLFVCSLDVLSSAFQLVGGKVAGQFFSNNSIMSNLMAGLVIRVLVTFMVQSSSTS
ParentalSSIIVSMVASSLLTVRAAIPIIMGANIGTSITNTIVALMQAGDRSEFRRAFAGATVHDFFNWLSVLVLLP
SSII.SMVASSLLTV.AAIPIIM.ANIGTSITNTI..LMQAGD.SEFRRAF.GAT.HDFFNWLSVLVLLP
RetrocopySSIIISMVASSLLTVWAAIPIIMRANIGTSITNTIALLMQAGDCSEFRRAFVGATIHDFFNWLSVLVLLP
ParentalLEAATHYLEILTNLVVDTFHFQNGEDAPALLKVITDPFTKLIIQLDKKVIHQIAMNDESAQNKSLIKIWC
LE.ATHYLEILTNLVVDTFHFQNGEDAPALLKVITDPFTKLIIQLDKKVIHQIAMNDE.AQNKSLIKIWC
RetrocopyLEVATHYLEILTNLVVDTFHFQNGEDAPALLKVITDPFTKLIIQLDKKVIHQIAMNDELAQNKSLIKIWC
ParentalKTFTNTTQMNVTVPSPENCTSPSLCWTDGIYTWTIKNVTYKENIAKCQHIFVNFNLPDLAVGIILLIVSL
KTFTNTTQMNV.VPSPENCTSPSLCWT.GIYTWTIKNVTYKENIAK.QHIFVNFNLPDLAVGII.LIVSL
RetrocopyKTFTNTTQMNVAVPSPENCTSPSLCWTEGIYTWTIKNVTYKENIAKYQHIFVNFNLPDLAVGIIMLIVSL
ParentalMVLCGCLIMIVKLLGSVLKGQVAVVIKKTINTDFPFPFAWVTGYLAILVGAGMTFIVQSSSVFTSAMTPL
MVLCGCLIMIVKLLGSVLKGQVA.VIKKTINTDFPFPFAWVTGYLAILVGAGMTFIVQSSSVFTSAMTPL
RetrocopyMVLCGCLIMIVKLLGSVLKGQVAIVIKKTINTDFPFPFAWVTGYLAILVGAGMTFIVQSSSVFTSAMTPL
ParentalIGIGVITIERAYPLTLGSNIGTTTTAILAALASPGNTLKSSLQIALCHFFFNISGILLWYPIPFTRLPIR
I.IGVITIERAYPLTLGSNIGTTTTAILAALASPGNTLKSSLQ..LCHFFFNISGILLWY.IPFTRLPI.
RetrocopyISIGVITIERAYPLTLGSNIGTTTTAILAALASPGNTLKSSLQLSLCHFFFNISGILLWYLIPFTRLPIC
ParentalLAKGLGNISAKYRWFAVFYLIFFFFLTPLAVFGLSLAGWPVLVGVGVPIILLLLLVICLRLLQSRCPRVL
LAKGLGNISAKYRWFAVFYLIFF.FLTPL.VFGLSLAG.PVLVGVGVPIILLLLLV.CLRLLQS.CPR.L
RetrocopyLAKGLGNISAKYRWFAVFYLIFFSFLTPLTVFGLSLAGSPVLVGVGVPIILLLLLVVCLRLLQSCCPRIL
ParentalPIKLRNWNFLPQWMHSLKPWDNLITLATSCCQQRCCC
PIKLRNW.FLPQWMHSLK.WDNLITLATSCCQQRCCC
RetrocopyPIKLRNWHFLPQWMHSLKHWDNLITLATSCCQQRCCC

Legend:
*Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide






RNA-Seq - click to see more details

Ictidomys tridecemlineatus was not studied using RNA-Seq expression data.

ChIP-Seq - click to see more details

Ictidomys tridecemlineatus was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_itri_207 retrocopy.

TSS - click to see more details

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab - click to see more details

retro_itri_207 was not experimentally validated.

Retrocopy orthology:
Ictidomys tridecemlineatus does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.
Parental genes homology:
Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species Parental gene accession Retrocopies number
Dipodomys ordii ENSDORG000000161051 retrocopy
retro_dord_479,
Myotis lucifugus ENSMLUG000000006941 retrocopy
retro_mluc_42,
Ictidomys tridecemlineatus ENSSTOG00000012971 1 retrocopy
retro_itri_207 ,


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