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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgcattttctatatgttaaattagttgccttattctggctataaagattggttggtcattgtttaagctttttctgataatgaaatcttacttttcagagTGTTACTCCGAACCTATCAATGGGAACTGAAATGTTCTGGCTTGGTCACCAAAGGAAGTCTGGAATTGGTTTTGCCTCTCGCTATAACACAGACAAAATG

Basic information

species Zea mays
transcript GRMZM2G174696_T02
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G174696_T02 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os03g20750.1 (Oryza sativa), 3'ss of exon 6
tgcattttctatatgttaaattagttgccttattctggctataaagattg--gttggtcattgtttaagctttt---tctgataatgaaatcttacttttcagagTGTTACTCCGAACCTATCAATGGGAACTGAAATGTTCTGGCTTGGTCACCAAAGGAAGTCTGGAATTGGTTTTGCCTCTCGCTATAACACAGACAAAATG
   ||||||| ||| |   |  |||    || |      || ||   |    |||     |||| ||  |||     |   | |||||| | || | |||||||||||||| |||||| | ||||||||||||||||| ||||||||||| |||||||||||||| |||||||||||||| ||||| |||||  |||| ||||  
--aattttctttatctagcacaagtacagttgtga-aattaaaatcttcactgttaaatcttgtctattcttgacagtgaaacaatgaacttttgcatttcagAGTGTTACGCCGAACTTGTCAATGGGAACTGAAATATTCTGGCTTGGCCACCAAAGGAAGTCAGGAATTGGTTTTGCTTCTCGATATAATTCAGATAAAA--
















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|31353843|gb|CD438200.1|CD438200
EST:     CACAATTCCAAATTGGGAACAATGCATTCTATGGTGCAAATTATATTCAG                         A
genomic: CACAATTCCAAATTGGGAACAATGCATTCTATGGTGCAAATTATATTCAGgtaaacactt ... cttttcagag-
EST: gi|31353843|gb|CD438200.1|CD438200
EST:     CACAATTCCAAATTGGGAACAATGCATTCTATGGTGCAAATTATATTCAG                         A
genomic: CACAATTCCAAATTGGGAACAATGCATTCTATGGTGCAAATTATATTCAGgtaaacactt ... cttttcagag-
EST: gi|31353843|gb|CD438200.1|CD438200
EST:     CACAATTCCAAATTGGGAACAATGCATTCTATGGTGCAAATTATATTCAG                         A
genomic: CACAATTCCAAATTGGGAACAATGCATTCTATGGTGCAAATTATATTCAGgtaaacactt ... cttttcagag-
EST: gi|37398312|gb|CF636468.1|CF636468
EST:     TATGGTGCAAATTATATTCAGAG                        
genomic: TATGGTGCAAATTATATTC--AGgtaaacactt ... cttttcaga
EST: gi|148944949|gb|EC890114.2|EC890114
EST:     CACAATTCCAAATTGGGAACAATGCATTCTATGGTGCAAATTATATTCAG                         A
genomic: CACAATTCCAAATTGGGAACAATGCATTCTATGGTGCAAATTATATTCAGgtaaacactt ... cttttcagag-
EST: gi|148944949|gb|EC890114.2|EC890114
EST:     CACAATTCCAAATTGGGAACAATGCATTCTATGGTGCAAATTATATTCAG                         A
genomic: CACAATTCCAAATTGGGAACAATGCATTCTATGGTGCAAATTATATTCAGgtaaacactt ... cttttcagag-
EST: gi|148944949|gb|EC890114.2|EC890114
EST:     CACAATTCCAAATTGGGAACAATGCATTCTATGGTGCAAATTATATTCAG                         A
genomic: CACAATTCCAAATTGGGAACAATGCATTCTATGGTGCAAATTATATTCAGgtaaacactt ... cttttcagag-
EST: gi|71428447|gb|DR809497.1|DR809497
EST:     CACAATTCCAAATTGGGAACAATGCATTCTATGGTGCAAATTATATTCAG                         A
genomic: CACAATTCCAAATTGGGAACAATGCATTCTATGGTGCAAATTATATTCAGgtaaacactt ... cttttcagag-
EST: gi|71428447|gb|DR809497.1|DR809497
EST:     CACAATTCCAAATTGGGAACAATGCATTCTATGGTGCAAATTATATTCAG                         A
genomic: CACAATTCCAAATTGGGAACAATGCATTCTATGGTGCAAATTATATTCAGgtaaacactt ... cttttcagag-
EST: gi|71428447|gb|DR809497.1|DR809497
EST:     CACAATTCCAAATTGGGAACAATGCATTCTATGGTGCAAATTATATTCAG                         A
genomic: CACAATTCCAAATTGGGAACAATGCATTCTATGGTGCAAATTATATTCAGgtaaacactt ... cttttcagag-
EST: gi|76294141|gb|DV033709.1|DV033709
EST:     CACAATTCCAAATTGGGAACAATGCATTCTATGGTGCAAATTATATTCAG                         A
genomic: CACAATTCCAAATTGGGAACAATGCATTCTATGGTGCAAATTATATTCAGgtaaacactt ... cttttcagag-
EST: gi|76294141|gb|DV033709.1|DV033709
EST:     CACAATTCCAAATTGGGAACAATGCATTCTATGGTGCAAATTATATTCAG                         A
genomic: CACAATTCCAAATTGGGAACAATGCATTCTATGGTGCAAATTATATTCAGgtaaacactt ... cttttcagag-
EST: gi|76294141|gb|DV033709.1|DV033709
EST:     CACAATTCCAAATTGGGAACAATGCATTCTATGGTGCAAATTATATTCAG                         A
genomic: CACAATTCCAAATTGGGAACAATGCATTCTATGGTGCAAATTATATTCAGgtaaacactt ... cttttcagag-
EST: gi|148937183|gb|EC881364.2|EC881364
EST:     CACAATTCCAAATTGAGAACAATGCATTCTATGGTGCAAATTATATTCAG                         A
genomic: CACAATTCCAAATTGGGAACAATGCATTCTATGGTGCAAATTATATTCAGgtaaacactt ... cttttcagag-
EST: gi|148937183|gb|EC881364.2|EC881364
EST:     CACAATTCCAAATTGAGAACAATGCATTCTATGGTGCAAATTATATTCAG                         A
genomic: CACAATTCCAAATTGGGAACAATGCATTCTATGGTGCAAATTATATTCAGgtaaacactt ... cttttcagag-
EST: gi|148937183|gb|EC881364.2|EC881364
EST:     CACAATTCCAAATTGAGAACAATGCATTCTATGGTGCAAATTATATTCAG                         A
genomic: CACAATTCCAAATTGGGAACAATGCATTCTATGGTGCAAATTATATTCAGgtaaacactt ... cttttcagag-
EST: gi|6095402|gb|AW120069.1|AW120069
EST:     CACAATTCCAAATTGGGAACAATGCATTCTATGGTGCAAATTATATTCAGAG                        
genomic: CACAATTCCAAATTGGGAACAATGCATTCTATGGTGCAAATTATATTC--AGgtaaacactt ... cttttcaga
EST: gi|6095403|gb|AW120070.1|AW120070
EST:     CACAATTCCAAATTGGGAACAATGCATTCTATGGTGCAAATTATATTCAGAG                        
genomic: CACAATTCCAAATTGGGAACAATGCATTCTATGGTGCAAATTATATTC--AGgtaaacactt ... cttttcaga
EST: gi|89762284|gb|DY689955.1|DY689955
EST:     CACAATTCCAAATTGGGAACAATGCATTCTATGGTGCAAATTATATTCAG                         A
genomic: CACAATTCCAAATTGGGAACAATGCATTCTATGGTGCAAATTATATTCAGgtaaacactt ... cttttcagag-
EST: gi|89762284|gb|DY689955.1|DY689955
EST:     CACAATTCCAAATTGGGAACAATGCATTCTATGGTGCAAATTATATTCAG                         A
genomic: CACAATTCCAAATTGGGAACAATGCATTCTATGGTGCAAATTATATTCAGgtaaacactt ... cttttcagag-
EST: gi|89762284|gb|DY689955.1|DY689955
EST:     CACAATTCCAAATTGGGAACAATGCATTCTATGGTGCAAATTATATTCAG                         A
genomic: CACAATTCCAAATTGGGAACAATGCATTCTATGGTGCAAATTATATTCAGgtaaacactt ... cttttcagag-
EST: gi|6095404|gb|AW120071.1|AW120071
EST:     CACAATTCCAAATTGGGAACAATGCATTCTATGGTGCAAATTATATTCAGAG                        
genomic: CACAATTCCAAATTGGGAACAATGCATTCTATGGTGCAAATTATATTC--AGgtaaacactt ... cttttcaga


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gattggttggtcattgtttaagctttttctgataatgaaatcttacttttcagagTGTTACTCCGAACCTATCAATGGGAACTGAAATGTTCTGGCTTGGTCACCAAAGGAAGTCTGGAATTGGTTTTGCCTCTCGCTATAACACAGACAAAATG
                                       atcttac  putative branch site (score: 3)
                                        tcttacttttc  CT-rich tract
                               ataatgaaatctta  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
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgcattttctatatgttaaattagttgccttattctggctataaagattggttggtcattgtttaagctttttctgataatgaaatcttacttttcagagTGTTACTCCGAACCTATCAATGGGAACTGAAATGTTCTGGCTTGGTCACCAAAGGAAGTCTGGAATTGGTTTTGCCTCTCGCTATAACACAGACAAAATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
tgcattt
- - - - - - - - - - - - -tgcctta
- - - - - - - - - - - - - - - - ttctggc
- - - - - - - - - - - - - - - - - - - - - - - -ttggttg