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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtactttattgctgctacaagatgcttgtttcttaagcacaattggatgaagcataatttactgcattttaattgacaaaaatgaataatgagctggaagtataacagttacatcttttctgcacttctgttgtggacacaaaaactgttagttaatagcatgaatccgtgttatggaatgtagTGTGGTCAATGGCGCACTTGAATATCTCGCGAAGGATCTTGGGATTGCTGAAAATGCTGTCTTGCAGGGTATG

Basic information

species Zea mays
transcript GRMZM2G153704_T03
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G153704_T03 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os01g04190.2 (Oryza sativa), 3'ss of exon 3
gtatgtactttattgctgctacaagatgcttgtttcttaagcacaattggatgaagcataatttactgcattttaattgacaaaaatgaata-atgagctggaagtata-aca-gttacatcttttctgcacttctgttg-tggaca-caaaaactgttagtt---aatagcatgaatccgtgttatggaatgtagTGTGGTCAATGGCGCACTTGAATATCTCGCGAAGGATCTTGGGATTGCTGAAAATGCTGTCTTGCAGGGTATG
                                                | ||| |   |   || |||  |   | ||| || || || ||| ||   |||  |  |   |||  || | | |   ||| | ||   ||| || | | ||| | ||| ||  |   |||| |     |     || ||   || || |||||||| ||||| ||||||||||| || ||||| ||||| ||| |||| |||||||| || || |     
------------------------------------------------gtatgtattgtg--ttgctgtttccaatttgtcataattgcatagattttctgtcaccacccacacattccttgtaacctgaatttaaattgatgaataacaatacctggtaaatctgaatatctcattttgaatttgtgttctgcagAGTGGTCAACGGCGCTCTTGAATATCTTGCAAAGGACCTTGGAATTTCTGAGAATGCTGTGTTACAAG-----

upper sequence: GRMZM2G153704_T03 (Zea mays), 3'ss of exon 3
lower sequence: AT5G16150.1 (Arabidopsis thaliana), 3'ss of exon 3
gtatgtactttattgctgctacaagatgcttgtttcttaagcacaattggatgaagcataatttactgcattttaattgacaaaaatgaataatgagctggaagtataacagttacatcttttctgcacttctgttgtggacacaaaaactgttagttaatagcatgaatccgtgttatggaatgtagTGTGGTCAATGGCGCACTTGAATATCTCGCGAAGGATCTTGGGATTGCTGAAAATGCTGTCTTGCAGGGTATG
                                                                                                   | | |  |||    ||||   ||| |    |  || ||||  ||   |          | ||    |   ||  |   |  ||||  || ||||| ||||| || ||||||||||| || |||||||||||||| || |||||| |||| ||||| |     
---------------------------------------------------------------------------------------------------gtatgactaaatactacactgttttta---tcttggtgtgatcatgga----------tgatgatgt---tctattggactgaat-cagGGTGGTTAATGGTGCTCTTGAATATCTTGCTAAGGATCTTGGGATCGCCGAAAATACTGTTTTGCAAG-----

upper sequence: GRMZM2G153704_T03 (Zea mays), 3'ss of exon 3
lower sequence: Vv14s0006g02720.t01 (Vitis vinifera), 3'ss of exon 3
gtatgtactttattgctgctacaagatgcttgtttcttaagcacaattggatgaagcataatttactgcattttaattgacaaaaatgaataatgagctggaagtataacagttacatcttttctgcacttctgttgtggacacaaaaactgttagttaatagcatgaatc-cgtgttatggaatgtagTGTGGTCAATGGCGCACTTGAATATCTCGCGAAGGATCTTGGGATTGCTGAAAATGCTGTCTTGCAGGGTATG
                                                                                  || |    |||     |     |  |||||     |||  | |  |  |    | |||  |  |    |||    ||| ||  |        | ||||       || ||||| ||||| || |||||||| ||  | ||||||||||| ||||||||||||||||| || || |     
----------------------------------------------------------------------------------aatacagttaagtctttttgtatgcaacagg---gtctcatgtataacttatctatgggtaaga----tgtactgtaacagtgtatgctattttttatttgccacagGGTGGTGAATGGTGCTCTTGAATACCTTTCCAAGGATCTTGGAATTGCTGAAAATGCTGTTTTACAAG-----

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|211360698|gb|FL393782.1|FL393782
EST:     TATGTTGGCGTTGCTTGTTTGGGGGCTATTCTGTTTGGTTACCATCTTGG                         TGTGGTCAATGGCGCACTTGAATATCTCGCGAAGGATCTTGGGATTGCTGA
genomic: TATGTTGGCGTTGCTTGTTTGGGGGCTATTCTGTTTGGTTACCATCTTGGgtatgtactt ... tggaatgtagTGTGGTCAATGGCGCACTTGAATATCTCGCGAAGGATCTTGGGATTGCTGA
EST: gi|31355374|gb|CD439731.1|CD439731
EST:     TATGTTGGCGTTGCTTGTTTGGGGGCTATTCTGTTTGGTTACCATCTTGG                         TGTGGTCAATGGCGCACTTGAATATCTCGCGAAGGATCTTGGGATTGCTGA
genomic: TATGTTGGCGTTGCTTGTTTGGGGGCTATTCTGTTTGGTTACCATCTTGGgtatgtactt ... tggaatgtagTGTGGTCAATGGCGCACTTGAATATCTCGCGAAGGATCTTGGGATTGCTGA
EST: gi|149082633|gb|EE171834.2|EE171834
EST:     TATGTTGGCGTTGCTTGTTTGGGGGCTATTCTGTTTGGTTACCATCTTGG                         TGTGGTCAATGGCGCACTTGAATATCTCGCGAAGGATCTTGGGATTGCTGA
genomic: TATGTTGGCGTTGCTTGTTTGGGGGCTATTCTGTTTGGTTACCATCTTGGgtatgtactt ... tggaatgtagTGTGGTCAATGGCGCACTTGAATATCTCGCGAAGGATCTTGGGATTGCTGA
EST: gi|149083192|gb|EE172463.2|EE172463
EST:     TATGTTGGCGTTGCTTGTTTGGGGGCTATTCTGTTTGGTTACCATCTTGG                         TGTGGTCAATGGCGCACTTGAATATCTCGCGAAGGATCTTGGGATTGCTGA
genomic: TATGTTGGCGTTGCTTGTTTGGGGGCTATTCTGTTTGGTTACCATCTTGGgtatgtactt ... tggaatgtagTGTGGTCAATGGCGCACTTGAATATCTCGCGAAGGATCTTGGGATTGCTGA
EST: gi|31355588|gb|CD439945.1|CD439945
EST:     TATGTTGGCGTTGCTTGTTTGGGGGCTATTCTGTTTGGTTACCATCTTGG                         TGTGGTCAATGGCGCACTTGAATATCTCGCGAAGGATCTTGGGATTGCTGA
genomic: TATGTTGGCGTTGCTTGTTTGGGGGCTATTCTGTTTGGTTACCATCTTGGgtatgtactt ... tggaatgtagTGTGGTCAATGGCGCACTTGAATATCTCGCGAAGGATCTTGGGATTGCTGA
EST: gi|148996907|gb|EE035711.2|EE035711
EST:     TATGTTGGCGTTGCTTGTTTGGGGGCTATTCTGTTTGGTTACCATCTTGG                         TGTGGTCAATGGCGCACTTGAATATCTCGCGAAGGATCTTGGGATTGCTGA
genomic: TATGTTGGCGTTGCTTGTTTGGGGGCTATTCTGTTTGGTTACCATCTTGGgtatgtactt ... tggaatgtagTGTGGTCAATGGCGCACTTGAATATCTCGCGAAGGATCTTGGGATTGCTGA
EST: gi|211063244|gb|FL401231.1|FL401231
EST:     TATGTTGGCGTTGCTTGTTTGGGGGCTATTCTGTTTGGTTACCATCTTGG                         TGTGGTCAATGGCGCACTTGAATATCTCGCCAAGGATCTTGGGATTGCTGA
genomic: TATGTTGGCGTTGCTTGTTTGGGGGCTATTCTGTTTGGTTACCATCTTGGgtatgtactt ... tggaatgtagTGTGGTCAATGGCGCACTTGAATATCTCGCGAAGGATCTTGGGATTGCTGA
EST: gi|211327531|gb|FL370114.1|FL370114
EST:     TATGTTGGCGTTGCTTGTTTGGGGGCTATTCTGTTTGGTTACCATCTTGG                         TGTGGTCAATGGCGCACTTGAATATCTCGCGAAGGATCTTGTGATTGCTGA
genomic: TATGTTGGCGTTGCTTGTTTGGGGGCTATTCTGTTTGGTTACCATCTTGGgtatgtactt ... tggaatgtagTGTGGTCAATGGCGCACTTGAATATCTCGCGAAGGATCTTGGGATTGCTGA
EST: gi|211266596|gb|FL404017.1|FL404017
EST:     TATGTTGGCGTTGCTTGTTTGGGGGCTATTCTGTTTGGTTACCATCTTGG                         TGTGGTCAATGGCGCACTTGAATATCTCGCGAAGGATCTTGTGATTGCTGA
genomic: TATGTTGGCGTTGCTTGTTTGGGGGCTATTCTGTTTGGTTACCATCTTGGgtatgtactt ... tggaatgtagTGTGGTCAATGGCGCACTTGAATATCTCGCGAAGGATCTTGGGATTGCTGA
EST: gi|211066519|gb|FL419923.1|FL419923
EST:     TGTTGGCGTTGCTTGTTTGGGGGCTAATTCTGTTTGGT-ACCATCCTTGG                         TGTGGTCAATGGCGCACTTGAATATCTCGCCAAGGNATCTTGGGATTGCT
genomic: TGTTGGCGTTGCTTGTTTGGGGGCTA-TTCTGTTTGGTTACCATC-TTGGgtatgtactt ... tggaatgtagTGTGGTCAATGGCGCACTTGAATATCTCGCGAAGG-ATCTTGGGATTGCT
EST: gi|31354767|gb|CD439124.1|CD439124
EST:     TATGTTGGCGTTGCTTGTTTGGGGGCTATTCTGTTTGGTTACCATCTTGG                         TGTGGTCAATGGCGCACTTGAATATCTCGCGAAGGATCTTGGGATTGCTGA
genomic: TATGTTGGCGTTGCTTGTTTGGGGGCTATTCTGTTTGGTTACCATCTTGGgtatgtactt ... tggaatgtagTGTGGTCAATGGCGCACTTGAATATCTCGCGAAGGATCTTGGGATTGCTGA
EST: gi|78078828|gb|DV507240.1|DV507240
EST:     TATGTTGGCGTTGCTTGTTTGGGGGCTATTCTGTTTGGTTACCATCTTGG                         TGTGGTCAATGGCGCACTTGAATATCTCGCGAAGGATCTTGGGATTGCTGA
genomic: TATGTTGGCGTTGCTTGTTTGGGGGCTATTCTGTTTGGTTACCATCTTGGgtatgtactt ... tggaatgtagTGTGGTCAATGGCGCACTTGAATATCTCGCGAAGGATCTTGGGATTGCTGA
EST: gi|148981335|gb|EE027589.2|EE027589
EST:     TATGTTGGCGTTGCTTGTTTGGGGGCTATTCTGTTTGGTTACCATCTTGG                         TGTGGTCAATGGCGCACTTGAATATCTCGCGAAGGATCTTGGGATTGCTGA
genomic: TATGTTGGCGTTGCTTGTTTGGGGGCTATTCTGTTTGGTTACCATCTTGGgtatgtactt ... tggaatgtagTGTGGTCAATGGCGCACTTGAATATCTCGCGAAGGATCTTGGGATTGCTGA
EST: gi|148977355|gb|EE026050.2|EE026050
EST:     TATGTTGGCGTTGCTTGTTTGGGGGCTATTCTGTTTGGTTACCATCTTGG                         TGTGGTCAATGGCGCACTTGAATATCTCGCGAAGGATCTTGGGATTGCTGA
genomic: TATGTTGGCGTTGCTTGTTTGGGGGCTATTCTGTTTGGTTACCATCTTGGgtatgtactt ... tggaatgtagTGTGGTCAATGGCGCACTTGAATATCTCGCGAAGGATCTTGGGATTGCTGA
EST: gi|211349168|gb|FL426325.1|FL426325
EST:     TATGTTGGCGTTGCTTGTTTGGGGGCTATTCTGTTTGGTTACCATCTTGG                         TGTGGTCAATGGCGCACTTGAATATCTCGCGAAGGATCTTGGGATTGCTGA
genomic: TATGTTGGCGTTGCTTGTTTGGGGGCTATTCTGTTTGGTTACCATCTTGGgtatgtactt ... tggaatgtagTGTGGTCAATGGCGCACTTGAATATCTCGCGAAGGATCTTGGGATTGCTGA
EST: gi|148971787|gb|EE022525.2|EE022525
EST:     TATGTTGGCGTTGCTTGTTTGGGGGCTATTCTGTTTGGTTACCATCTTGG                         TGTGGTCAATGGCGCACTTGAATATCTCGCGAAGGATCTTGGGATTGCTGA
genomic: TATGTTGGCGTTGCTTGTTTGGGGGCTATTCTGTTTGGTTACCATCTTGGgtatgtactt ... tggaatgtagTGTGGTCAATGGCGCACTTGAATATCTCGCGAAGGATCTTGGGATTGCTGA
EST: gi|148953947|gb|EC899333.2|EC899333
EST:     TATGTTGGCGTTGCTTGTTTGGGGGCTATTCTGTTTGGTTACCATCTTGG                         TGTGGTCAATGGCGCACTTGAATATCTCGCGAAGGATCTTGGGATTGCTGA
genomic: TATGTTGGCGTTGCTTGTTTGGGGGCTATTCTGTTTGGTTACCATCTTGGgtatgtactt ... tggaatgtagTGTGGTCAATGGCGCACTTGAATATCTCGCGAAGGATCTTGGGATTGCTGA
EST: gi|211369268|gb|FL413710.1|FL413710
EST:     TGTTGGCGTTGCTTGTTTGGGGGCTAATTCTGTTTGGT-ACCCATCTTGG                         TGTGGTCAATGGCGCACTTGA-TATCTCGCGAAGGATCTTGGGATTGCTG
genomic: TGTTGGCGTTGCTTGTTTGGGGGCTA-TTCTGTTTGGTTACC-ATCTTGGgtatgtactt ... tggaatgtagTGTGGTCAATGGCGCACTTGAATATCTCGCGAAGGATCTTGGGATTGCTG
EST: gi|211416246|gb|FL417246.1|FL417246
EST:     TATGTTGGCGTTGCTTGTTTGGGGGCTATTCTGTTTGGTTACCATCTTGG                         TGTGGTCAATGGCGCACTTGAATATCTCGCGAAGGATCTTGGGATTGCTGA
genomic: TATGTTGGCGTTGCTTGTTTGGGGGCTATTCTGTTTGGTTACCATCTTGGgtatgtactt ... tggaatgtagTGTGGTCAATGGCGCACTTGAATATCTCGCGAAGGATCTTGGGATTGCTGA
EST: gi|31355150|gb|CD439507.1|CD439507
EST:     TATGTTGGCGTTGCTTGTTTGGGGGCTATTCTGTTTGGTTACCATCTTGG                         TGTGGTCAATGGCGCACTTGAATATCTCGCGAAGGATCTTGGGATTGCTGA
genomic: TATGTTGGCGTTGCTTGTTTGGGGGCTATTCTGTTTGGTTACCATCTTGGgtatgtactt ... tggaatgtagTGTGGTCAATGGCGCACTTGAATATCTCGCGAAGGATCTTGGGATTGCTGA
EST: gi|211485157|gb|FL401977.1|FL401977
EST:     TATGTTGGCGTTGCTTGTTTGGGGGCTATTCTGTTTGGTTACCATCTTGG                         TGTGGTCAATGGCG
genomic: TATGTTGGCGTTGCTTGTTTGGGGGCTATTCTGTTTGGTTACCATCTTGGgtatgtactt ... tggaatgtagTGTGGTCAATGGCG
EST: gi|211244572|gb|FL131421.1|FL131421
EST:     TATGTTGGCGTTGCTTGTTTGGGGGCTATTCTGTTTGGTTACCATCTTGG                         TGTGGTCAATGGCGCACTTGAATATCTCGCCAARGATCTTGGGATTGCTGA
genomic: TATGTTGGCGTTGCTTGTTTGGGGGCTATTCTGTTTGGTTACCATCTTGGgtatgtactt ... tggaatgtagTGTGGTCAATGGCGCACTTGAATATCTCGCGAAGGATCTTGGGATTGCTGA
EST: gi|78075828|gb|DV504262.1|DV504262
EST:     TATGTTGGCGTTGCTTGTTTGGGGGCTATTCTGTTTGGTTACCATCTTGG                         TGTGGTCAATGGCGCACTTGAATATCTCGCGAAGGATCTTGGGATTGCTGA
genomic: TATGTTGGCGTTGCTTGTTTGGGGGCTATTCTGTTTGGTTACCATCTTGGgtatgtactt ... tggaatgtagTGTGGTCAATGGCGCACTTGAATATCTCGCGAAGGATCTTGGGATTGCTGA
EST: gi|211465272|gb|FL339432.1|FL339432
EST:     TATGTTGGCGTTGCTTGTTTGGGGGCTATTCTGTTTGGTTACCATCTTGG                         TGTGGTCAATGGCGCACTTGAATATCTCGCGAAGGATCTTGGGATTGCTGA
genomic: TATGTTGGCGTTGCTTGTTTGGGGGCTATTCTGTTTGGTTACCATCTTGGgtatgtactt ... tggaatgtagTGTGGTCAATGGCGCACTTGAATATCTCGCGAAGGATCTTGGGATTGCTGA
EST: gi|211210064|gb|FL412311.1|FL412311
EST:     TATGTTGGCGTTGCTTGTTTGGGGGCTATTCTGTTTGGTTACCATCTTGG                         TGTGGTCAATGGCGCACTTGAATATCTCGCGAAGGATCTTGGGATTGCTGA
genomic: TATGTTGGCGTTGCTTGTTTGGGGGCTATTCTGTTTGGTTACCATCTTGGgtatgtactt ... tggaatgtagTGTGGTCAATGGCGCACTTGAATATCTCGCGAAGGATCTTGGGATTGCTGA
EST: gi|211441205|gb|FL381373.1|FL381373
EST:     TATGTTGGCGTTGCTTGTTTGGGGGCTATTCTGTTTGGTTACCATCTTGG                         TGTGGTCAATGGCGCAC
genomic: TATGTTGGCGTTGCTTGTTTGGGGGCTATTCTGTTTGGTTACCATCTTGGgtatgtactt ... tggaatgtagTGTGGTCAATGGCGCAC
EST: gi|149055222|gb|EE156147.2|EE156147
EST:     TATGTTGGCGTTGCTTGTTTGGGGGCTATTCTGTTTGGTTACCATCTTGG                         TGTGGTCAATGGCGCACTTGAATATCTCGCGAAGGATCTTGGGATTGCTGA
genomic: TATGTTGGCGTTGCTTGTTTGGGGGCTATTCTGTTTGGTTACCATCTTGGgtatgtactt ... tggaatgtagTGTGGTCAATGGCGCACTTGAATATCTCGCGAAGGATCTTGGGATTGCTGA
EST: gi|211157837|gb|FL370475.1|FL370475
EST:     TATGTTGGCGTTGCTTGTTTGGGGGCTATTCTGTTTGGTTACCATCTTGG                         TGTGGTCAATGGCGCACTTGAATATCTCGCGAAGGATCTTGGGATTGCTGA
genomic: TATGTTGGCGTTGCTTGTTTGGGGGCTATTCTGTTTGGTTACCATCTTGGgtatgtactt ... tggaatgtagTGTGGTCAATGGCGCACTTGAATATCTCGCGAAGGATCTTGGGATTGCTGA
EST: gi|211244570|gb|FL131419.1|FL131419
EST:     TATGTTGGCGTTGCTTGTTTGGGGGCTATTCTGTTTGGTTACCATCTTGG                         TGTGGTCAATGGCGCACT
genomic: TATGTTGGCGTTGCTTGTTTGGGGGCTATTCTGTTTGGTTACCATCTTGGgtatgtactt ... tggaatgtagTGTGGTCAATGGCGCACT
EST: gi|211153701|gb|FL418638.1|FL418638
EST:     TATGTTGGCGTTGCTTGTTTGGGGGCTATTCTGTTTTGTTACCATCTTGG                         TGTGGTCAATGGCGCACTTGAATATCTCGCGAAGGATCTTGGGATTGCTGA
genomic: TATGTTGGCGTTGCTTGTTTGGGGGCTATTCTGTTTGGTTACCATCTTGGgtatgtactt ... tggaatgtagTGTGGTCAATGGCGCACTTGAATATCTCGCGAAGGATCTTGGGATTGCTGA
EST: gi|211471554|gb|FL402494.1|FL402494
EST:     TATGTTGGCGTTGCTTGTTTGGGGGCTATTCTGTTTGGTTACCATCTTGG                         TGTGGTCAATGGCGCACTTGAATATCTCGCCAAGGATCTTGG
genomic: TATGTTGGCGTTGCTTGTTTGGGGGCTATTCTGTTTGGTTACCATCTTGGgtatgtactt ... tggaatgtagTGTGGTCAATGGCGCACTTGAATATCTCGCGAAGGATCTTGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttgtggacacaaaaactgttagttaatagcatgaatccgtgttatggaatgtagTGTGGTCAATGGCGCACTTGAATATCTCGCGAAGGATCTTGGGATTGCTGAAAATGCTGTCTTGCAGGGTATG
                     agttaat  putative branch site (score: 4)
                   ttagttaata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtactttattgctgctacaagatgcttgtttcttaagcacaattggatgaagcataatttactgcattttaattgacaaaaatgaataatgagctggaagtataacagttacatcttttctgcacttctgttgtggacacaaaaactgttagttaatagcatgaatccgtgttatggaatgtagTGTGGTCAATGGCGCACTTGAATATCTCGCGAAGGATCTTGGGATTGCTGAAAATGCTGTCTTGCAGGGTATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG