RetrogeneDB ID:

retro_itri_687

Retrocopy
location
Organism:Squirrel (Ictidomys tridecemlineatus)
Coordinates:JH393311.1:8286149..8288456(-)
Located in intron of:ENSSTOG00000022925
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:GTF3C4
Ensembl ID:ENSSTOG00000004976
Aliases:None
Description:general transcription factor IIIC, polypeptide 4, 90kDa [Source:HGNC Symbol;Acc:4667]


Retrocopy-Parental alignment summary:






>retro_itri_687
CAGGAACCAGCCGTGAAGCTGCAGTACGCGGTGAGCGGCCTGGAGCCACTGGCCTGGTCGGAGAACCACTGTGTGTAGGT
GTCCACGGCCTGCAGCATCGCCGTGCTGGAGCTCATCTGCCACGTGCGCAACCCGGGCCAGGACCTGGTGATCCACCGCA
CCTCAGTGCCCGCCCCTCTCAACAGCTGCCTGCTCAAAGTTGGCTCAAAATCAGAAGTTGCTGAGTGCAAGGAGAAATTT
GCCAGCTCCAAAGACCCCACCATCATCCAGACTTTCATGTTGGACAGGGTGTTCAACCCTAAGGGAAAGGCCTTGCCACC
AATGAGAGGGTTCAAATGCACCAGCTGGTCTCCCATGGGTTGCAATGCAAATGGCAGGTGCCTCTTGGCAGCGCTGACCA
TGGACAATCGCCTGACTGTCCAGGTGAACCTCAACAGACTCCAGTGGGTCCAGCTGGTTGATCTGACTGAGATTTACGGA
GAGCGTCTCTATGAGACCAGTTACAGGCTCTCTAACAATGAGGCTCCAGAGGGAAATCTCGGGGATTTTGCCGAATTTCA
GAGGAGGCACAGCATGCAGACCCCAGTCAGAATGGAGTGGTCGGGCATCTGCACCACTCAGCAGGTCAAGCACAACAATG
AGTGCCGGGATGTGGGCAGTGTGCTCTTGGCTGTCCTCTTTGAGAACGGTAACATTGCCGTGTGGCAATTTCAGCTGCCC
TTTGTAGGAAAGGAGTCCATCTCCTCATGCAACACGATCGAGTCTGGAATCAGCTCCCCTAGTGTTTTATTCTGGTGGGA
ATATGAGCACAATAATCGGAAAATGAGTGGCCTTATTGTGGGGAGTGCTTTTGGACCCGTAAAAATTCTCCCTGTCAATC
TCAAAGCAGTCAAGGGCTACTTCACCTTGAGGCAGCCTGTTGTCTTGTGGAAAGAAATGGACCAGTTGCCTGTGCACAGC
ATTAAGTGCGTGCCGCTTTATCACCCCTACCGGAAGTGCAGCTGCAGCCTGGTGGTGGCTGCAAGAGGCTCCTACGTGTT
TTGGTGTCTTCTTTTGATCTCCAAGGCAGGTCTGAATGTTCACAATTCCCACGTCACAGGCCTTCACTCCCTGCCCATTG
TCTCCATGACTGCAGACAAACAGAACGGAACCATGTACACTTGTTCCAGGGATGGGAAAGTGAGGCAGTTGATTCCCATC
TTCACAGATGTCGCATTAAAGTTCGAGCACCAGTTAATTAAACTCTCAGATGTGTCTGGCTCAGTGAGGACTCATGGGAT
AGCAGTGAGCCTGTGTGGTGCGTATCTGGCCATCATCACAACTGAGGGCATGGTCAATGGCCTTCATCCTGTCAACAAAA
ATTATCAGGTCCAGTTCGTTACTCTCAAAACCTTTGAGGAGGCAGCTGCTCAGCTCCTGGAGTCTTCAGTGCAGAACCTC
TTTAAGCAGGTGGATTTAATAGACCTAGTACGCTGGAAAATTTTAAAAGATAAACATATCCCTCAGTTTTTACATGAAGC
TTTGGAAAAAAAGATCGAAAGCAGTGGAGTCACCTATTTTTGGCATTTTAAGCTTTTTCTCCTGAGGATTTTATACCAGT
CAATGCAGAAAACTCCTTCAGAAGCCTTATGGAAACCTGCCCATGAAGACTCAAAAATCTTGATCGTTGACTGTCCTGGG
ATGGGCAATGCAGAGGATGAGCAGCAAGAAGAAGGCGCCTCTTCCAGGCAGGTGACTAAGCCAGGCCTGCAGGAGAGGAG
CAGAGAGGGCGAAGCAGAGGAGCCCACAGACGACTCACTGCCCCCATCGGGAGACGGTGGAGGCCACGAGGCAGTGGAGG
AGAAGCTCCTTGAGATCCAAGGGAAGATCGAGGCTGTGGAGATGCACCTGACCAGGGAGCACATGAAGCGCGTCCTGGGG
GAAGTGTACCTGCACACCTGGATCACGGAGAACACCAGCATCCCCACCAGAGGGCTCTGCAACTTTCTAATGTCTGATGA
AGAGTATGAGGACAGAACGGCTCGGGTGCTGATCGGACACATCTCAAAGAAGATGAATAAACGGACTTTCCCTGAACACT
GCAGCTTGTGTAAAGAGATCTTGCCGTTCACAGATCGCAAGCAGGCCATCTGCTCTAATGGGCACATCTGGCTCCGGTGC
TTCTTAACCTACCAGTCCTGCCAGAGCTTGATATACAGACAGTGTTTGCTCCATGACAGCATCGCTCGGCACCCAGCCCC
AGAAGATCCTAACTGGATTAAGAGGTTGCTGCAGAGCCCCTGTCCTTTCTGTGATTCTCCTGTCTTC

ORF - retro_itri_687 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 96.75 %
Parental protein coverage: 99.48 %
Number of stop codons detected: 1
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalREPAVKLQYAVSGLEPLAWSEDHRVSVSTARSIAVLELICDVHNPGQDLVIHRTSVPAPLNSCLLKVGSK
.EPAVKLQYAVSGLEPLAWSE.H.V.VSTA.SIAVLELIC.V.NPGQDLVIHRTSVPAPLNSCLLKVGSK
RetrocopyQEPAVKLQYAVSGLEPLAWSENHCV*VSTACSIAVLELICHVRNPGQDLVIHRTSVPAPLNSCLLKVGSK
ParentalSEVAECKEKFASSKDPTISQTFMLDRVFNPEGKALPPMRGFKYTSWSPMGCDANGRCLLAALTMDNRLTV
SEVAECKEKFASSKDPTI.QTFMLDRVFNP.GKALPPMRGFK.TSWSPMGC.ANGRCLLAALTMDNRLTV
RetrocopySEVAECKEKFASSKDPTIIQTFMLDRVFNPKGKALPPMRGFKCTSWSPMGCNANGRCLLAALTMDNRLTV
ParentalQVNLNRLQWVQLVDLTEIYGERLYETSYRLSKNEAPEGNLGDFAEFQRRHSMQTPVRMEWSGICTTQQVK
QVNLNRLQWVQLVDLTEIYGERLYETSYRLS.NEAPEGNLGDFAEFQRRHSMQTPVRMEWSGICTTQQVK
RetrocopyQVNLNRLQWVQLVDLTEIYGERLYETSYRLSNNEAPEGNLGDFAEFQRRHSMQTPVRMEWSGICTTQQVK
ParentalHNNECRDVGSVLLAVLFENGNIAVWQFQLPFVGKESISSCNTIESGISSPSVLFWWEYEHNNRKMSGLIV
HNNECRDVGSVLLAVLFENGNIAVWQFQLPFVGKESISSCNTIESGISSPSVLFWWEYEHNNRKMSGLIV
RetrocopyHNNECRDVGSVLLAVLFENGNIAVWQFQLPFVGKESISSCNTIESGISSPSVLFWWEYEHNNRKMSGLIV
ParentalGSAFGPVKIIPVNLKAVKGYFTLRQPVVLWKEMDQLPVHSIKCVPLYHPYQKCSCSLVVAARGSYVFWCL
GSAFGPVKI.PVNLKAVKGYFTLRQPVVLWKEMDQLPVHSIKCVPLYHPY.KCSCSLVVAARGSYVFWCL
RetrocopyGSAFGPVKILPVNLKAVKGYFTLRQPVVLWKEMDQLPVHSIKCVPLYHPYRKCSCSLVVAARGSYVFWCL
ParentalLLISKAGLNVHNSHVTGLHSLPIVSMTADKQNGTVYTCSSDGKVRQLIPIFTDVALKFEHQLIKLSDVFG
LLISKAGLNVHNSHVTGLHSLPIVSMTADKQNGT.YTCS.DGKVRQLIPIFTDVALKFEHQLIKLSDV.G
RetrocopyLLISKAGLNVHNSHVTGLHSLPIVSMTADKQNGTMYTCSRDGKVRQLIPIFTDVALKFEHQLIKLSDVSG
ParentalSVRTHGIAVSPCGAYLAIITTEGMVNGLHPVNKNYQVQFVTLKTFEEAAAQLLESSVQNLFKQVDLIDLV
SVRTHGIAVS.CGAYLAIITTEGMVNGLHPVNKNYQVQFVTLKTFEEAAAQLLESSVQNLFKQVDLIDLV
RetrocopySVRTHGIAVSLCGAYLAIITTEGMVNGLHPVNKNYQVQFVTLKTFEEAAAQLLESSVQNLFKQVDLIDLV
ParentalRWKILKDKHIPQFLHEALEKKIESSGVTYFWRFKLFLLRILYQSMQKTPSEALWKPAHEDSKILIVDSPG
RWKILKDKHIPQFLHEALEKKIESSGVTYFW.FKLFLLRILYQSMQKTPSEALWKPAHEDSKILIVD.PG
RetrocopyRWKILKDKHIPQFLHEALEKKIESSGVTYFWHFKLFLLRILYQSMQKTPSEALWKPAHEDSKILIVDCPG
ParentalMGNAEDEQQEEGTSSRQVTKPGLQERSREGEAEEPTDDSLPPSGDGGGHEAVEEKLLEIQGKIEAVEMHL
MGNAEDEQQEEG.SSRQVTKPGLQERSREGEAEEPTDDSLPPSGDGGGHEAVEEKLLEIQGKIEAVEMHL
RetrocopyMGNAEDEQQEEGASSRQVTKPGLQERSREGEAEEPTDDSLPPSGDGGGHEAVEEKLLEIQGKIEAVEMHL
ParentalTREHMKRVLGEVYLHTWITENTSIPTRGLCNFLMSDEEYEDRTARVLIGHISKKMNKQTFPEHCSLCKEI
TREHMKRVLGEVYLHTWITENTSIPTRGLCNFLMSDEEYEDRTARVLIGHISKKMNK.TFPEHCSLCKEI
RetrocopyTREHMKRVLGEVYLHTWITENTSIPTRGLCNFLMSDEEYEDRTARVLIGHISKKMNKRTFPEHCSLCKEI
ParentalLPFTDRKQAVCSNGHIWLRCFLTYQSCQSLIYRRCLLHDSIARHPAPEDPDWIKRLLQSPCPFCDSPVF
LPFTDRKQA.CSNGHIWLRCFLTYQSCQSLIYR.CLLHDSIARHPAPEDP.WIKRLLQSPCPFCDSPVF
RetrocopyLPFTDRKQAICSNGHIWLRCFLTYQSCQSLIYRQCLLHDSIARHPAPEDPNWIKRLLQSPCPFCDSPVF

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_687 retrocopy.

TSS - click to see more details

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab - click to see more details

retro_itri_687 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 ENSSTOG00000004976 1 retrocopy
retro_itri_687 ,




Copyright © RetrogeneDB 2014-2017