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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagtactactattactagtcactttgcttcctcatgccttagcatgcaacctacatttactgctatttgcattctcaaacatcactgtgagtgtttctatagtctcttcattttgctattgcagCATGTTCCTAAAACTAATGGAGAGATTCCTTCTGTTGACGAAGCCATTTCAGATCATCAAAGACTTCTTGACAG

Basic information

species Zea mays
transcript GRMZM2G035150_T02
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G035150_T02 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os03g64219.1 (Oryza sativa), 3'ss of exon 2
----------------------------gttagtactactattactagtcactttgcttcctcatgccttagcatgcaacctacatttactgctatttgcattctcaaacatcactgtgagtgtttctatag--------tctcttcattttgctattgcagCATGTTCCTAAAACTAATGGAGAGATTCCTTCTGTTGACGAAGCCATTTCAGATCATCAAAGACTTCTTGACAG
                                   || |    | |  ||| |||   |  || || |  |  ||  | ||   | | | | |  |     |||     | ||    |||   |   | | |        |  |||| || |  ||||| |||||||||| |||||||| || || |||||||||||||| |||||| |||||||||| |||||||| ||| ||||
gtaactaactctctactgcttattccccaccttctcttcacccattcatca-tttaaatattcttgtcaaaatattaatccattaatgattaccttgcttcttcctcttcttcttcttgatgctacttgttggttaccctttccttccttctcttattgtagCATGTTCCAAAAACTAACGGGGACATTCCTTCTGTTGATGAAGCCTTTTCAGATCACCAAAGACTCCTTCACAG

upper sequence: GRMZM2G035150_T02 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA10G35300.3 (Glycine max), 3'ss of exon 3
gttagtactactattactagtcactttgcttcctcatgccttagcatgcaacctacatttactgctatttgcattctcaaacatcactgtgagtgtttctatagtctcttcattttgctattgcagCATGTTCCTAAAACTAATGGAGAGATTCCTTCTGTTGACGAAGCCATTTCAGATCATCAAAGACTTCTTGACAG
                  |  ||  |   || || ||   | ||||   |   |||| | |  | |||  | |||   ||      |    | |  |||  |    | |    ||     |||||||||||||||||||| |||| | | || || |||| ||||||||  || |||||||||||||||||||| |||||
------------------atacatatgaatttctaat--ttaagca---atattacagt-atagatat--gaatttctaatttaagcaacaattcattcacttacttttcttgttcatgtttgcagCATGTTCCTAAAACCAATGAAAAAATACCATCTGATGACGAAGAAATATCAGATCATCAAAGACTTCTAGACAG

upper sequence: GRMZM2G035150_T02 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA20G32220.1 (Glycine max), 3'ss of exon 3
gttagtactactattactagtcactttgcttcctcatgccttagcatgcaacctacatttactgct---atttgcattctcaaacatcactgtgagtgtttctatagtctcttcattttgctattgcagCATGTTCCTAAAACTAATGGAGAGATTCCTTCTGTTGACGAAGCCATTTCAGATCATCAAAGACTTCTTGACAG
                        | | |           ||   | |  | | | ||| || | |   || || |||   ||   |    || |   ||  |  | |    |  ||      |||||||||||||||||||| |||| | | || || |||| ||| ||||  || |||||||||||||| ||||| |||||
------------------------tgtacaagactgaagtttgataggttatcaatatt-acagtttaaatatggatttctaa---tttaagtaacaattcatgcacttctcttgttc-atgtttgcagCATGTTCCTAAAACCAATGAAAAAATACCATCTGATGATGAAGAAATATCAGATCATCAAAGGCTTCTAGACAG

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|78092884|gb|DV521258.1|DV521258
EST:     TCATTGACGGTGAAGTGGGCAAAAGATTGAACAACATGGTTCCTGTTCCT                         CATGTTCCTAAAACTAATGGAGAGATTCCTTCTGTTGACGAAGCCATTTCA
genomic: TCATTGACGGTGAAGTGGGCAAAAGATTGAACAACATGGTTCCTGTTCCTgttagtacta ... gctattgcagCATGTTCCTAAAACTAATGGAGAGATTCCTTCTGTTGACGAAGCCATTTCA
EST: gi|50324082|gb|CO519208.1|CO519208
EST:     TCATTGACGGTGAAGTGGGCAAAAGATTGAACAACATGGTTCCTGTTCCT                         CATGTTCCTAAAACTAATGGAGAGATTCCTTCTGTTGACGAAGCCATTTCA
genomic: TCATTGACGGTGAAGTGGGCAAAAGATTGAACAACATGGTTCCTGTTCCTgttagtacta ... gctattgcagCATGTTCCTAAAACTAATGGAGAGATTCCTTCTGTTGACGAAGCCATTTCA
EST: gi|71427954|gb|DR809004.1|DR809004
EST:     TCATTGACGGTGAAGTGGGCAAAAGATTGAACAACATGGTTCCTGTTCCT                         CATGTTCCTAANACTAATGGAGAGATTCCTTCTGTTGACGAAGCCATTTCA
genomic: TCATTGACGGTGAAGTGGGCAAAAGATTGAACAACATGGTTCCTGTTCCTgttagtacta ... gctattgcagCATGTTCCTAAAACTAATGGAGAGATTCCTTCTGTTGACGAAGCCATTTCA
EST: gi|74235679|gb|DT643593.1|DT643593
EST:     TCATTGACGGTGAAGTGGGCAAAAGATTGAACAACATGGTTCCTGTTCCT                         CATGTTCCTAANACTAATGGAGAGATTCCTTCTGTTGACGAAGCCATTTCA
genomic: TCATTGACGGTGAAGTGGGCAAAAGATTGAACAACATGGTTCCTGTTCCTgttagtacta ... gctattgcagCATGTTCCTAAAACTAATGGAGAGATTCCTTCTGTTGACGAAGCCATTTCA
EST: gi|71449152|gb|DR830202.1|DR830202
EST:     TCATTGACGGTGAAGTGGGCAAAAGATTGAACAACATGGTTCTTGTTCCT                         CATGTTCCTAAAACTAATGGAGAGATTCCTT
genomic: TCATTGACGGTGAAGTGGGCAAAAGATTGAACAACATGGTTCCTGTTCCTgttagtacta ... gctattgcagCATGTTCCTAAAACTAATGGAGAGATTCCTT
EST: gi|71427181|gb|DR808231.1|DR808231
EST:     TCATTGACGGTGAAGTGGGCAAAAGATTGAACAACATGGTTCCTGTTCCT                         CATGTTCCTAAAACTAATGGAGAGAT
genomic: TCATTGACGGTGAAGTGGGCAAAAGATTGAACAACATGGTTCCTGTTCCTgttagtacta ... gctattgcagCATGTTCCTAAAACTAATGGAGAGAT
EST: gi|76291810|gb|DV031378.1|DV031378
EST:     TCATTGACGGTGAAGTGGGCAAAAGATTGAACAACATGGTTCCTGTTCCT                         CATGTTCCTAAAACTAATGGAGAGATTCCTTCTGTTGACGAAGCCATTTCA
genomic: TCATTGACGGTGAAGTGGGCAAAAGATTGAACAACATGGTTCCTGTTCCTgttagtacta ... gctattgcagCATGTTCCTAAAACTAATGGAGAGATTCCTTCTGTTGACGAAGCCATTTCA
EST: gi|50327717|gb|CO522843.1|CO522843
EST:     TCATTGACGGTGAAGTGGGCAAAAGATTGAACAACATGGTTCCTGTTCCT                         CATGTTCCTAAAACTAATGGAGAGATTCCTTCTGTTGACGAAGCCATTTC
genomic: TCATTGACGGTGAAGTGGGCAAAAGATTGAACAACATGGTTCCTGTTCCTgttagtacta ... gctattgcagCATGTTCCTAAAACTAATGGAGAGATTCCTTCTGTTGACGAAGCCATTTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cattctcaaacatcactgtgagtgtttctatagtctcttcattttgctattgcagCATGTTCCTAAAACTAATGGAGAGATTCCTTCTGTTGACGAAGCCATTTCAGATCATCAAAGACTTCTTGACAG
                                 tctcttcattttgct  CT-rich tract
                        tttctata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagtactactattactagtcactttgcttcctcatgccttagcatgcaacctacatttactgctatttgcattctcaaacatcactgtgagtgtttctatagtctcttcattttgctattgcagCATGTTCCTAAAACTAATGGAGAGATTCCTTCTGTTGACGAAGCCATTTCAGATCATCAAAGACTTCTTGACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA