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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaattccttctattatcatcaattctattgtttcatactatctgttctgcttgatgtagtctatataacacctttctgttatagGCACGACCGACCATATATCAAGTTGTCAAGGAAATGATTGATAAAATGGGTTATGAG

Basic information

species Zea mays
transcript GRMZM2G053531_T02
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G053531_T02 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os08g26870.4 (Oryza sativa), 3'ss of exon 4
gtaattccttctattatcatcaattctattgtttcatactatctgttctgcttgatgtagtctatataacacctttctgttatagGCACGACCGACCATATATCAAGTTGTCAAGGAAATGATTGATAAAATGGGTTATGAG
|||||  ||| | |||| |      |||   |||  | || | | || |||||||||   | ||||  || | ||    ||  ||||| |||| ||||||||||||||||| ||||| ||||||||||| ||||||||||||
gtaatatcttgttttatta------ctacaatttgctccttttt-ttttgcttgatgcgatttata--accctttctcattgcagGCAAGACCAACCATATATCAAGTTGTGAAGGAGATGATTGATAAGATGGGTTATGAG
















Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|50323662|gb|CO518788.1|CO518788
EST:     TGGAGATGCCAAGCGTTCTTCTGATGGCAGCTATTCGTAATGTCCACATT                         GCACGACCGACCATATATCAAGTTGTCAAGGAAATGATTGATAAAATGGGT
genomic: TGGAGATGCCAAGCGTTCTTCTGATGGCAGCTATTCGTAATGTCCACATTgtaattcctt ... tctgttatagGCACGACCGACCATATATCAAGTTGTCAAGGAAATGATTGATAAAATGGGT
EST: gi|60353122|gb|DN220095.1|DN220095
EST:     TGGAGATGCCAAGCGTTCTTCTGATGGCAGCTATTCGTAATGTCCACATT                         GCACGACCGACCATATATCAAGTTGTCAAGGAAATGATTGATAAAATGGGT
genomic: TGGAGATGCCAAGCGTTCTTCTGATGGCAGCTATTCGTAATGTCCACATTgtaattcctt ... tctgttatagGCACGACCGACCATATATCAAGTTGTCAAGGAAATGATTGATAAAATGGGT
EST: gi|84969850|gb|DW468264.1|DW468264
EST:     TGATGGCAGCTATTCGTAATGTCCACACT                         GCACGCCCGCCCATATATCAAGTTGTCAAGGAAATGATTGATAAAATGGGT
genomic: TGATGGCAGCTATTCGTAATGTCCACATTgtaattcctt ... tctgttatagGCACGACCGACCATATATCAAGTTGTCAAGGAAATGATTGATAAAATGGGT
EST: gi|211437854|gb|FL220477.1|FL220477
EST:     TGGAGATGCCAAGCGTTCTTCTGATGGCAGCTATTCGTAATGTCCACATT                         GCACGACCGACCATATATCAAGTTGTCAAGGAAATGATTGATAAAATGGGT
genomic: TGGAGATGCCAAGCGTTCTTCTGATGGCAGCTATTCGTAATGTCCACATTgtaattcctt ... tctgttatagGCACGACCGACCATATATCAAGTTGTCAAGGAAATGATTGATAAAATGGGT
EST: gi|78109883|gb|DV528299.1|DV528299
EST:     TGGAGATGCCAAGCGTTCTTCTGATGGCAGCTATTCGTAATGTCCACATT                         GCACGACCGACCATATATCAAGTTGTCAAGGAAATGATTGATAAAATGGGT
genomic: TGGAGATGCCAAGCGTTCTTCTGATGGCAGCTATTCGTAATGTCCACATTgtaattcctt ... tctgttatagGCACGACCGACCATATATCAAGTTGTCAAGGAAATGATTGATAAAATGGGT
EST: gi|60341680|gb|DN208653.1|DN208653
EST:     TGGAGATGCCAAGCGTTCTTCTGATGGCAGCTATTCGTAATGTCCACATT                         GCACGACCGACCATATATCAAGTTGTCAAGGAAATGATTGATAAAATGGGT
genomic: TGGAGATGCCAAGCGTTCTTCTGATGGCAGCTATTCGTAATGTCCACATTgtaattcctt ... tctgttatagGCACGACCGACCATATATCAAGTTGTCAAGGAAATGATTGATAAAATGGGT
EST: gi|113702906|gb|EE680410.1|EE680410
EST:     TGGAGATGCCAAGCGTTCTTCTGATGGCAGCTATTCGTAATGTCCACATT                         GCACGACCGACCATATATCAAGTTGTCAAGGAAATGATTGATAAAATGGGT
genomic: TGGAGATGCCAAGCGTTCTTCTGATGGCAGCTATTCGTAATGTCCACATTgtaattcctt ... tctgttatagGCACGACCGACCATATATCAAGTTGTCAAGGAAATGATTGATAAAATGGGT
EST: gi|78109884|gb|DV528300.1|DV528300
EST:     TGGAGATGCCAAGCGTTCTTCTGATGGCAGCTATTCGTAATGTCCACATT                         GCACGACCGACCATATATCAAGTTGTCAAGGAAATGATTGATAAAATGGGT
genomic: TGGAGATGCCAAGCGTTCTTCTGATGGCAGCTATTCGTAATGTCCACATTgtaattcctt ... tctgttatagGCACGACCGACCATATATCAAGTTGTCAAGGAAATGATTGATAAAATGGGT
EST: gi|93281145|gb|EB673409.1|EB673409
EST:     TGGAGATGCCAAGCGTTCTTCTGATGGCAGCTATTCGTAATGTCCACATT                         GCACGACCGACCATATATCAAGTTGTCAAGGAAATGATTGATAAAATGGGT
genomic: TGGAGATGCCAAGCGTTCTTCTGATGGCAGCTATTCGTAATGTCCACATTgtaattcctt ... tctgttatagGCACGACCGACCATATATCAAGTTGTCAAGGAAATGATTGATAAAATGGGT
EST: gi|60394174|gb|DN227044.1|DN227044
EST:     TGGAGATGCCAAGCGTTCTTCTGATGGCAGCTATTCGTAATGTCCACATT                         GCACGACCGACCATATATCAAGTTGTCAAGGAAATGATTGATAAAATGGGT
genomic: TGGAGATGCCAAGCGTTCTTCTGATGGCAGCTATTCGTAATGTCCACATTgtaattcctt ... tctgttatagGCACGACCGACCATATATCAAGTTGTCAAGGAAATGATTGATAAAATGGGT
EST: gi|6227143|gb|AW155672.1|AW155672
EST:     TGGAGATGCCAAGCGTTCTTCTAATGGCAGCTATTCGTAATGTCCACATT                         GCACGACCGACCATATATCAAGTTGTCAAGGAAATGATTGATAAAATGGGT
genomic: TGGAGATGCCAAGCGTTCTTCTGATGGCAGCTATTCGTAATGTCCACATTgtaattcctt ... tctgttatagGCACGACCGACCATATATCAAGTTGTCAAGGAAATGATTGATAAAATGGGT
EST: gi|93016890|gb|EB642410.1|EB642410
EST:     TGGAGATGCCAAGCGTTCTTCTGATGGCAGCTATTCGTAATGTCCACATT                         GCACGACCGACCATATATCAAGTTGTCAAGGAAATGATTGATAAAATGGGT
genomic: TGGAGATGCCAAGCGTTCTTCTGATGGCAGCTATTCGTAATGTCCACATTgtaattcctt ... tctgttatagGCACGACCGACCATATATCAAGTTGTCAAGGAAATGATTGATAAAATGGGT
EST: gi|76926083|gb|DV170714.1|DV170714
EST:     TGGAGATGCCAAGCGTTCTTCTGATGGCAGCTATTCGTAATGTCCACATT                         GCACGACCGACCATATATCAAGTTGTCAAGGAAATGATTGATAAAATGGGT
genomic: TGGAGATGCCAAGCGTTCTTCTGATGGCAGCTATTCGTAATGTCCACATTgtaattcctt ... tctgttatagGCACGACCGACCATATATCAAGTTGTCAAGGAAATGATTGATAAAATGGGT
EST: gi|78021679|gb|DV490066.1|DV490066
EST:     TGGAGATGCCAAGCGTTCTTCTAATGGCAGCTATTCGTAATGTCCACATT                         GCACGACCGACCATATATCAAGTTGTCAAGGAAATGATTGATAAAATGGGT
genomic: TGGAGATGCCAAGCGTTCTTCTGATGGCAGCTATTCGTAATGTCCACATTgtaattcctt ... tctgttatagGCACGACCGACCATATATCAAGTTGTCAAGGAAATGATTGATAAAATGGGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtttcatactatctgttctgcttgatgtagtctatataacacctttctgttatagGCACGACCGACCATATATCAAGTTGTCAAGGAAATGATTGATAAAATGGGTTATGAG
                                 atataac  putative branch site (score: 3)
                                         cctttctgtt  CT-rich tract
                              tctatataa  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
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---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaattccttctattatcatcaattctattgtttcatactatctgttctgcttgatgtagtctatataacacctttctgttatagGCACGACCGACCATATATCAAGTTGTCAAGGAAATGATTGATAAAATGGGTTATGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA