RetrogeneDB ID:

retro_itri_1267

Retrocopy
location
Organism:Squirrel (Ictidomys tridecemlineatus)
Coordinates:JH393419.1:192340..194069(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSSTOG00000025133
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:WWC1
Ensembl ID:ENSSTOG00000015095
Aliases:None
Description:WW and C2 domain containing 1 [Source:HGNC Symbol;Acc:29435]


Retrocopy-Parental alignment summary:






>retro_itri_1267
AAGGTGGAGCTTCTGCTCCTGGAAGGCACCACGGGCTTCCGGCCCTCGGGTTGCATCACCACTATCCAGGAGGACGAGGT
GGCCAAGACCCAGAAGGCAGAGGGAGGTGGCCGCTTGCCGGCCCTGCGCTCCCTGTCTGGCACCCCAAAGTCCATGACTT
CCCTGTCCCCACTTTCTTCCCTCTCCTCCCCGTCCCCGCCCTGCTCCCCTCTCATTGCTGACCCCCTTCTGACTGGAGAT
ACCTTTCTGAGCCCAGTGGAGTTTGAAGACCCAGAGCTAAGTGCCACTCTGTGTGAGCTGAGCCTCAGGAGCGGCACCCC
GGAGAGATACCGGCTGGAAGAACCAGGAGCAGAGGGCAAGCCTTTGGGCCAAGCTGTGAATGCAGCCCAAGGGTGCGGCC
TCAAAGTGGCCTGTGTCTCAGCCACAGTGTCAGACGAGTCAGTGGCTGGGGACAGTGGTGTGTACCAGGCTTCTGTGCAG
AGACTGGGTGCTTCAGAAGCCACTGCTGCATTCGACAGTGATGAATCAGAAGCAGCAGGTGCCACTCGGATTCAGATTGC
CCTGAAGTATGATGAGAAGAATAAACAATTTGCAATATTAATCATCCAACTGAGTAACCTTTCTGCTCTTTCCCTGCTGC
AAGATCAGAGAGTGAACATCCTCGTGGCTATCCTCCCTTGCTCTGAAAGCACCACCTGCCTATTCAGGACCCGGTTCCTG
GACGCCTCGGACACCCTCTTGTTCAACGAGATGTTCTGGGTGTCGGTGTCCTACCAAGCCCTTCACCAGAAGACCTTAAG
AGTCGATGTCTGCACCACTGACAGGAGCCACGTGGAAGAGTGCCTGAGAGGTGCCCAGATCAGACTGGCAGAGGTGTGCT
GCTCTGGGGAGAGGTCGACTCGCTGGTACAACCTCTTGAGCTACAAATACTTGAAGAAGCAGAGCAGCGGTCCCAAGGCA
GCTGGAGTTGCGGGCCCCAGCCCAGGGCCTGAACGCATGGACGCTGTGTCTGCCCTGCTGGAGCAGATGGCAGTGGAGCT
AGAGAAGAGGCAGGAGAGCAGGAGCAGCCCACAGGTGCTAGAAGACAGCTGGAGGTACGAGGAGGAGACCTGCGAGAATG
AGGCTGTGGCTGAGGAGGAGGAGGACGAAGAGGGGGAGGAAGCGGAGGGAGAAGATTTTTTTTTTGCAGAGAAAGCCTCC
CCAGATGATCACCCGGCATTGAAGGCATTGAAGGTGGATAAAGAGACCAACACAGACACAGTGGCCCCATCCCCCACAGT
GGTGCGGCTCAAGGACCGGCGTGTGGGCACCCCATCGCCAGGGCCATTTCTTCAGGGGGAGCACCATCATCCGCTCCAAG
ACCTTCTCCCCAGGGCCCCAGAGCCAGTACGTGTGCCGGCTGAATCGGAGCAACAGTGATAGCTCCACTCTCTCCAAAAA
GCCACCTTTTGTGCGAAACTCCCTGGAGCAGCGCAGCGTCAGGATGAAGCGGCCTTCCTCTGTGAAATCCCTGTGCACCG
GGCGCCTGATCCGCACCTCGCTGGACCTTGAGCTGGACCTGCAGGCAACGCGAACCTGGCACAGCCAACTGACTCAGGAG
ACTTCGGTGCTGCGGGAGCTCAAGGAGCGGCTGGAGCAAGCCAAGAGCCACAGGGAGAAGGAGCTGCCACAGTGGCTGCG
CGAGGATGAGCGCATCCACCTGCTGCTGAGGATGCTAGAGAAGAGGATG

ORF - retro_itri_1267 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 88.39 %
Parental protein coverage: 54.47 %
Number of stop codons detected: 0
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalKVELLLLEGTTGFRPSGCITTIHEDEVAKTQKAEGGGRLQALRSLSGTPKSMTSLSPRSSLSSPSPPCSP
KVELLLLEGTTGFRPSGCITTI.EDEVAKTQKAEGGGRL.ALRSLSGTPKSMTSLSP.SSLSSPSPPCSP
RetrocopyKVELLLLEGTTGFRPSGCITTIQEDEVAKTQKAEGGGRLPALRSLSGTPKSMTSLSPLSSLSSPSPPCSP
ParentalLIADPLLTGDAFLSPLEFEDPELSATLCELSLGSGTRERYRLEEPGAEGKPLGQAVNAAQGCGLKVACVS
LIADPLLTGD.FLSP.EFEDPELSATLCELSL.SGT.ERYRLEEPGAEGKPLGQAVNAAQGCGLKVACVS
RetrocopyLIADPLLTGDTFLSPVEFEDPELSATLCELSLRSGTPERYRLEEPGAEGKPLGQAVNAAQGCGLKVACVS
ParentalAAVSDESVAGDSGVYEASVQRLGASEATAAFDSDESEAAGATRIQIALKYDEKNKQFAILIIQLSNLSAL
A.VSDESVAGDSGVY.ASVQRLGASEATAAFDSDESEAAGATRIQIALKYDEKNKQFAILIIQLSNLSAL
RetrocopyATVSDESVAGDSGVYQASVQRLGASEATAAFDSDESEAAGATRIQIALKYDEKNKQFAILIIQLSNLSAL
ParentalSLLQDQRVNIRVAILPCSESTTCLFRTRPLDASDTLLFNEMFWVSASYQALHQKTLRVDVCTTDRSHVEE
SLLQDQRVNI.VAILPCSESTTCLFRTR.LDASDTLLFNEMFWVS.SYQALHQKTLRVDVCTTDRSHVEE
RetrocopySLLQDQRVNILVAILPCSESTTCLFRTRFLDASDTLLFNEMFWVSVSYQALHQKTLRVDVCTTDRSHVEE
ParentalCLGGAQISLAEVCRSGERSTRWYNLLSYKYLKKQSSGPKAAGAAGPSPGPEHTDAVSALLEQTAVELEKR
CL.GAQI.LAEVC.SGERSTRWYNLLSYKYLKKQSSGPKAAG.AGPSPGPE..DAVSALLEQ.AVELEKR
RetrocopyCLRGAQIRLAEVCCSGERSTRWYNLLSYKYLKKQSSGPKAAGVAGPSPGPERMDAVSALLEQMAVELEKR
ParentalQESRSSSQVLEDSWRYEEETCENEAVAEEEEDEEGEEVEGEEDFFAEKASPDDH-PALKVDKETNTDTVA
QESRSS.QVLEDSWRYEEETCENEAVA.............E....AEKASPDDH...........T.T..
RetrocopyQESRSSPQVLEDSWRYEEETCENEAVAXXXXXXXXXXXXXEXXXXAEKASPDDHXXXXXXXXDKETNTDT
ParentalPSP--TVVRPKDRRVGIPSPGPFL-RGSTIIRSKTFSPGPQSQYVCRLNRSDSDSSTLSKKPPFVRNSLE
..P..TVVR.KDRRVG.PSPGPFL.RGSTIIRSKTFSPGPQSQYVCRLNRS.SDSSTLSKKPPFVRNSLE
RetrocopyVAPSPTVVRLKDRRVGTPSPGPFL>RGSTIIRSKTFSPGPQSQYVCRLNRSNSDSSTLSKKPPFVRNSLE
ParentalRRSVRMKRPSSVKSLRTERLIRTSLDLELDLQATRTWHSQLTQEISVLRELKERLEQAKSHGEKELPQWL
.RSVRMKRPSSVKSL.T.RLIRTSLDLELDLQATRTWHSQLTQE.SVLRELKERLEQAKSH.EKELPQWL
RetrocopyQRSVRMKRPSSVKSLCTGRLIRTSLDLELDLQATRTWHSQLTQETSVLRELKERLEQAKSHREKELPQWL
ParentalREDERFRLLLRMLEKRV
REDER..LLLRMLEKR.
RetrocopyREDERIHLLLRMLEKRM

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_1267 retrocopy.

TSS - click to see more details

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab - click to see more details

retro_itri_1267 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 ENSSTOG00000015095 1 retrocopy
retro_itri_1267 ,


Copyright © RetrogeneDB 2014-2017