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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGAAGCTGATCCTGGCCAAGGGCAACCCGCACTTCATCTGCGACGCGCGCGTGCTCGTGAAGCCCTACAAGGAGAAGGGCAAGGTCCCCGACAAGTACAGgcacgcctcccccttccttttttcaattcgctctacctacgatcgacatcatgtcatgaccgatcgctccgctgctgctgctctgcag

Basic information

species Zea mays
transcript GRMZM2G311665_T01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G311665_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os07g48410.2 (Oryza sativa), 5'ss of exon 3
TGAAGCTGATCCTGGCCAAGGGCAACCCGCACTTCATCTGCGACGCGCGCGTGCTCGTGAAGCCCTACAAGGAGAAGGGCAAGGTCCCCGACAAGTACAGgcacgcctcccccttccttttttcaattcgctctacctacgatcgacatcatgtcatgaccgatcgctccgctgctgctgctctgcag
|||||||||| || |||||||||||||||||||||||||||||||| ||||||||||| ||||| |||||||||||||||||||||||||||||||||||||| |||   |          | ||  | || ||  ||| | | ||   | |   || ||| ||   |    ||||| | || |||||
TGAAGCTGATTCTCGCCAAGGGCAACCCGCACTTCATCTGCGACGCCCGCGTGCTCGTCAAGCCATACAAGGAGAAGGGCAAGGTCCCCGACAAGTACAGgcaagccgagcttacttacagtccacattgc-ctctcta-ggttgatcccct---ataaccaatttgtaacttgctgttactttgcag

upper sequence: GRMZM2G311665_T01 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA12G01350.1 (Glycine max), 5'ss of exon 3
TGAAGCTGATCCTGGCCAAGGGCAACCCGCACTTCATCTGCGACGCGCGCGTGCTCGTGAAGCCCTACAAGGAGAAGGGCAAGGTCCCCGACAAGTACAGgcacgcctcccccttcctttttt--caattcgctctacctacgatcgacatca---tgtcatgaccgatcgctccgctgctgct---gctctgcag
||||||| || ||  | || || ||||| || ||  | || || || || ||||| || ||||| ||||||||||||||||| ||||| ||||||||||||||| ||  |    | || || |   || |   | |   |   ||   | | |   |||  |||  |  | | |   || | ||   | | |||||
TGAAGCTTATTCTATCTAAAGGAAACCCTCATTTTGTGTGTGATGCACGAGTGCTTGTTAAGCCTTACAAGGAGAAGGGCAAAGTCCCAGACAAGTACAGgcaccccctctttctactcttatgttaactttttgtttttgttattcccttgagtttgttttgaatgtgctcactattgtttcttgtgatttgcag

upper sequence: GRMZM2G311665_T01 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA11G01780.1 (Glycine max), 5'ss of exon 3
------TGAAGCTGATCCTGGCCAAGGGCAACCCGCACTTCATCTGCGACGCGCGCGTGCTCGTGAAGCCCTACAAGGAGAAGGGCAAGGTCCCCGACAAGTACAGgcacgcctcccccttccttttttcaattcgctctacctacgatcgacatcatgtcatgaccgatcgctccgctgctgctgctctgcag
      |||  || ||  |  |||| || || || || || ||||| ||  | || || || || |||||||||||||||||||| || ||||| ||||||||      |  |      ||  ||  || |  ||   |||      | |   |   || | | |   ||    | |                 
AGACAGTGAGACTCATATTATCCAAAGGGAATCCTCATTTTATCTGTGATTCACGTGTACTTGTCAAGCCCTACAAGGAGAAGGGAAAAGTCCCTGACAAgtaagtatgcatcatgtttttaattggtttatatcttactattcctaaac--taatgtgac-taatttattatgcag-----------------

upper sequence: GRMZM2G311665_T01 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA12G01350.2 (Glycine max), 5'ss of exon 3
------TGAAGCTGATCCTGGCCAAGGGCAACCCGCACTTCATCTGCGACGCGCGCGTGCTCGTGAAGCCCTACAAGGAGAAGGGCAAGGTCCCCGACAAGTACAGgcacgcctcccccttcctttttt--caattcgctctacctacgatcgacatca---tgtcatgaccgatcgctccgctgctgct---gctctgcag
      ||||||| || ||  | || || ||||| || ||  | || || || || ||||| || ||||| ||||||||||||||||| ||||| ||||||||||||||| ||  |    | || || |   || |   | |   |   ||   | | |   |||  |||  |  | | |   || | ||   | | |||||
AGACCGTGAAGCTTATTCTATCTAAAGGAAACCCTCATTTTGTGTGTGATGCACGAGTGCTTGTTAAGCCTTACAAGGAGAAGGGCAAAGTCCCAGACAAgtacaggcaccccctctttctactcttatgttaactttttgtttttgttattcccttgagtttgttttgaatgtgctcactattgtttcttgtgatttgcag

upper sequence: GRMZM2G311665_T01 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA01G43700.1 (Glycine max), 5'ss of exon 3
------TGAAGCTGATCCTGGCCAAGGGCAACCCGCACTTCATCTGCGACGCGCGCGTGCTCGTGAAGCCCTACAAGGAGAAGGGCAAGGTCCCCGACAAGTACAGgcacgcc---tcccccttccttttttcaattcgctctacctacgatcgacatcatgtcatgaccgatc-gctccgctgctgctgctctgcag
      |||  || ||  |  |||| || || || || || ||||| ||  | || || || || |||||||||||||||||||| || ||||| ||||||||      |  |   |     ||  ||| |  |  |  || | ||||  |   | |  ||    ||||  ||    |  || |              
AGACAGTGAGACTCATATTATCCAAAGGGAATCCTCATTTTATCTGTGATTCACGTGTACTTGTCAAGCCCTACAAGGAGAAGGGAAAAGTCCCTGACAAgtaagtatgcatcatgttttaattggtttctgtatcttactattccta-aactaatactat--tgtgactaatttattatgcag--------------

upper sequence: GRMZM2G311665_T01 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA12G01340.1 (Glycine max), 5'ss of exon 4
------TGAAGCTGATCCTGGCCAAGGGCAACCCGCACTTCATCTGCGACGCGCGCGTGCTCGTGAAGCCCTACAAGGAGAAGGGCAAGGTCCCCGACAAGTACAGgcacgcctcccccttcctttt--------ttcaattcgctctacctacgatcgacatcatgtcatgaccgatcgctccgctgctgct---gctctgcag
      ||||||| || ||  | || || ||||| || ||  | || || || || ||||| || ||||| ||||||||||||||||| ||||| ||||||||||||||| ||  |    | || ||        ||   || | | |   ||    |   |   |||  |||  |  | | |   || | ||   | | |||||
AGACCGTGAAGCTTATTCTATCTAAAGGAAACCCTCATTTTGTGTGTGATGCACGAGTGCTTGTTAAGCCTTACAAGGAGAAGGGCAAAGTCCCAGACAAgtacaggcaccccctctttctactcttatgttatcttttttttgtttttgttattcccttgagtttgttttgaatgtgctcactattgtttcttgtgatttgcag

upper sequence: GRMZM2G311665_T01 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA09G35990.1 (Glycine max), 5'ss of exon 7
TGAAGCTGATCCTGGCCAAGGGCAACCCGCACTTCATCTGCGACGCGCGCGTGCTCGTGAAGCCCTACAAGGAGAAGGGCAAGGTCCCCGACAAGTACAGgcacgcctcccccttccttttttcaattcgctctacctacgatcgacatcatgtcatgaccgatcgctccgctgctgctgctctgcag------------------------------
||||||| || ||  |||| || || || || ||  | || || || || ||||| || ||||| ||||||||||||||||| ||||| ||||||||||||||| |  ||||  |   |  |   ||    |||   |    ||       | |  |    | |   |    ||    |  | || |                               
TGAAGCTTATTCTATCCAAAGGAAATCCTCATTTTGTGTGTGATGCTCGAGTGCTTGTTAAGCCTTACAAGGAGAAGGGCAAAGTCCCAGACAAGTACAGgcacccaccccctctttctactcttatgttatcttttttttttcttttcttttttctttttggttattgtcttgagtttattttgaatgtcctcattgatgtttcttgtgatttgcag

upper sequence: GRMZM2G311665_T01 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA09G35980.1 (Glycine max), 5'ss of exon 4
------TGAAGCTGATCCTGGCCAAGGGCAACCCGCACTTCATCTGCGACGCGCGCGTGCTCGTGAAGCCCTACAAGGAGAAGGGCAAGGTCCCCGACAAGTACAGgcacgcctcccccttccttttttcaattcgctctacctacgatcgacatcatgtcatgaccgatcgctccgctgctgctgctctgcag------------------------------
      ||||||| || ||  |||| || || || || ||  | || || || || ||||| || ||||| ||||||||||||||||| ||||| ||||||||||||||| |  ||||  |   |  |   ||    |||   |    ||       | |  |    | |   |    ||    |  | || |                               
AGACTGTGAAGCTTATTCTATCCAAAGGAAATCCTCATTTTGTGTGTGATGCTCGAGTGCTTGTTAAGCCTTACAAGGAGAAGGGCAAAGTCCCAGACAAgtacaggcacccaccccctctttctactcttatgttatcttttttttttcttttcttttttctttttggttattgtcttgagtttattttgaatgtcctcattgatgtttcttgtgatttgcag

upper sequence: GRMZM2G311665_T01 (Zea mays), 5'ss of exon 3
lower sequence: AT3G63450.1 (Arabidopsis thaliana), 5'ss of exon 3
------TGAAGCTGATCCTGGCCAAGGGCAACCCGCACTTCATCTGCGACGCGCGCGTGCTCGTGAAGCCCTACAAGGAGAAGGGCAAGGTCCCCGACAAGTACAGgcacgcctcccccttccttttttcaattcgctctacctacgatcgacatcatgtcatgaccgatcgctccgctgctgctgctctgcag
      |||||   || |||||||| || ||||| |||||  | ||  |  |  | || || || ||||| ||||||||||| ||||| ||||| |||||||||||| |  | |   | || | |  || |  |    ||   | |      | | | | |      |||  ||| ||||| |           
AGACTGTGAAGAGCATTCTGGCCAAAGGGAACCCTCACTTTGTGTGTCATTCCAGGGTTCTTGTTAAGCCTTACAAGGAGAAAGGCAAAGTCCCAGACAAgtacaggta--ctttggcttttcctccttgagctgctcctgattcctcatctctttacgacgct-ttgattcctctgctgcag-----------

upper sequence: GRMZM2G311665_T01 (Zea mays), 5'ss of exon 3
lower sequence: AT3G63450.3 (Arabidopsis thaliana), 5'ss of exon 3
TGAAGCTGATCCTGGCCAAGGGCAACCCGCACTTCATCTGCGACGCGCGCGTGCTCGTGAAGCCCTACAAGGAGAAGGGCAAGGTCCCCGACAAGTACAGgcacgcctcccccttccttttttcaattcgctctacctacgatcgacatcatgtcatgaccgatcgctccgctgctgctgctctgcag
|||||   || |||||||| || ||||| |||||  | ||  |  |  | || || || ||||| ||||||||||| ||||| ||||| |||||||||||| |  | |   | || | |  || |  |    ||   | |      | | | | |      |||  ||| ||||| |           
TGAAGAGCATTCTGGCCAAAGGGAACCCTCACTTTGTGTGTCATTCCAGGGTTCTTGTTAAGCCTTACAAGGAGAAAGGCAAAGTCCCAGACAAGTACAGgta--ctttggcttttcctccttgagctgctcctgattcctcatctctttacgacgct-ttgattcctctgctgcag-----------

upper sequence: GRMZM2G311665_T01 (Zea mays), 5'ss of exon 3
lower sequence: Vv13s0158g00370.t01 (Vitis vinifera), 5'ss of exon 4
------TGAAGCTGATCCTGGCCAAGGGCAACCCGCACTTCATCTGCGACGCGCGCGTGCTCGTGAAGCCCTACAAGGAGAAGGGCAAGGTCCCCGACAAGTACAGgcacgcctcccccttccttttttcaattcgctc-tacctacgatcgacatcatgtcatgaccgatcgctccgctgctgctgctctgcag
      ||||||| ||  |||| || || ||||| || ||  | || || || || || || || |||||||| |||||||||||||| ||||| ||||||||||||||| |    |   ||    | | ||| |  |  |   |  | |  |  |       |  | ||| |      |  || |  || |   
AGACAGTGAAGCTCATTTTGGCTAAAGGGAACCCTCATTTTGTTTGTGATGCTCGGGTTCTGGTTAAGCCCTATAAGGAGAAGGGCAAAGTCCCGGACAAgtacaggcactctcttctgctctccctctaaatgccttggtttttttggtgcatcttgcagagtagctgatggta--atttttggt-ttcag---

