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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCCAAAATGATATGAGTGAATGGAAACAGGGACGCTCCTCAAAGAAAAATAACAAATTTGCGCCCAAAAAATCAAGGAACTCTTTTAAGAGCAAAGCAAGgtatgcagcaatggtttaaattagaactgtttgtattgccagtcaactggaaatggaaatggctaaatgacgccgttgagctcttgttaccacatgattcagcctaacaatttttcgcatgtgatgaggatgttggtactacagcattcgtaattgagttttttccccttcatttttggcag

Basic information

species Zea mays
transcript GRMZM2G420865_T02
intron # 19
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G420865_T04 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os12g29660.1 (Oryza sativa), 5'ss of exon 18
---TCCAAAATGATATGAGTGAATGGAAACAGGGACGCTCCTCAAAGAAAAATAACAAATTTGCGCCCAAAAAATCAAGGAACTCTTTTAAGAGCAAAGCAAGgtatgcagcaatggtttaaattagaactgtttgtattgccagtcaactggaaatggaaatggctaaatgacgccgttgagctcttgttaccacatgattcagcctaa--caatttttcgcatgtgatgaggatgttggta-ctacagcattcgtaattgagttttttccccttcatttttggcag
   |||| |||||||||||||||||||| ||||| ||||||| ||||||||||||     ||  ||  || ||||| |  || ||||||||||||||| | ||||||| | ||||| |          | ||  ||   |   | | ||  | |||           | |   |   |   |  | || | |    |   | | | ||||  || ||| |  |   ||| |   ||  | |   |  ||  |||  ||| ||||  ||   |  | | ||||  |   
TGTTCCAGAATGATATGAGTGAATGGAAGCAGGGCCGCTCCTTAAAGAAAAATAATG---TTATGCGAAAGAAATCGAAAAATTCTTTTAAGAGCAAATCCAGgtatgtaacaatgtt----------attgcctgcccttgtatttaatcgaaaa-----------atacaccttagcatattttttatcatacaaaactactgtctaattcattttattaccactgacgctaatactagggtccccaaaatttctaaatgagagttccactttcctttttcag---
















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|211343050|gb|FL472500.1|FL472500
EST:     AACAAATTTGCGCCCAAAAAATCAAGGAACTCTTTTAAGAGCAAAGCAAG                         GTACAAGCGGAAGTAGAAGACTCGGCCATCTCCGGGTTTATATTACACTCC
genomic: AACAAATTTGCGCCCAAAAAATCAAGGAACTCTTTTAAGAGCAAAGCAAGgtatgcagca ... tttttggcagGTACAAGCGGAAGTAGAAGACTCGGCCATCTCCGGGTTTATATTACATTCC
EST: gi|78090028|gb|DV518402.1|DV518402
EST:     AACAAATTTGCGCCCAAAAAATCAAGGAACTCTTTTAAGAGCAAAGCAAG                         GTACAAGCGGAAGTAGAAGACTCGGCCATCTCCGGGTTTATATTACATTCC
genomic: AACAAATTTGCGCCCAAAAAATCAAGGAACTCTTTTAAGAGCAAAGCAAGgtatgcagca ... tttttggcagGTACAAGCGGAAGTAGAAGACTCGGCCATCTCCGGGTTTATATTACATTCC
EST: gi|32906964|gb|CF011777.1|CF011777
EST:     AACAAATTTGCGCCCAAAAAATCAAGGAACTCTTTTAAGAGCAAAGCAAG                         GTACAAGCGGAAGTAGAAGACTCGGCCATCTCCGGGTTTATATTACATTCC
genomic: AACAAATTTGCGCCCAAAAAATCAAGGAACTCTTTTAAGAGCAAAGCAAGgtatgcagca ... tttttggcagGTACAAGCGGAAGTAGAAGACTCGGCCATCTCCGGGTTTATATTACATTCC
EST: gi|211343049|gb|FL472499.1|FL472499
EST:     AACAAATTTGCGCCCAAAAAATCAAGGAACTCTTTTAAGAGCAAAGCAAG                         GTACAAGCGGAAGTAGAAGACTCGGCCATCTCCGGGTTTATATTACACTCC
genomic: AACAAATTTGCGCCCAAAAAATCAAGGAACTCTTTTAAGAGCAAAGCAAGgtatgcagca ... tttttggcagGTACAAGCGGAAGTAGAAGACTCGGCCATCTCCGGGTTTATATTACATTCC
EST: gi|166480470|gb|EG173915.1|EG173915
EST:     ACAAATTTGACGCCCAAAAAATCAAGGAACTCTTTTAAGAGCAAAGCAAG                         GTACAAGCGGAAG
genomic: ACAAATTTG-CGCCCAAAAAATCAAGGAACTCTTTTAAGAGCAAAGCAAGgtatgcagca ... tttttggcagGTACAAGCGGAAG
EST: gi|37373944|gb|CF623297.1|CF623297
EST:     AACAAATTTGCGCCCAAAAAATCAAGGAACTCTTTTAAGAGCAAAGCAAG                         GTACAAGCGGAAGTAGAAGACTCGGCCATCTCCGGGTTTATATTACATTCC
genomic: AACAAATTTGCGCCCAAAAAATCAAGGAACTCTTTTAAGAGCAAAGCAAGgtatgcagca ... tttttggcagGTACAAGCGGAAGTAGAAGACTCGGCCATCTCCGGGTTTATATTACATTCC
EST: gi|14203521|gb|BG837198.1|BG837198
EST:     AACAAATTTGCGCCCAAAAAATCAAGGAACTCTTTTAAGAGCAAAGCAAG                         GTACAAGCGGAAGTAGAAGACTCGGCCATCTCCGGGTTTWTATTACATTCC
genomic: AACAAATTTGCGCCCAAAAAATCAAGGAACTCTTTTAAGAGCAAAGCAAGgtatgcagca ... tttttggcagGTACAAGCGGAAGTAGAAGACTCGGCCATCTCCGGGTTTATATTACATTCC
EST: gi|166480367|gb|EG112632.1|EG112632
EST:     GAACTCTTTTAAGAGCAAAGCAAG                         GTACAAGCGGAAGTAGAAGACTCGGCCATCTCCGGGTTTATATTACATTCC
genomic: GAACTCTTTTAAGAGCAAAGCAAGgtatgcagca ... tttttggcagGTACAAGCGGAAGTAGAAGACTCGGCCATCTCCGGGTTTATATTACATTCC
EST: gi|60396007|gb|DN228877.1|DN228877
EST:     AACAAATTTGCGCCCAAAAAATCAAGGAACTCTTTTAAGAGCAAAGCAAG                         GTACAAGCGGAAGTAGAAGACTCGGCCATCTCCGGGTTTATATTACATTCC
genomic: AACAAATTTGCGCCCAAAAAATCAAGGAACTCTTTTAAGAGCAAAGCAAGgtatgcagca ... tttttggcagGTACAAGCGGAAGTAGAAGACTCGGCCATCTCCGGGTTTATATTACATTCC
EST: gi|37398106|gb|CF636362.1|CF636362
EST:     AACAAATTTGCGCCCAAAAAATCAAGGAACTCTTTTAAGAGCAAAGCAAG                         GTACAAGCGGAAGTAGAAGACTCGGCCATCTCCGGGTTTATATTACATTCC
genomic: AACAAATTTGCGCCCAAAAAATCAAGGAACTCTTTTAAGAGCAAAGCAAGgtatgcagca ... tttttggcagGTACAAGCGGAAGTAGAAGACTCGGCCATCTCCGGGTTTATATTACATTCC
EST: gi|40337352|gb|CK371422.1|CK371422
EST:     AACAAATTTGCGCCCAAAAAATCAAGGAACTCTTTTAAGAGCAAAGCAAG                         GTACAAGCGGAAGTAGAAGACTCGGCCATCTCCGGGTTTATATTACATTCC
genomic: AACAAATTTGCGCCCAAAAAATCAAGGAACTCTTTTAAGAGCAAAGCAAGgtatgcagca ... tttttggcagGTACAAGCGGAAGTAGAAGACTCGGCCATCTCCGGGTTTATATTACATTCC
EST: gi|166491346|gb|EG261747.1|EG261747
EST:     AACAAATTTGCGCCCAAAAAATCAAGGAACTCTTTTAAGAGCAAAGCAAG                         GTACAAGCGGAAGTAGAAG
genomic: AACAAATTTGCGCCCAAAAAATCAAGGAACTCTTTTAAGAGCAAAGCAAGgtatgcagca ... tttttggcagGTACAAGCGGAAGTAGAAG
EST: gi|78022212|gb|DV490599.1|DV490599
EST:     AACAAATTTGCGCCCAAAAAATCAAGGAACTCTTTTAAGAGCAAAGCAAG                         GTACAAGCGGAAGTAGAAGACTCGGCCATCTCCGGGTTTATATTACATTCC
genomic: AACAAATTTGCGCCCAAAAAATCAAGGAACTCTTTTAAGAGCAAAGCAAGgtatgcagca ... tttttggcagGTACAAGCGGAAGTAGAAGACTCGGCCATCTCCGGGTTTATATTACATTCC
EST: gi|211354282|gb|FK984305.1|FK984305
EST:     AACAAATTTGCGCCCAAAAAATCAAGGAACTCTTTTAAGAGCAAAGCAAG                         GTACAAGCGGAAGTAGAAGACTCGGCCATCTCCGGGTTTATATTACATTCC
genomic: AACAAATTTGCGCCCAAAAAATCAAGGAACTCTTTTAAGAGCAAAGCAAGgtatgcagca ... tttttggcagGTACAAGCGGAAGTAGAAGACTCGGCCATCTCCGGGTTTATATTACATTCC
EST: gi|5740651|gb|AI948341.1|AI948341
EST:     ACCAAATTTGCGCCCAAAAAATCAAGGAACTCTTTTAAGAGCAAAGCAAG                         GTACAAACGGAAGTAGAAGACTCGGCCATCTCCGGGTTTATATTACATTCC
genomic: AACAAATTTGCGCCCAAAAAATCAAGGAACTCTTTTAAGAGCAAAGCAAGgtatgcagca ... tttttggcagGTACAAGCGGAAGTAGAAGACTCGGCCATCTCCGGGTTTATATTACATTCC
EST: gi|166436022|gb|EG187628.1|EG187628
EST:     AAAAAATACAAGGAACTCTTTTAAGAGCAAAGCAAG                         GTACAAGCGGAAGTAGAAGACTCGGCCATCTCCGGGTTTATATTACATTCC
genomic: AAAAAAT-CAAGGAACTCTTTTAAGAGCAAAGCAAGgtatgcagca ... tttttggcagGTACAAGCGGAAGTAGAAGACTCGGCCATCTCCGGGTTTATATTACATTCC
EST: gi|67016515|gb|CO445264.1|CO445264
EST:     AACAAATTTGCGCCCAAAAAATCAAGGAACTCTTTTAAGAGCAAAGCAAG                         GTACAAGCGGAAGTAGAAGACTCGGCCATCTCCGGGTTTATATTACATTCC
genomic: AACAAATTTGCGCCCAAAAAATCAAGGAACTCTTTTAAGAGCAAAGCAAGgtatgcagca ... tttttggcagGTACAAGCGGAAGTAGAAGACTCGGCCATCTCCGGGTTTATATTACATTCC
EST: gi|32801098|gb|CD953334.1|CD953334
EST:     TAAGAGCAAAGCACG                         GTACAAGCGGAAGTAGAAGACTCGGCCATCTCCGGGTTTATATTACATTCC
genomic: TAAGAGCAAAGCAAGgtatgcagca ... tttttggcagGTACAAGCGGAAGTAGAAGACTCGGCCATCTCCGGGTTTATATTACATTCC
EST: gi|60344195|gb|DN211168.1|DN211168
EST:     AACAAATTTGCGCCCAAAAAATCAAGGAACTCTTTTAAGAGCAAAGCAAG                         GTACAAGCGGAAGTAGAAGACTCGGCCATCTCCGGGTTTATATTACATTCC
genomic: AACAAATTTGCGCCCAAAAAATCAAGGAACTCTTTTAAGAGCAAAGCAAGgtatgcagca ... tttttggcagGTACAAGCGGAAGTAGAAGACTCGGCCATCTCCGGGTTTATATTACATTCC
EST: gi|60341880|gb|DN208853.1|DN208853
EST:     AACAAATTTGCGCCCAAAAAATCAAGGAACTCTTTTAAGAGCAAAGCAAG                         GTACAAGCGGAAGTAGAAGACTCGGCCATCTCCGGGTTTATATTACATTCC
genomic: AACAAATTTGCGCCCAAAAAATCAAGGAACTCTTTTAAGAGCAAAGCAAGgtatgcagca ... tttttggcagGTACAAGCGGAAGTAGAAGACTCGGCCATCTCCGGGTTTATATTACATTCC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCCAAAATGATATGAGTGAATGGAAACAGGGACGCTCCTCAAAGAAAAATAACAAATTTGCGCCCAAAAAATCAAGGAACTCTTTTAAGAGCAAAGCAAGgtatgcagcaatggtttaaattagaactgtttgtattgccagtcaactggaaatggaaatggctaaatgacgccgttgagctcttgttaccacatgattcagcctaacaatttttcgcatgtgatgaggatgttggtactacagcattcgtaattgagttttttccccttcatttttggcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG