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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgatccatatcatttttatattgtcaattgtgtcctgtctaaagttttgagtcataattctctagctcttatcagaacttgtttttcctgaatttcgcagGAGTGGGATGCTCTCATGCTTTCTAATTTTGCTTTGGAGCAGCAGCTTCACACAGCAAGACAAGAACTTAGTCATGCACTCTACCAG

Basic information

species Zea mays
transcript GRMZM2G324540_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G324540_T02 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os10g32880.1 (Oryza sativa), 3'ss of exon 2
--tgat----ccatatcatttttatattgtcaattgtgtcctgtctaaagttttgagtcataattc--tctagctcttatcagaacttgtttttcctgaatttcgcagGAGTGGGATGCTCTCATGCTTTCTAATTTTGCTTTGGAGCAGCAGCTTCACACAGCAAGACAAGAACTTAGTCATGCACTCTACCAG
  ||||    ||| |  ||  | ||      ||   |||| |||   ||        |||| ||||   |||||||| |  |||||     |  | ||  |||  ||||||||||||||| |||||||||||| |||||||||||||||||||||||| |||||||||||||||||||||||||| || || |||
cttgattttgccacaa-ataatcatggaactaaaaatgtcttgtgagaaccc----atcatgattcaccctagctctcactagaacaa---taccatggcttttacagGAGTGGGATGCTATCATGCTTTCTAGTTTTGCTTTGGAGCAGCAGCTTCATACAGCAAGACAAGAACTTAGTCATGCGCTATATCAG

upper sequence: GRMZM2G324540_T02 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA20G21330.1 (Glycine max), 3'ss of exon 4
--tgatccatat-catttttatat-tgtcaattgtgtcctgtctaaagttttgagtcataattctctagctcttatcagaacttgtttttcctgaatttcgcagGAGTGGGATGCTCTCATGCTTTCTAATTTTGCTTTGGAGCAGCAGCTTCACACAGCAAGACAAGAACTTAGTCATGCACTCTACCAG
    ||  | |     ||  |||| |||    |   | ||||  |||      | |  | |  ||   ||   ||  |  | ||| ||| ||| |  || | |||| |||||||   | ||||| ||||||||||| |||||||| ||  | ||||||||||||||||| || ||||||||  | || |||
aaatatttagacatgcttagatatgtgtaggcttctttctgttgaaaaaaacaattatttaggcttccgca--taagatgatttggtttgcctaa--tttgtagGAATGGGATGGATTGATGCTATCTAATTTTGCATTGGAGCAACAATTGCACACAGCAAGACAAGAGCTGAGTCATGCTTTGTATCAG

upper sequence: GRMZM2G324540_T02 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA10G26870.1 (Glycine max), 3'ss of exon 4
tgatccatat-catttttatattgtcaattgtgtcctgtctaaagttttgagtcataattct--ctagctcttatcagaacttgtttttcctgaatttcgcagGAGTGGGATGCTCTCATGCTTTCTAATTTTGCTTTGGAGCAGCAGCTTCACACAGCAAGACAAGAACTTAGTCATGCACTCTACCAG
  ||   ||  |||  ||| || ||   | || | || |||   |     ||| || |||    ||  | |||   |  | ||| ||| ||| |  || | |||| |||||||   | ||||| ||||||||||| |||||||| ||  | |||||||||||||| || || |||||||| || || |||
aaatatttagacatgcttagat-gtgtgtagtcttctttctgttgaaaaaagtaattatttaggcttccacttgagatgatttggtttgcctaa--tttgtagGAATGGGATGGATTGATGCTATCTAATTTTGCATTGGAGCAACAATTGCACACAGCAAGACAGGAGCTGAGTCATGCTCTGTATCAG