upper sequence: GRMZM2G311665_T01 (Zea mays), 5'ss of exon 3
lower sequence: Vv06s0061g00150.t01 (Vitis vinifera), 5'ss of exon 3
------TGAAGCTGATCCTGGCCAAGGGCAACCCGCACTTCATCTGCGACGCGCGCGTGCTCGTGAAGCCCTACAAGGAGAAGGGCAAGGTCCCCGACAAGTACAGgcacgcctcccccttccttttttcaattcgctctacctacgatcgacatcatgtcatgaccgatcgctccgctgctgctgct-ctgcag
      ||||||| ||  | || || || ||||| || ||| | || ||  |||| |||||||| |||||||| ||||||||||| || ||||| || ||||| |||||      | | ||  |  |||   || |   |   |   |   || |||| |  |||  | |  |   | || |    |   |||||
AGACTGTGAAGCTCATTTTAGCTAAAGGGAACCCCCATTTCGTATGTGATTCGCGTGTGCTCGTAAAGCCCTATAAGGAGAAGGGAAAAGTCCCGGAAAAgtataggcattttctctcttttgtgcttttgttttg---tgtgtgttactcacttcatatattgat-gttaacattgttgattgaacaattgcag

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|148933686|gb|EC877586.2|EC877586
EST:     GCTCGTGAAGCCCTACAAGGAGAAGGGCAAAGGTCCCCGGACAAGTACAG                         GAAGCAGCAGCTGCAAGGCGAGAGGGCGGTGGATTTCTTCTCCAACGGGTT
genomic: GCTCGTGAAGCCCTACAAGGAGAAGGGC-AAGGTCCCC-GACAAGTACAGgcacgcctcc ... tgctctgcagGAAGCAGCAGCTGCAAGGCGAGAGGGCGGTGGATTTCTTCTCCAACGGGTT
EST: gi|87157568|gb|DY402357.1|DY402357
EST:     GTGCTCGTGAAGCCCTACAAGGAGAAGGGCAAGGTCCCCGACAAGTACAG                         GAAGCAGCAGCTGCAAGGCGAGAGGGCGGTGGATTTCTTCTCCAACGGGTT
genomic: GTGCTCGTGAAGCCCTACAAGGAGAAGGGCAAGGTCCCCGACAAGTACAGgcacgcctcc ... tgctctgcagGAAGCAGCAGCTGCAAGGCGAGAGGGCGGTGGATTTCTTCTCCAACGGGTT
EST: gi|149096961|gb|EE182760.2|EE182760
EST:     GTGCTCGTGAAGCCCTACAAGGAGAAGGGCAAGGTCCCCGACAAGTACAG                         GAAGCAGCAGCTGCAAGGCGAGAGGGCGGTGGATTTCTTCTCCAACGGGTT
genomic: GTGCTCGTGAAGCCCTACAAGGAGAAGGGCAAGGTCCCCGACAAGTACAGgcacgcctcc ... tgctctgcagGAAGCAGCAGCTGCAAGGCGAGAGGGCGGTGGATTTCTTCTCCAACGGGTT
EST: gi|88756925|gb|DY541066.1|DY541066
EST:     GTGCTCGTGAAGCCCTACAAGGAGAAGGGCAAGGTCCCCGACAAGTACAG                         GAAGCAGCAGCTGCAAGGCGAGAGGGCGGTGGATTTCTTCTCCAACGGGTT
genomic: GTGCTCGTGAAGCCCTACAAGGAGAAGGGCAAGGTCCCCGACAAGTACAGgcacgcctcc ... tgctctgcagGAAGCAGCAGCTGCAAGGCGAGAGGGCGGTGGATTTCTTCTCCAACGGGTT
EST: gi|148937220|gb|EC881402.2|EC881402
EST:     GTGCTCGTGAAGCCCTACAAGGAGAAGGGCAAGGTCCCCGACAAGTACAG                         GAAGCAGCAGCTGCAAGGCGAGAGGGCGGTGGATTTCTTCTCCAACGGGTT
genomic: GTGCTCGTGAAGCCCTACAAGGAGAAGGGCAAGGTCCCCGACAAGTACAGgcacgcctcc ... tgctctgcagGAAGCAGCAGCTGCAAGGCGAGAGGGCGGTGGATTTCTTCTCCAACGGGTT
EST: gi|149088773|gb|EE177898.2|EE177898
EST:     GTGCTCGTGAAGCCCTACAAGGAGAAGGGCAAGGTCCCCGACAAGTACAG                         GAAGCAGCAGCTGCAAGGCGAGAGGGCGGTGGATTTCTTCTCCAACGGGTT
genomic: GTGCTCGTGAAGCCCTACAAGGAGAAGGGCAAGGTCCCCGACAAGTACAGgcacgcctcc ... tgctctgcagGAAGCAGCAGCTGCAAGGCGAGAGGGCGGTGGATTTCTTCTCCAACGGGTT
EST: gi|22520971|gb|BU079782.1|BU079782
EST:     GTGCTCGTGAAGCCCTACAAGGAGAAGGGCAAGGTCCCCGACAAGTACAG                         GAAGCAGCAGCTGCAAGGCGAGAGGGCGGTGGATTTCTTCTCCAACGGGTT
genomic: GTGCTCGTGAAGCCCTACAAGGAGAAGGGCAAGGTCCCCGACAAGTACAGgcacgcctcc ... tgctctgcagGAAGCAGCAGCTGCAAGGCGAGAGGGCGGTGGATTTCTTCTCCAACGGGTT
EST: gi|71771644|gb|DR969581.1|DR969581
EST:     GTGCTCGTGAAGCCCTACAAGGAGAAGGGCAAGGTCCCCGACAAGTACAG                         GAAGCAGCAGCTGCAAGGCGAGAGGGCGGTGGATTTCTTCTCCAACGGGTT
genomic: GTGCTCGTGAAGCCCTACAAGGAGAAGGGCAAGGTCCCCGACAAGTACAGgcacgcctcc ... tgctctgcagGAAGCAGCAGCTGCAAGGCGAGAGGGCGGTGGATTTCTTCTCCAACGGGTT
EST: gi|148962434|gb|EE013289.2|EE013289
EST:     GTGCTCGTGAAGCCCTACAAGGAGAAGGGCAAGGTCCCCGACAAGTACAG                         GAAGCAGCAGCTGCAAGGCGAGAGGGCGGTGGATTTCTTCTCCAACGGGTT
genomic: GTGCTCGTGAAGCCCTACAAGGAGAAGGGCAAGGTCCCCGACAAGTACAGgcacgcctcc ... tgctctgcagGAAGCAGCAGCTGCAAGGCGAGAGGGCGGTGGATTTCTTCTCCAACGGGTT
EST: gi|148933685|gb|EC877585.2|EC877585
EST:     GTGCTCGTGAAGCCCTACAAGGAGAAGGGCAAGGTCCCCGACAAGTACAG                         GAAGCAGCAGCTGCAAGGCGAGAGGGCGGTGGATTTCTTCTCCAACGGGTT
genomic: GTGCTCGTGAAGCCCTACAAGGAGAAGGGCAAGGTCCCCGACAAGTACAGgcacgcctcc ... tgctctgcagGAAGCAGCAGCTGCAAGGCGAGAGGGCGGTGGATTTCTTCTCCAACGGGTT
EST: gi|149072206|gb|EE160452.2|EE160452
EST:     GTGCTCGTGAAGCCCTACAAGGAGAAGGGCAAGGTCCCCGACAAGTACAG                         GAAGCAGCAGCTGCAAGGCGAGAGGGCGGTGGATTTCTTCTCCAACGGGTT
genomic: GTGCTCGTGAAGCCCTACAAGGAGAAGGGCAAGGTCCCCGACAAGTACAGgcacgcctcc ... tgctctgcagGAAGCAGCAGCTGCAAGGCGAGAGGGCGGTGGATTTCTTCTCCAACGGGTT
EST: gi|149015392|gb|EE045235.2|EE045235
EST:     GTGCTCCTGAAGCCCTACAAGGAGAAGGGCAAGGTCCCCGACAAGTACAG                         GAAGCAGCAGCTGCCAGGCGAGAGGGCGGTGGATTTCTTCTCCAACGGGTT
genomic: GTGCTCGTGAAGCCCTACAAGGAGAAGGGCAAGGTCCCCGACAAGTACAGgcacgcctcc ... tgctctgcagGAAGCAGCAGCTGCAAGGCGAGAGGGCGGTGGATTTCTTCTCCAACGGGTT
EST: gi|149082408|gb|EE171596.2|EE171596
EST:     GTGCTCGTGAAGCCCTACAAGGAGAAGGGCAAGGTCCCCGACAAGTACAG                         GAAGCAGCAGCTGCAAGGCGAGAGGGCGGTGGATTTCTTCTCCAACGGGTT
genomic: GTGCTCGTGAAGCCCTACAAGGAGAAGGGCAAGGTCCCCGACAAGTACAGgcacgcctcc ... tgctctgcagGAAGCAGCAGCTGCAAGGCGAGAGGGCGGTGGATTTCTTCTCCAACGGGTT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGAAGCTGATCCTGGCCAAGGGCAACCCGCACTTCATCTGCGACGCGCGCGTGCTCGTGAAGCCCTACAAGGAGAAGGGCAAGGTCCCCGACAAGTACAGgcacgcctcccccttccttttttcaattcgctctacctacgatcgacatcatgtcatgaccgatcgctccgctgctgctgctctgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA