RetrogeneDB ID:

retro_itri_1436

Retrocopy
location
Organism:Squirrel (Ictidomys tridecemlineatus)
Coordinates:JH393486.1:2917713..2919372(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSSTOG00000009226
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:GK
Ensembl ID:ENSSTOG00000008732
Aliases:None
Description:glycerol kinase [Source:HGNC Symbol;Acc:4289]


Retrocopy-Parental alignment summary:






>retro_itri_1436
ATGGCAGCCCCAAAGAAAGGAGCTGTGGGGCCGTTGGTGGGGGCAGTGGTCCAGGGTACCAACTCCACTCGCTTTCTGGT
TTTTAATTCAAAAACAGCAGAACTACTTAGTCATCATCAAGTGGAATTGACCCAAGAGTTCCCCAGAGAAGGATGGGTGG
AGCAGGACCCTAAGGAAATTCTTCAGTCCGTCTATGAGTGTATAGAGAGAACGTGTGAGAAACTTGATGAAGTGAACGTT
GATATCGCCAACATAAAAGCGATCGGAGTCAGCAATCAGAGGGAAACCACTGTCATCTGGGACAAGTTAACTGGAGAGCC
TCTCTACAATGCTGTGGTGTGGCTTGATCTCAGAACCCAGTCTACCGTTGAGAATCTCAGTAAAAAAATTCCGGGAAATA
ATAACTTTGTCAAGTCTAAGACTGGCCTTCCACTTAGCACTTACTTCAGTGCAGTGAAACTTCGCTGGATGCTTGACAAT
GTGAGAAACGTTCAAAAAGCTGTTGAAGAAGGTAGAGCTCTTTTTGGTACCATTGATTCATGGCTTATCTGGAGCATGAC
AGGAGGAGTTAATGGAGGTGTCCATTGTACAGATGTGACAAATGCAAGTAGGACAATGCTTTTCAACATCCATTCTTTAG
AATGGGATAAAGAGCTCTGTGACTTTTTTGAAATTCCAATGAATATTCTTCCAAATGTCTGGAGTTCTTCTGAGATCTAT
GGCCTGATGAAAAGTGGAGCCTTGGAAGGTGTACCAATATCTGGGTGTTTGGGGGACCAGTCTGCTGCATTGGTAGGACA
GATGTGCTTCCAGGAAGGACAAGCCAAAAACACATACGGAACAGGCTGTTTCTTATTATGTAATACAGGTCGTAAATGTG
TATTTTCTGAACATGGCCTTCTGACAACTGTGGCTTACAAACTAGGCAGAGACAAGCCAGTATGTTATGCATTGGAAGGT
TCTGTTGCTATAGCTGGTGCTGTTATTCGTTGGCTAAGAGACAATCTTGGAATTATAGAAACCTCAGAAGAAGTTGAAAA
ACTTGCTAAAGAAGCAGGTACTTCTTATGGCTGCTACTTTGTCCCAGCCTTTTCAGGGTTATATGCACCTTATTGGGAGC
CCAGTGCAAGAGGGATAATCTGTGGTCTCACTCATTTTACCAACAAATATCATATTGCTTTCGCAGCATTAGAAGCTGTT
TGTTTCCAAACCCGAGAGATTTTGGATGCCATGAATCGTGATTGTGGAATTCCACTCACTCATTTGCAGGTTGATGGAGC
AATGACCAACAACAATATTCTTATGCAACTACAAGCAGATATTCTGCATATTCCAGTAGTAAAATCTTCCATGCCTGAAA
CAACTGCTTTGGGAGCTGCCATGGCAGCAGGAGCTGCAGAAGGAATAGGCGTTTGGAGTCTTGAACCTGAGAATTTGTCG
GCAATCACAATGGAAAAGTTTGAACCACAGATACAGGCTACAGAAAGCGATATTCGTTATGCTACATGGAAGAAAGCTGT
GATGAAGTCAATGGGTTGGGTTACAGCTCAGTCTTCTGAAAATGATGATACTGCTATCTTCTCTAGTCTGCCTTTGGGAT
TTTTTGTAGTGAGTAGCATGATAATGTTAATTGGGGCAAGATACATCTCAGGTATTCCA

ORF - retro_itri_1436 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 89.51 %
Parental protein coverage: 100. %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMAAAKKAVLGPLVGAVDQGTSSTRFLVFNSKTAELLSHHQVEIKQEFPREGWVEQDPKEILQSVYECIEK
MAA.KK...GPLVGAV.QGT.STRFLVFNSKTAELLSHHQVE..QEFPREGWVEQDPKEILQSVYECIE.
RetrocopyMAAPKKGAVGPLVGAVVQGTNSTRFLVFNSKTAELLSHHQVELTQEFPREGWVEQDPKEILQSVYECIER
ParentalTCEKLGQLNIDISNIKAIGVSNQRETTVVWDKLTGEPLYNAVVWLDLRTQSTVENLYKRIPGNNNFVKSK
TCEKL...N.DI.NIKAIGVSNQRETTV.WDKLTGEPLYNAVVWLDLRTQSTVENL.K.IPGNNNFVKSK
RetrocopyTCEKLDEVNVDIANIKAIGVSNQRETTVIWDKLTGEPLYNAVVWLDLRTQSTVENLSKKIPGNNNFVKSK
ParentalTGLPLSTYFSAVKLRWLLDNVRKVQKAVEENRALFGTIDSWLIWSLTGGVNGGVHCTDVTNASRTMLFNI
TGLPLSTYFSAVKLRW.LDNVR.VQKAVEE.RALFGTIDSWLIWS.TGGVNGGVHCTDVTNASRTMLFNI
RetrocopyTGLPLSTYFSAVKLRWMLDNVRNVQKAVEEGRALFGTIDSWLIWSMTGGVNGGVHCTDVTNASRTMLFNI
ParentalHSLEWDKELCDFFGIPMEILPNVRSSSEIYGLMKAGALEGVPISGCLGDQSAALVGQMCFQDGQAKNTYG
HSLEWDKELCDFF.IPM.ILPNV.SSSEIYGLMK.GALEGVPISGCLGDQSAALVGQMCFQ.GQAKNTYG
RetrocopyHSLEWDKELCDFFEIPMNILPNVWSSSEIYGLMKSGALEGVPISGCLGDQSAALVGQMCFQEGQAKNTYG
ParentalTGCFLLCNTGHKCVFSEHGLLTTVAYKLGRDKPVYYALEGSVAIAGAVIRWLRDNLGIIKSSEEIEKLAK
TGCFLLCNTG.KCVFSEHGLLTTVAYKLGRDKPV.YALEGSVAIAGAVIRWLRDNLGII..SEE.EKLAK
RetrocopyTGCFLLCNTGRKCVFSEHGLLTTVAYKLGRDKPVCYALEGSVAIAGAVIRWLRDNLGIIETSEEVEKLAK
ParentalEVGTSYGCYFVPAFSGLYAPYWEPSARGIICGLTQFTNKCHIAFAALEAVCFQTREILDAMNRDCGIPLS
E.GTSYGCYFVPAFSGLYAPYWEPSARGIICGLT.FTNK.HIAFAALEAVCFQTREILDAMNRDCGIPL.
RetrocopyEAGTSYGCYFVPAFSGLYAPYWEPSARGIICGLTHFTNKYHIAFAALEAVCFQTREILDAMNRDCGIPLT
ParentalHLQVDGGMTSNKILMQLQADILYIPVVKPSMPETTALGAAMAAGAAEGVGVWSLEPEDLSAVTMERFEPQ
HLQVDG.MT.N.ILMQLQADIL.IPVVK.SMPETTALGAAMAAGAAEG.GVWSLEPE.LSA.TME.FEPQ
RetrocopyHLQVDGAMTNNNILMQLQADILHIPVVKSSMPETTALGAAMAAGAAEGIGVWSLEPENLSAITMEKFEPQ
ParentalINAEESEIRYSTWKKAVMKSMGWVTTQSPESGDPSIFCSLPLGIFIVSSMVMLIGARYISGIP
I.A.ES.IRY.TWKKAVMKSMGWVT.QS.E..D..IF.SLPLG.F.VSSM.MLIGARYISGIP
RetrocopyIQATESDIRYATWKKAVMKSMGWVTAQSSENDDTAIFSSLPLGFFVVSSMIMLIGARYISGIP

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_1436 retrocopy.

TSS - click to see more details

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab - click to see more details

retro_itri_1436 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 14 parental genes, and 25 retrocopies.

Species Parental gene accession Retrocopies number
Callithrix jacchus ENSCJAG000000076333 retrocopies
retro_cjac_125, retro_cjac_3161, retro_cjac_4035,
Cavia porcellus ENSCPOG000000032612 retrocopies
retro_cpor_11, retro_cpor_20,
Echinops telfairi ENSETEG000000082792 retrocopies
retro_etel_2000, retro_etel_247,
Felis catus ENSFCAG000000042641 retrocopy
retro_fcat_140,
Homo sapiens ENSG000001988144 retrocopies
retro_hsap_3087, retro_hsap_3120, retro_hsap_4885, retro_hsap_70,
Loxodonta africana ENSLAFG000000076321 retrocopy
retro_lafr_30,
Monodelphis domestica ENSMODG000000024171 retrocopy
retro_mdom_234,
Mus musculus ENSMUSG000000250592 retrocopies
retro_mmus_119, retro_mmus_97,
Nomascus leucogenys ENSNLEG000000101022 retrocopies
retro_nleu_1650, retro_nleu_771,
Oryctolagus cuniculus ENSOCUG000000130232 retrocopies
retro_ocun_2, retro_ocun_81,
Rattus norvegicus ENSRNOG000000341162 retrocopies
retro_rnor_114, retro_rnor_34,
Sarcophilus harrisii ENSSHAG000000064701 retrocopy
retro_shar_35,
Ictidomys tridecemlineatus ENSSTOG00000008732 1 retrocopy
retro_itri_1436 ,
Tarsius syrichta ENSTSYG000000082491 retrocopy
retro_tsyr_29,




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