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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gagtgagtcagttgtcgtgtcacaagcataatcatagacacacagacagatcttgcaacatttactcattaatgtggttcatgggttctgaagctcacagGATTTGATAATGAGCTGTCTTGGACTTCATTGGACAAATGATCTACCTGGAGCAATGATACAG

Basic information

species Zea mays
transcript GRMZM2G087692_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G087692_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os12g10200.1 (Oryza sativa), 3'ss of exon 2
----------gagtgagtcagttgtcgtgtcacaagcataatcatagacacacagacagatcttgcaacatttactcattaatgtggttcatgggttctgaagctcacagGATTTGATAATGAGCTGTCTTGGACTTCATTGGACAAATGATCTACCTGGAGCAATGATACAG
           | | | | ||||   ||   ||||   |   |  |    |  |     || ||||  ||| |  | |||||||||||| ||||  |||||||||| ||||||  |||||| || |||||||| |||||||||||||||||||||||||||||||||||||||
gcagttctcacaattatttagtttaagtcaaacaa-tgtttcccgatcttcctatctgcatattgct-catgtcattattaatgtggtt-atggtctctgaagCTCGCAGGATACGATAATAAGTTGTCTTGGGCTTCATTGGACAAATGATCTACCTGGAGCAATGATACAG

upper sequence: GRMZM2G087692_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA04G43650.1 (Glycine max), 3'ss of exon 3
gagtgagtcagttgtcgtgtcacaagcataatcatagacacacagacagatcttgcaacatttactcattaatgtggttcatgggttctgaagctcacagGATTTGATAATGAGCTGTCTTGGACTTCATTGGACAAATGATCTACCTGGAGCAATGATACAG
        || || |  |      |   || |    | ||| |       | ||| |   ||  || | | || |  ||  |  ||| || |||||   ||||||| |  | || ||  | ||||| || ||||| |||||||| ||||||||||||||||||
-------gcaattataat----tgattttatttcatgtcacgcttttctgttttggattgtt--cttacttatata-ttggtttgtt-tgcagCTCTGTGGATTTGGTTGTTAGTTGCTTGGGACTACACTGGACTAATGATCTGCCTGGAGCAATGATACAG

upper sequence: GRMZM2G087692_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA12G37130.2 (Glycine max), 3'ss of exon 4
gagtgagtcagttgtcgtgtcacaagcataatcatagacacacaga-cagatcttgcaacatttactcattaatgtggttcatgggttctgaagctcacagGATTTGATAATGAGCTGTCTTGGACTTCATTGGACAAATGATCTACCTGGAGCAATGATACAG
        || || |  |      |   || |    | ||| |    |   | ||| |   ||    | |  || | | |  ||   | || |||||   ||||||| |  | || ||  | ||||| || ||||| |||||||| ||||||||||||||||||
-------gcaattataat----tgattttatttcatgtcacgcttttcctgttttggattgttcttacttagatattggtt-tg---tttgcagCTCTGTGGATTTGGTTGTTAGTTGCTTGGGACTACACTGGACTAATGATCTGCCTGGAGCAATGATACAG

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|74241982|gb|DT649896.1|DT649896
EST:     GAGACCCACTTTGTTATCGGCGATGAGGAGTTTCTTCCAATCAAAGAGAG                         C
genomic: GAGACCCACTTTGTTATCGGCGATGAGGAGTTTCTTCCAATCAAAGAGAGgtgatttcac ... aagctcacag-
EST: gi|74241982|gb|DT649896.1|DT649896
EST:     GAGACCCACTTTGTTATCGGCGATGAGGAGTTTCTTCCAATCAAAGAGAG                         C
genomic: GAGACCCACTTTGTTATCGGCGATGAGGAGTTTCTTCCAATCAAAGAGAGgtgatttcac ... aagctcacag-
EST: gi|74241982|gb|DT649896.1|DT649896
EST:     GAGACCCACTTTGTTATCGGCGATGAGGAGTTTCTTCCAATCAAAGAGAG                         C
genomic: GAGACCCACTTTGTTATCGGCGATGAGGAGTTTCTTCCAATCAAAGAGAGgtgatttcac ... aagctcacag-
EST: gi|74241982|gb|DT649896.1|DT649896
EST:     GAGACCCACTTTGTTATCGGCGATGAGGAGTTTCTTCCAATCAAAGAGAG                         C
genomic: GAGACCCACTTTGTTATCGGCGATGAGGAGTTTCTTCCAATCAAAGAGAGgtgatttcac ... aagctcacag-
EST: gi|74241982|gb|DT649896.1|DT649896
EST:     GAGACCCACTTTGTTATCGGCGATGAGGAGTTTCTTCCAATCAAAGAGAG                         C
genomic: GAGACCCACTTTGTTATCGGCGATGAGGAGTTTCTTCCAATCAAAGAGAGgtgatttcac ... aagctcacag-
EST: gi|74241982|gb|DT649896.1|DT649896
EST:     GAGACCCACTTTGTTATCGGCGATGAGGAGTTTCTTCCAATCAAAGAGAG                         C
genomic: GAGACCCACTTTGTTATCGGCGATGAGGAGTTTCTTCCAATCAAAGAGAGgtgatttcac ... aagctcacag-
EST: gi|74241982|gb|DT649896.1|DT649896
EST:     GAGACCCACTTTGTTATCGGCGATGAGGAGTTTCTTCCAATCAAAGAGAG                         C
genomic: GAGACCCACTTTGTTATCGGCGATGAGGAGTTTCTTCCAATCAAAGAGAGgtgatttcac ... aagctcacag-
EST: gi|71440891|gb|DR821941.1|DR821941
EST:     GAGACCCACTTTGTTATCGGCGATGAGGAGTTTCTTCCAATCAAAGAGAG                         C
genomic: GAGACCCACTTTGTTATCGGCGATGAGGAGTTTCTTCCAATCAAAGAGAGgtgatttcac ... aagctcacag-
EST: gi|71440891|gb|DR821941.1|DR821941
EST:     GAGACCCACTTTGTTATCGGCGATGAGGAGTTTCTTCCAATCAAAGAGAG                         C
genomic: GAGACCCACTTTGTTATCGGCGATGAGGAGTTTCTTCCAATCAAAGAGAGgtgatttcac ... aagctcacag-
EST: gi|71440891|gb|DR821941.1|DR821941
EST:     GAGACCCACTTTGTTATCGGCGATGAGGAGTTTCTTCCAATCAAAGAGAG                         C
genomic: GAGACCCACTTTGTTATCGGCGATGAGGAGTTTCTTCCAATCAAAGAGAGgtgatttcac ... aagctcacag-
EST: gi|71440891|gb|DR821941.1|DR821941
EST:     GAGACCCACTTTGTTATCGGCGATGAGGAGTTTCTTCCAATCAAAGAGAG                         C
genomic: GAGACCCACTTTGTTATCGGCGATGAGGAGTTTCTTCCAATCAAAGAGAGgtgatttcac ... aagctcacag-
EST: gi|71440891|gb|DR821941.1|DR821941
EST:     GAGACCCACTTTGTTATCGGCGATGAGGAGTTTCTTCCAATCAAAGAGAG                         C
genomic: GAGACCCACTTTGTTATCGGCGATGAGGAGTTTCTTCCAATCAAAGAGAGgtgatttcac ... aagctcacag-
EST: gi|71440891|gb|DR821941.1|DR821941
EST:     GAGACCCACTTTGTTATCGGCGATGAGGAGTTTCTTCCAATCAAAGAGAG                         C
genomic: GAGACCCACTTTGTTATCGGCGATGAGGAGTTTCTTCCAATCAAAGAGAGgtgatttcac ... aagctcacag-
EST: gi|71440891|gb|DR821941.1|DR821941
EST:     GAGACCCACTTTGTTATCGGCGATGAGGAGTTTCTTCCAATCAAAGAGAG                         C
genomic: GAGACCCACTTTGTTATCGGCGATGAGGAGTTTCTTCCAATCAAAGAGAGgtgatttcac ... aagctcacag-
EST: gi|78078319|gb|DV506734.1|DV506734
EST:     GAGACCCACTTTGTTATCGGCGATGAGGAGTTTCTTCCAATCAAAGAGAG                         C
genomic: GAGACCCACTTTGTTATCGGCGATGAGGAGTTTCTTCCAATCAAAGAGAGgtgatttcac ... aagctcacag-
EST: gi|78078319|gb|DV506734.1|DV506734
EST:     GAGACCCACTTTGTTATCGGCGATGAGGAGTTTCTTCCAATCAAAGAGAG                         C
genomic: GAGACCCACTTTGTTATCGGCGATGAGGAGTTTCTTCCAATCAAAGAGAGgtgatttcac ... aagctcacag-
EST: gi|78078319|gb|DV506734.1|DV506734
EST:     GAGACCCACTTTGTTATCGGCGATGAGGAGTTTCTTCCAATCAAAGAGAG                         C
genomic: GAGACCCACTTTGTTATCGGCGATGAGGAGTTTCTTCCAATCAAAGAGAGgtgatttcac ... aagctcacag-
EST: gi|78078319|gb|DV506734.1|DV506734
EST:     GAGACCCACTTTGTTATCGGCGATGAGGAGTTTCTTCCAATCAAAGAGAG                         C
genomic: GAGACCCACTTTGTTATCGGCGATGAGGAGTTTCTTCCAATCAAAGAGAGgtgatttcac ... aagctcacag-
EST: gi|78078319|gb|DV506734.1|DV506734
EST:     GAGACCCACTTTGTTATCGGCGATGAGGAGTTTCTTCCAATCAAAGAGAG                         C
genomic: GAGACCCACTTTGTTATCGGCGATGAGGAGTTTCTTCCAATCAAAGAGAGgtgatttcac ... aagctcacag-
EST: gi|78078319|gb|DV506734.1|DV506734
EST:     GAGACCCACTTTGTTATCGGCGATGAGGAGTTTCTTCCAATCAAAGAGAG                         C
genomic: GAGACCCACTTTGTTATCGGCGATGAGGAGTTTCTTCCAATCAAAGAGAGgtgatttcac ... aagctcacag-
EST: gi|78078319|gb|DV506734.1|DV506734
EST:     GAGACCCACTTTGTTATCGGCGATGAGGAGTTTCTTCCAATCAAAGAGAG                         C
genomic: GAGACCCACTTTGTTATCGGCGATGAGGAGTTTCTTCCAATCAAAGAGAGgtgatttcac ... aagctcacag-
EST: gi|89762249|gb|DY689931.1|DY689931
EST:     GAGACCCACTTTGTTATCGGCGATGAGGAGTTTCTTCCAATCAAAGAGAG                         C
genomic: GAGACCCACTTTGTTATCGGCGATGAGGAGTTTCTTCCAATCAAAGAGAGgtgatttcac ... aagctcacag-
EST: gi|89762249|gb|DY689931.1|DY689931
EST:     GAGACCCACTTTGTTATCGGCGATGAGGAGTTTCTTCCAATCAAAGAGAG                         C
genomic: GAGACCCACTTTGTTATCGGCGATGAGGAGTTTCTTCCAATCAAAGAGAGgtgatttcac ... aagctcacag-
EST: gi|89762249|gb|DY689931.1|DY689931
EST:     GAGACCCACTTTGTTATCGGCGATGAGGAGTTTCTTCCAATCAAAGAGAG                         C
genomic: GAGACCCACTTTGTTATCGGCGATGAGGAGTTTCTTCCAATCAAAGAGAGgtgatttcac ... aagctcacag-
EST: gi|89762249|gb|DY689931.1|DY689931
EST:     GAGACCCACTTTGTTATCGGCGATGAGGAGTTTCTTCCAATCAAAGAGAG                         C
genomic: GAGACCCACTTTGTTATCGGCGATGAGGAGTTTCTTCCAATCAAAGAGAGgtgatttcac ... aagctcacag-
EST: gi|89762249|gb|DY689931.1|DY689931
EST:     GAGACCCACTTTGTTATCGGCGATGAGGAGTTTCTTCCAATCAAAGAGAG                         C
genomic: GAGACCCACTTTGTTATCGGCGATGAGGAGTTTCTTCCAATCAAAGAGAGgtgatttcac ... aagctcacag-
EST: gi|89762249|gb|DY689931.1|DY689931
EST:     GAGACCCACTTTGTTATCGGCGATGAGGAGTTTCTTCCAATCAAAGAGAG                         C
genomic: GAGACCCACTTTGTTATCGGCGATGAGGAGTTTCTTCCAATCAAAGAGAGgtgatttcac ... aagctcacag-
EST: gi|89762249|gb|DY689931.1|DY689931
EST:     GAGACCCACTTTGTTATCGGCGATGAGGAGTTTCTTCCAATCAAAGAGAG                         C
genomic: GAGACCCACTTTGTTATCGGCGATGAGGAGTTTCTTCCAATCAAAGAGAGgtgatttcac ... aagctcacag-
EST: gi|101393422|gb|EB818643.1|EB818643
EST:     GAGACCCACTTTGTTATCGGCGATGAGGAGTTTCTTCCAATCAAAGAGAG                         C
genomic: GAGACCCACTTTGTTATCGGCGATGAGGAGTTTCTTCCAATCAAAGAGAGgtgatttcac ... aagctcacag-