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|211270237|gb|FL344649.1|FL344649
EST:     GGCCTTTGCAGGCTGCAAGCATTCCAGGACTCCTTGGGATTTTTCAGAAC                         GAGNGGGATGCTCTCATGCTTTCTAATTTTGCTTTGGAGCAGCAGCTTCAC
genomic: GGCCTTTGCAGGCTGCAAGCATTCCAGGACTCCTTGGGATTTTTCAGAACgtaaggggtt ... aatttcgcagGAGTGGGATGCTCTCATGCTTTCTAATTTTGCTTTGGAGCAGCAGCTTCAC
EST: gi|211156212|gb|FL365662.1|FL365662
EST:     GGCCTTTGCAGGCTGCAAGCATTCCAGGACTCCTTGGGATTTTTCAGAAC                         GAGTGGGATGCTCTCATGCTTTCTAATTTTGCTTTGGAGCAGCAGCTTCAC
genomic: GGCCTTTGCAGGCTGCAAGCATTCCAGGACTCCTTGGGATTTTTCAGAACgtaaggggtt ... aatttcgcagGAGTGGGATGCTCTCATGCTTTCTAATTTTGCTTTGGAGCAGCAGCTTCAC
EST: gi|211089285|gb|FL354017.1|FL354017
EST:     GGCCTTTGCAGGCTGCAAGCATTCCAGGACTCCTTGGGATTTTTCANAAC                         GAGGGGGATGCTCTCATGCTTTCTAATTTTGCTTTGGAGCAGCAGCTTCAC
genomic: GGCCTTTGCAGGCTGCAAGCATTCCAGGACTCCTTGGGATTTTTCAGAACgtaaggggtt ... aatttcgcagGAGTGGGATGCTCTCATGCTTTCTAATTTTGCTTTGGAGCAGCAGCTTCAC
EST: gi|211206059|gb|FL353696.1|FL353696
EST:     GCCTTTGCAGGCTGCAAGCATTCCCAGGACTCCTTGGGATTTTTCAGAAC                         GAGTGGGATGCTCTCATGCTTTCTAATTTTGCTTTGGAGCAGCAGCTTCAC
genomic: GCCTTTGCAGGCTGCAAGCATTCC-AGGACTCCTTGGGATTTTTCAGAACgtaaggggtt ... aatttcgcagGAGTGGGATGCTCTCATGCTTTCTAATTTTGCTTTGGAGCAGCAGCTTCAC
EST: gi|211228973|gb|FL343790.1|FL343790
EST:     GGCCTTTGCAGGCTGCAAGCATTCCAGGACTCCTTGGGATTTTTCAGAAC                         GAGTGGGATGCTCTCATGCTTTCTAATTTTGCTTTGGAGCAGCAGCTTCAC
genomic: GGCCTTTGCAGGCTGCAAGCATTCCAGGACTCCTTGGGATTTTTCAGAACgtaaggggtt ... aatttcgcagGAGTGGGATGCTCTCATGCTTTCTAATTTTGCTTTGGAGCAGCAGCTTCAC
EST: gi|211232319|gb|FK959916.1|FK959916
EST:     GGCCTTTGCAGGCTGCAAGCATTCCAGGACTCCTTGGGATTTTTCAGAAC                         GAGTGGGATGCTCTCATGCTTTCTAATTTTTGCTTTGGAGCAG
genomic: GGCCTTTGCAGGCTGCAAGCATTCCAGGACTCCTTGGGATTTTTCAGAACgtaaggggtt ... aatttcgcagGAGTGGGATGCTCTCATGCTTTCTAATTTT-GCTTTGGAGCAG
EST: gi|211040670|gb|FL334591.1|FL334591
EST:     GGCCTTTGCAGGCTGCAAGCATTCCAGGACTCCTTGGGATTTTTCAGAAC                         GAGTGGGATGCTCTCATGCTTTCTAATTTTGCTTTGGAGCAGCAGCTTCAC
genomic: GGCCTTTGCAGGCTGCAAGCATTCCAGGACTCCTTGGGATTTTTCAGAACgtaaggggtt ... aatttcgcagGAGTGGGATGCTCTCATGCTTTCTAATTTTGCTTTGGAGCAGCAGCTTCAC
EST: gi|211158673|gb|FL319015.1|FL319015
EST:     GGCCTTTGCAGGCTGCAAGCATTCCAGGACTCCTTGGGATTTTTCAGAAC                         GAGTGGGATGCTCTCATGCTTTCTAATTTTGCTTTGGAGCAGCAGCTTCAC
genomic: GGCCTTTGCAGGCTGCAAGCATTCCAGGACTCCTTGGGATTTTTCAGAACgtaaggggtt ... aatttcgcagGAGTGGGATGCTCTCATGCTTTCTAATTTTGCTTTGGAGCAGCAGCTTCAC
EST: gi|211165501|gb|FL341377.1|FL341377
EST:     GGCCTTTGCAGGCTGCAAGCATTCCAGGACTCCTTGGGATTTTTCAGAAC                         GAGTGGGATGCTCTCATGCTTTCTAATTTTGCTTTGGAGCAGCAGCTTCAC
genomic: GGCCTTTGCAGGCTGCAAGCATTCCAGGACTCCTTGGGATTTTTCAGAACgtaaggggtt ... aatttcgcagGAGTGGGATGCTCTCATGCTTTCTAATTTTGCTTTGGAGCAGCAGCTTCAC
EST: gi|211227097|gb|FL350438.1|FL350438
EST:     GCCTTTGCAGGCTGCAAGCATTCCAGGACTCCCTTGGGATTTTTCAGAAC                         GAGTGGGATGCTCTCATGCTTTCTAATTTTGCTTTGGAGCAGCAGCTTCAC
genomic: GCCTTTGCAGGCTGCAAGCATTCCAGGACTCC-TTGGGATTTTTCAGAACgtaaggggtt ... aatttcgcagGAGTGGGATGCTCTCATGCTTTCTAATTTTGCTTTGGAGCAGCAGCTTCAC
EST: gi|211108070|gb|FL361613.1|FL361613
EST:     GGCCTTTGCAGGCTGCAAGCATTCCAGGACTCCTTGGGATTTTTCAGAAC                         GAGTGGGATGCTCTCATGCTTTCTAATTTTGCTTTGGAGCAGCAGCTTCAC
genomic: GGCCTTTGCAGGCTGCAAGCATTCCAGGACTCCTTGGGATTTTTCAGAACgtaaggggtt ... aatttcgcagGAGTGGGATGCTCTCATGCTTTCTAATTTTGCTTTGGAGCAGCAGCTTCAC
EST: gi|211399607|gb|FL346420.1|FL346420
EST:     GGCCTTTGCAGGCTGCAAGCATTCCAGGACTCCTTGGGATTTTTCAGAAC                         GAGTGGGATGCTCTCATGCTTTCTAATTTTGCTTTGGAGCAGCAGCTTCAC
genomic: GGCCTTTGCAGGCTGCAAGCATTCCAGGACTCCTTGGGATTTTTCAGAACgtaaggggtt ... aatttcgcagGAGTGGGATGCTCTCATGCTTTCTAATTTTGCTTTGGAGCAGCAGCTTCAC
EST: gi|211444525|gb|FL325223.1|FL325223
EST:     GGCCTTTGCAGGCTGCAAGCATTCCAGGACTCCTTGGGATTTTTCAGAAC                         GAGTGGGATGCTCTCATGCTTTCTAATTTTGCTTTGGAGCAGCAGCTTCAC
genomic: GGCCTTTGCAGGCTGCAAGCATTCCAGGACTCCTTGGGATTTTTCAGAACgtaaggggtt ... aatttcgcagGAGTGGGATGCTCTCATGCTTTCTAATTTTGCTTTGGAGCAGCAGCTTCAC
EST: gi|211050070|gb|FL348912.1|FL348912
EST:     GGCCTTTGCAGGCTGCAAGCATTCCAGGACTCCTTGGGATTTTTCAGAAC                         GAGTGGGATGCTCTCATGCTTTCTAATTTTGCTTTGGAGCAGCAGCTTCAC
genomic: GGCCTTTGCAGGCTGCAAGCATTCCAGGACTCCTTGGGATTTTTCAGAACgtaaggggtt ... aatttcgcagGAGTGGGATGCTCTCATGCTTTCTAATTTTGCTTTGGAGCAGCAGCTTCAC
EST: gi|9254345|gb|BE344813.1|BE344813
EST:     GGCCTTTGCAGGCTGCAAGCATTCCAGGACTCCTTGGGATTTTTCAGAAC                         GAGTGGGATGCTCTCATGCTTTCTAATTTTGCTTTGGAGCAGCAGCTTCAC
genomic: GGCCTTTGCAGGCTGCAAGCATTCCAGGACTCCTTGGGATTTTTCAGAACgtaaggggtt ... aatttcgcagGAGTGGGATGCTCTCATGCTTTCTAATTTTGCTTTGGAGCAGCAGCTTCAC
EST: gi|211367120|gb|FL319134.1|FL319134
EST:     GGCCTTTGCAGGCTGCAAGCATTCCAGGACTCCTTGGGATTTTTCAGAAC                         GAGTGGGATGCTCTCATGCTTTCTAATTTTGCTTTGGAGCAGCAGCTTCAC
genomic: GGCCTTTGCAGGCTGCAAGCATTCCAGGACTCCTTGGGATTTTTCAGAACgtaaggggtt ... aatttcgcagGAGTGGGATGCTCTCATGCTTTCTAATTTTGCTTTGGAGCAGCAGCTTCAC
EST: gi|211096168|gb|FL332998.1|FL332998
EST:     GGCCTTTGCAGGCTGCAAGCATTCCAGGACTCCTTGGGATTTTTCAGAAC                         GAGTGGGATGCTCTCATGCTTTCTAATTTTGCTTTGGAGCAGCAGCTTCAC
genomic: GGCCTTTGCAGGCTGCAAGCATTCCAGGACTCCTTGGGATTTTTCAGAACgtaaggggtt ... aatttcgcagGAGTGGGATGCTCTCATGCTTTCTAATTTTGCTTTGGAGCAGCAGCTTCAC
EST: gi|211320067|gb|FL327288.1|FL327288
EST:     GGCCTTTGCAGGCTGCAAGCATTCCAGGACTCCTTGGGATTTTTCAGAAC                         GAGTGGGATGCTCTCATGCTTTCTAATTTTGCTTTGGAGCA
genomic: GGCCTTTGCAGGCTGCAAGCATTCCAGGACTCCTTGGGATTTTTCAGAACgtaaggggtt ... aatttcgcagGAGTGGGATGCTCTCATGCTTTCTAATTTTGCTTTGGAGCA
EST: gi|211262919|gb|FL344603.1|FL344603
EST:     GGCCTTTGCAGGCTGCAAGCATTCCAGGACTCCTTGGGATTTTTCAGAAC                         GAGTGGGATGCTCTCATGCTTTCTAATTTTGCTTTGGAGCAGCAGCTTCAC
genomic: GGCCTTTGCAGGCTGCAAGCATTCCAGGACTCCTTGGGATTTTTCAGAACgtaaggggtt ... aatttcgcagGAGTGGGATGCTCTCATGCTTTCTAATTTTGCTTTGGAGCAGCAGCTTCAC
EST: gi|211012592|gb|FL327139.1|FL327139
EST:     GGCCTTTGCAGGCTGCAAGCATTCCAGGACTCCTTGGGATTTTTCAGAAC                         GAGTGGGATGCTCTCATGCYTTCTAATTTTGCYTTGGAGCAGCAGCTTCAC
genomic: GGCCTTTGCAGGCTGCAAGCATTCCAGGACTCCTTGGGATTTTTCAGAACgtaaggggtt ... aatttcgcagGAGTGGGATGCTCTCATGCTTTCTAATTTTGCTTTGGAGCAGCAGCTTCAC
EST: gi|211180977|gb|FL324623.1|FL324623
EST:     GGCCTTTGCAGGCTGCAAGCATTCCAGGACTCCTTGGGATTTTTCAGAAC                         GAGTGGGATGCTCTCATGCTTTCTAATTTTGC
genomic: GGCCTTTGCAGGCTGCAAGCATTCCAGGACTCCTTGGGATTTTTCAGAACgtaaggggtt ... aatttcgcagGAGTGGGATGCTCTCATGCTTTCTAATTTTGC
EST: gi|211162340|gb|FL348127.1|FL348127
EST:     GGCCTTTGCAGGCTGCAAGCATTCCAGGACTCTTTGGGATTTTTCAGAAC                         GAGTGGGATGCTCTCATGGCTT-CTAATTTTGCTTTGAAGCAGCAGCTTCA
genomic: GGCCTTTGCAGGCTGCAAGCATTCCAGGACTCCTTGGGATTTTTCAGAACgtaaggggtt ... aatttcgcagGAGTGGGATGCTCTCATG-CTTTCTAATTTTGCTTTGGAGCAGCAGCTTCA
EST: gi|211320874|gb|FL365294.1|FL365294
EST:     GGCCTTTGCAGGCTGCAAGCATTCCAGGACTCCTTGGGAYTTTTCAGAAC                         GAGTGGGATGCTCTCAT
genomic: GGCCTTTGCAGGCTGCAAGCATTCCAGGACTCCTTGGGATTTTTCAGAACgtaaggggtt ... aatttcgcagGAGTGGGATGCTCTCAT
EST: gi|211411809|gb|FL328773.1|FL328773
EST:     GGCCTTTGCAGGCTGCAAGCATTCCAGGACTCCTTGGGATTTTTCAGAAC                         GAGTGGGATGCTCTCATGCTTTCTAATTTTGCTTTGGAGCAGCAGCTTCAC
genomic: GGCCTTTGCAGGCTGCAAGCATTCCAGGACTCCTTGGGATTTTTCAGAACgtaaggggtt ... aatttcgcagGAGTGGGATGCTCTCATGCTTTCTAATTTTGCTTTGGAGCAGCAGCTTCAC
EST: gi|211170529|gb|FL341423.1|FL341423
EST:     GCCTTTGCAGGCTGCAAGCATTCCAGGAACTCCTTGGGATTTTTCAGAAC                         GAGTGGGATGCTCTCATGCTTTCTAATTTTGCTTTGGAGCAGCAGCTTCAC
genomic: GCCTTTGCAGGCTGCAAGCATTCCAGGA-CTCCTTGGGATTTTTCAGAACgtaaggggtt ... aatttcgcagGAGTGGGATGCTCTCATGCTTTCTAATTTTGCTTTGGAGCAGCAGCTTCAC
EST: gi|211306361|gb|FL348172.1|FL348172
EST:     GGCCTTTGCAGGCTGCAAGCATTCCAGGACTCCTTGGGATTTTTCAGAAC                         GAGTGGGATGCTCTCATGCTTTCTAATTTTGCTTTGGAGCAGCAGCTTCAC
genomic: GGCCTTTGCAGGCTGCAAGCATTCCAGGACTCCTTGGGATTTTTCAGAACgtaaggggtt ... aatttcgcagGAGTGGGATGCTCTCATGCTTTCTAATTTTGCTTTGGAGCAGCAGCTTCAC
EST: gi|211314342|gb|FL341215.1|FL341215
EST:     GGCCTTTGCAGGCTGCAAGCATTCCAGGACTCCTTGGGATTTTTCAGAAC                         GAGTGGGATGCTCTCATGCTTTCTAATTTTGCTTTGGAGCAGCAGCTTCAC
genomic: GGCCTTTGCAGGCTGCAAGCATTCCAGGACTCCTTGGGATTTTTCAGAACgtaaggggtt ... aatttcgcagGAGTGGGATGCTCTCATGCTTTCTAATTTTGCTTTGGAGCAGCAGCTTCAC
EST: gi|148945896|gb|EC891188.2|EC891188
EST:     GGCCTTTGCAGGCTGCAAGCATTCCAGGACTCCTTGGGATTTTTCAGAAC                         GAGTGGGATGCTCTCATGCTTTCTAATTTTGCTTTGGAGCAGCAGCTTCAC
genomic: GGCCTTTGCAGGCTGCAAGCATTCCAGGACTCCTTGGGATTTTTCAGAACgtaaggggtt ... aatttcgcagGAGTGGGATGCTCTCATGCTTTCTAATTTTGCTTTGGAGCAGCAGCTTCAC
EST: gi|67020062|gb|CO448811.1|CO448811
EST:     GGCCTTTGCAGGCTGCAAGCATTCCAGGACTCCTTGGGATTTTTCAGAAC                         GAGTGGGATGCTCTCATGCTTTCTAATTTTGCTTTGGAGCAGCAGCTTCAC
genomic: GGCCTTTGCAGGCTGCAAGCATTCCAGGACTCCTTGGGATTTTTCAGAACgtaaggggtt ... aatttcgcagGAGTGGGATGCTCTCATGCTTTCTAATTTTGCTTTGGAGCAGCAGCTTCAC
EST: gi|211108071|gb|FL361614.1|FL361614
EST:     GCCTTTGCAGGCTGCAAGCATTCCAGGNACTCCTTGGGATTTTTCAGAAC                         GAGTGGGATGCTCTCATGCTTTCTAATTTTGCTTTGGAGCAGCAGCTTCAC
genomic: GCCTTTGCAGGCTGCAAGCATTCCAGG-ACTCCTTGGGATTTTTCAGAACgtaaggggtt ... aatttcgcagGAGTGGGATGCTCTCATGCTTTCTAATTTTGCTTTGGAGCAGCAGCTTCAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgagtcataattctctagctcttatcagaacttgtttttcctgaatttcgcagGAGTGGGATGCTCTCATGCTTTCTAATTTTGCTTTGGAGCAGCAGCTTCACACAGCAAGACAAGAACTTAGTCATGCACTCTACCAG
      tcataatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgatccatatcatttttatattgtcaattgtgtcctgtctaaagttttgagtcataattctctagctcttatcagaacttgtttttcctgaatttcgcagGAGTGGGATGCTCTCATGCTTTCTAATTTTGCTTTGGAGCAGCAGCTTCACACAGCAAGACAAGAACTTAGTCATGCACTCTACCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC