RetrogeneDB ID:

retro_itri_654

Retrocopy
location
Organism:Squirrel (Ictidomys tridecemlineatus)
Coordinates:JH393309.1:12078442..12080184(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:CLCN2
Ensembl ID:ENSSTOG00000008267
Aliases:None
Description:chloride channel, voltage-sensitive 2 [Source:HGNC Symbol;Acc:2020]


Retrocopy-Parental alignment summary:






>retro_itri_654
CAGTACACGGAGATGGCGGACTCGGCGGCCATGGCGGCCGAGGAGGGGATGGAGCCACGAGAGCTGCAGTAGGAGCAGAC
CCTGATGTATGGCCGGTATACTCAGGAACTCGGGCCTTTGCCAAAGAGGAAGCTGCTCGGATTCCCTGGGAGGCCCTGAG
CCCTGGAAGGGGCCCCCTTCCCCTCGGGCTCCCCCAGAGCTCTTGGAATATGGACAGAGACAATGTGTCAGATGCCGCAT
CTGTTCAGTATGCTGCCACAAGGTCCTAGTATCCAGGGTTGGTGAAGACTGGATCTTTCTGGTCCTCCTGGGGCTCCTCA
TGGCACTAGTCAGCTGGGCCATGGATTATGCCATTGCTGTTTGTCCACAGGCCCAGCAGTGGATGTCCTGGGGCTTAAAC
ACCAGCATCTTACTCCAGTACCTGGCCTGGGTTACCTACCCTTGTCGTTCTTATCAGTTTCTCAGCTGGATTCACACAGA
TCCTAGCCCCTCAGGCTGTTGGGTCTGGCATCCCGGAGATTAAGACCATCTTGTGAGGAGTGGTGCTGAAAGAATACCTC
ACTCTCAAGACCTTTGTGGCTAAGGTCATTGGGCTGACCTGTGCCTTGGGCAGTGGAATGCCCCTTGGCAAAGAGGGCCC
TTTTGTGCATATTGAGAGCATGTGTGCTGCCCTTCTCAGCAAGTTCCTTTCTCTCTTTGGGGGTATCTACGAGAATGAAT
CTTGGAACACGGAGATGCTGGCTGCTGCCTCTGCTGTGGGTGTGGGCTTCTGCTTTGCAGCACCTATTGGAGGTGTCCTG
TTCAGTATTGAGTTCACCTCCACCTTCTTCGCTGTGCGAAACTACTGGTGGGGCTTTTTTGCTGCAACCTTCAGTGCCTT
CATCTTCCGGGTCTTGGCAGTCTGGAACCATGATGAATAGACCATTACTGCTCTCTTCAAAACCCGGTTCCGGCTCGGCT
TTCCCTTTGACCTGCAGGAGTTGCCAGCCATTGCTGTCATTGGCATTGCTAGTGGCTTTGGGGGAGCCCTCTTTGTCTAC
CTGAACCAGAAGATTGTCCAGGTGATGCGGAAACAGAAACCATCAATCGCTTCCTCATGAGGAAACGCCTGCTCTTCCCG
GCTCTGGTGACCCTGCTCATCTCTACTCTGACTTTCCTCCCTGGCTTTGGGCAGTTCATGGATGGACAGCTTTCACAGAA
GGAGACATTGGTCACCTTGTTTGACAACAGGACATGGGTCCACCAGGGCCTAGTAGAAGAGCTAGAGCCATCCAGCACCT
CACAGGCCTGGAGCCCACCCCATGCCAATGTCCTCCTCACCCTGGTCATCTTCATTCTGATGAAGTTCTGGATGTCTGCA
CTGGCCACAACGATCCCTGTGCCTTGCGGGGCCTTCATGCCTGTCTTTGTAATCGGAGCAGCATTTGGAGGTCTGGTGGG
TGAAAGCATGGCTGCCTGGTTCCCAGATGGGATTCACACAGACAGCAGTACCTACCGAATTGTGCCTGGGGCTATGCAGT
GGTTGGGGCAGCTGCACTGACAGGAGCAGTGACACACACACAGTATCTACAGCCGTGATTGTGTTCGAGCTCACGGGGCA
GATCGCCCATATCCTGCCTGTCATGATTGCCCTCATCCTGGCCAATGCTGTTGCCCAGAGCCTACAGCCCTCACTCTATG
ACAGCATCATCAGGATCAAGACACTGCCCTACCTGCCTGATCTGGGCTGGGGCTGCCACCAG

ORF - retro_itri_654 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 90.78 %
Parental protein coverage: 64.06 %
Number of stop codons detected: 3
Number of frameshifts detected 5


Retrocopy - Parental Gene Alignment:

ParentalQYTEMAASAAVAAEEGMEPRALQYEQTLMYGRYTQELG-AFAKEEAARI-RLGGPEPWKGPPSPRAPPEL
QYTEMA.SAA.AAEEGMEPR.LQ.EQTLMYGRYTQELG.AFAKEEAARI..LGGPEPWKGPPSPRAPPEL
RetrocopyQYTEMADSAAMAAEEGMEPRELQ*EQTLMYGRYTQELG<AFAKEEAARI<SLGGPEPWKGPPSPRAPPEL
ParentalLEYGQSRCARCRICSVRCHKFLVSRVGEDWIFLVLLGLLMALVSWAMDYAIAVCLQAQQWMSRGLNTSIL
LEYGQ..C.RCRICSV.CHK.LVSRVGEDWIFLVLLGLLMALVSWAMDYAIAVC.QAQQWMS.GLNTSIL
RetrocopyLEYGQRQCVRCRICSVCCHKVLVSRVGEDWIFLVLLGLLMALVSWAMDYAIAVCPQAQQWMSWGLNTSIL
ParentalLQYLAWVTYP-VVLITFSAGFTQILAPQAVGSGIPEMKTILRGVVLKEYLTLKTFVAKVIGLTCALGSGM
LQYLAWVTYP.VVLI.FSAGFTQILAPQAVGSGIPE.KTIL.GVVLKEYLTLKTFVAKVIGLTCALGSGM
RetrocopyLQYLAWVTYP>VVLISFSAGFTQILAPQAVGSGIPEIKTIL*GVVLKEYLTLKTFVAKVIGLTCALGSGM
ParentalPLGKEGPFVHIASMCAALLSKFLSLFGGIYENESRNTEMLAAACAVGVGCCFAAPIGGVLFSIEVTSTFF
PLGKEGPFVHI.SMCAALLSKFLSLFGGIYENES.NTEMLAAA.AVGVG.CFAAPIGGVLFSIE.TSTFF
RetrocopyPLGKEGPFVHIESMCAALLSKFLSLFGGIYENESWNTEMLAAASAVGVGFCFAAPIGGVLFSIEFTSTFF
ParentalAVRNYWRGFFAATFSAFIFRVLAVWNRDEETITALFKTRFRLDFPFDLQELPAFAVIGIASGFGGALFVY
AVRNYW.GFFAATFSAFIFRVLAVWN.DE.TITALFKTRFRL.FPFDLQELPA.AVIGIASGFGGALFVY
RetrocopyAVRNYWWGFFAATFSAFIFRVLAVWNHDE*TITALFKTRFRLGFPFDLQELPAIAVIGIASGFGGALFVY
ParentalLNRKIVQVMRKQK-TINRFLMRKRLLFPALVTLLISTLTFPPGFGQFMAGQLSQKETLVTLFDNRTWVRQ
LN.KIVQVMRKQK.TINRFLMRKRLLFPALVTLLISTLTF.PGFGQFM.GQLSQKETLVTLFDNRTWV.Q
RetrocopyLNQKIVQVMRKQK<TINRFLMRKRLLFPALVTLLISTLTFLPGFGQFMDGQLSQKETLVTLFDNRTWVHQ
ParentalGLVEELEPSSTSQAWSPPRANVFLTLVIFILMKFWMSALATTIPVPCGAFMPVFVIGAAFGRLVGESMAA
GLVEELEPSSTSQAWSPP.ANV.LTLVIFILMKFWMSALATTIPVPCGAFMPVFVIGAAFG.LVGESMAA
RetrocopyGLVEELEPSSTSQAWSPPHANVLLTLVIFILMKFWMSALATTIPVPCGAFMPVFVIGAAFGGLVGESMAA
ParentalWFPDGIHTDSSTYRIVPGGYAVV-GAAALAGAVTHTVSTAVIVFELTGQIAHILPVMIAVILANAVAQSL
WFPDGIHTDSSTYRIVPG......G........THTVSTAVIVFELTGQIAHILPVMIA.ILANAVAQSL
RetrocopyWFPDGIHTDSSTYRIVPGAMQWL>GSCTDRSSDTHTVSTAVIVFELTGQIAHILPVMIALILANAVAQSL
ParentalQPSLYDSIIRIKKLPYLPELGWGRHQ
QPSLYDSIIRIK.LPYLP.LGWG.HQ
RetrocopyQPSLYDSIIRIKTLPYLPDLGWGCHQ

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_654 retrocopy.

TSS - click to see more details

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab - click to see more details

retro_itri_654 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 1 parental gene, and 1 retrocopy.

Species Parental gene accession Retrocopies number
Ictidomys tridecemlineatus ENSSTOG00000008267 1 retrocopy
retro_itri_654 ,




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