EST: gi|101393422|gb|EB818643.1|EB818643
EST:     GAGACCCACTTTGTTATCGGCGATGAGGAGTTTCTTCCAATCAAAGAGAG                         C
genomic: GAGACCCACTTTGTTATCGGCGATGAGGAGTTTCTTCCAATCAAAGAGAGgtgatttcac ... aagctcacag-
EST: gi|101393422|gb|EB818643.1|EB818643
EST:     GAGACCCACTTTGTTATCGGCGATGAGGAGTTTCTTCCAATCAAAGAGAG                         C
genomic: GAGACCCACTTTGTTATCGGCGATGAGGAGTTTCTTCCAATCAAAGAGAGgtgatttcac ... aagctcacag-
EST: gi|101393422|gb|EB818643.1|EB818643
EST:     GAGACCCACTTTGTTATCGGCGATGAGGAGTTTCTTCCAATCAAAGAGAG                         C
genomic: GAGACCCACTTTGTTATCGGCGATGAGGAGTTTCTTCCAATCAAAGAGAGgtgatttcac ... aagctcacag-
EST: gi|101393422|gb|EB818643.1|EB818643
EST:     GAGACCCACTTTGTTATCGGCGATGAGGAGTTTCTTCCAATCAAAGAGAG                         C
genomic: GAGACCCACTTTGTTATCGGCGATGAGGAGTTTCTTCCAATCAAAGAGAGgtgatttcac ... aagctcacag-
EST: gi|101393422|gb|EB818643.1|EB818643
EST:     GAGACCCACTTTGTTATCGGCGATGAGGAGTTTCTTCCAATCAAAGAGAG                         C
genomic: GAGACCCACTTTGTTATCGGCGATGAGGAGTTTCTTCCAATCAAAGAGAGgtgatttcac ... aagctcacag-
EST: gi|101393422|gb|EB818643.1|EB818643
EST:     GAGACCCACTTTGTTATCGGCGATGAGGAGTTTCTTCCAATCAAAGAGAG                         C
genomic: GAGACCCACTTTGTTATCGGCGATGAGGAGTTTCTTCCAATCAAAGAGAGgtgatttcac ... aagctcacag-
EST: gi|13316098|gb|BG410545.1|BG410545
EST:     GAGACCCACTTTGTTATCGGCGATGAGGAGTTTCTTCCAATCAAAGAGAG                         C
genomic: GAGACCCACTTTGTTATCGGCGATGAGGAGTTTCTTCCAATCAAAGAGAGgtgatttcac ... aagctcacag-
EST: gi|13316098|gb|BG410545.1|BG410545
EST:     GAGACCCACTTTGTTATCGGCGATGAGGAGTTTCTTCCAATCAAAGAGAG                         C
genomic: GAGACCCACTTTGTTATCGGCGATGAGGAGTTTCTTCCAATCAAAGAGAGgtgatttcac ... aagctcacag-
EST: gi|13316098|gb|BG410545.1|BG410545
EST:     GAGACCCACTTTGTTATCGGCGATGAGGAGTTTCTTCCAATCAAAGAGAG                         C
genomic: GAGACCCACTTTGTTATCGGCGATGAGGAGTTTCTTCCAATCAAAGAGAGgtgatttcac ... aagctcacag-
EST: gi|13316098|gb|BG410545.1|BG410545
EST:     GAGACCCACTTTGTTATCGGCGATGAGGAGTTTCTTCCAATCAAAGAGAG                         C
genomic: GAGACCCACTTTGTTATCGGCGATGAGGAGTTTCTTCCAATCAAAGAGAGgtgatttcac ... aagctcacag-
EST: gi|13316098|gb|BG410545.1|BG410545
EST:     GAGACCCACTTTGTTATCGGCGATGAGGAGTTTCTTCCAATCAAAGAGAG                         C
genomic: GAGACCCACTTTGTTATCGGCGATGAGGAGTTTCTTCCAATCAAAGAGAGgtgatttcac ... aagctcacag-
EST: gi|13316098|gb|BG410545.1|BG410545
EST:     GAGACCCACTTTGTTATCGGCGATGAGGAGTTTCTTCCAATCAAAGAGAG                         C
genomic: GAGACCCACTTTGTTATCGGCGATGAGGAGTTTCTTCCAATCAAAGAGAGgtgatttcac ... aagctcacag-
EST: gi|13316098|gb|BG410545.1|BG410545
EST:     GAGACCCACTTTGTTATCGGCGATGAGGAGTTTCTTCCAATCAAAGAGAG                         C
genomic: GAGACCCACTTTGTTATCGGCGATGAGGAGTTTCTTCCAATCAAAGAGAGgtgatttcac ... aagctcacag-
EST: gi|50328095|gb|CO523221.1|CO523221
EST:     GAGACCCACTTTGTTATCGGCGATGAGGAGTTTCTTCCAATCAAAGAGAG                         GATTTGATAATGAGCTGTCTTGGACTTCATTGGACAAATGATCTACCTGGA
genomic: GAGACCCACTTTGTTATCGGCGATGAGGAGTTTCTTCCAATCAAAGAGAGgtgatttcac ... aagctcacagGATTTGATAATGAGCTGTCTTGGACTTCATTGGACAAATGATCTACCTGGA
EST: gi|93282992|gb|EB675256.1|EB675256
EST:     GAGACCCACTTTGTTATCGGCGATGAGGAGTTTCTTCCAATCAAAGAGAG                         GATTTGATAATGAGCTGTCTTGGACTTCATTGGACAAATGATCTACCTGGA
genomic: GAGACCCACTTTGTTATCGGCGATGAGGAGTTTCTTCCAATCAAAGAGAGgtgatttcac ... aagctcacagGATTTGATAATGAGCTGTCTTGGACTTCATTGGACAAATGATCTACCTGGA
EST: gi|87157627|gb|DY402416.1|DY402416
EST:     GAGACCCACTTTGTTATCGGCGATGAGGAGTTTCTTCCAATCAAAGAGAG                         C
genomic: GAGACCCACTTTGTTATCGGCGATGAGGAGTTTCTTCCAATCAAAGAGAGgtgatttcac ... aagctcacag-
EST: gi|87157627|gb|DY402416.1|DY402416
EST:     GAGACCCACTTTGTTATCGGCGATGAGGAGTTTCTTCCAATCAAAGAGAG                         C
genomic: GAGACCCACTTTGTTATCGGCGATGAGGAGTTTCTTCCAATCAAAGAGAGgtgatttcac ... aagctcacag-
EST: gi|87157627|gb|DY402416.1|DY402416
EST:     GAGACCCACTTTGTTATCGGCGATGAGGAGTTTCTTCCAATCAAAGAGAG                         C
genomic: GAGACCCACTTTGTTATCGGCGATGAGGAGTTTCTTCCAATCAAAGAGAGgtgatttcac ... aagctcacag-
EST: gi|87157627|gb|DY402416.1|DY402416
EST:     GAGACCCACTTTGTTATCGGCGATGAGGAGTTTCTTCCAATCAAAGAGAG                         C
genomic: GAGACCCACTTTGTTATCGGCGATGAGGAGTTTCTTCCAATCAAAGAGAGgtgatttcac ... aagctcacag-
EST: gi|87157627|gb|DY402416.1|DY402416
EST:     GAGACCCACTTTGTTATCGGCGATGAGGAGTTTCTTCCAATCAAAGAGAG                         C
genomic: GAGACCCACTTTGTTATCGGCGATGAGGAGTTTCTTCCAATCAAAGAGAGgtgatttcac ... aagctcacag-
EST: gi|87157627|gb|DY402416.1|DY402416
EST:     GAGACCCACTTTGTTATCGGCGATGAGGAGTTTCTTCCAATCAAAGAGAG                         C
genomic: GAGACCCACTTTGTTATCGGCGATGAGGAGTTTCTTCCAATCAAAGAGAGgtgatttcac ... aagctcacag-
EST: gi|87157627|gb|DY402416.1|DY402416
EST:     GAGACCCACTTTGTTATCGGCGATGAGGAGTTTCTTCCAATCAAAGAGAG                         C
genomic: GAGACCCACTTTGTTATCGGCGATGAGGAGTTTCTTCCAATCAAAGAGAGgtgatttcac ... aagctcacag-


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acagatcttgcaacatttactcattaatgtggttcatgggttctgaagctcacagGATTTGATAATGAGCTGTCTTGGACTTCATTGGACAAATGATCTACCTGGAGCAATGATACAG
                     cattaat  putative branch site (score: 3)
              atttactcattaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gagtgagtcagttgtcgtgtcacaagcataatcatagacacacagacagatcttgcaacatttactcattaatgtggttcatgggttctgaagctcacagGATTTGATAATGAGCTGTCTTGGACTTCATTGGACAAATGATCTACCTGGAGCAATGATACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - cacaagc
- - - - - - - - - - - - - - - - - - -acacaca
- - - - - - - - - - - - - - - - - - - - - - - - - tcttgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gttcatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggttctg