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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgttctgtctcgaattgcgatgcactcatcatcccttttccttctcggggttctgggttttgtgtgagtatgtgttcggtggcgtgtttctttgcagAGCAAGCAAGAAGAGGAAGCGAAGAAGCTCATGGAGAGCACAGACGAAATTAAGAAAAGGTTGGCAGCCAAAGAAGTTGAGGTGCAGGAGGCCAAGAGCA

Basic information

species Zea mays
transcript GRMZM2G172101_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G172101_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os03g10190.1 (Oryza sativa), 3'ss of exon 2
gtacgttctgtctcgaattgcgatgcactcatcatcccttttccttctcggggttctgggttttgtgtgagtatgtgttcggtggcgtgtttctttgcagAGCAAGCAAGAAGAGGAAGCGAAGAAGCTCATGGAGAGCACAGACGAAATTAAGAAAAGGTTGGCAGCCAAAGAAGTTGAGGTGCAGGAGGCCAAGAGCA------
|||||||||   |||| |||             ||||| |||  |   |  |     |||||||   |  |  ||||   | | || ||   || ||||||      || | ||||| ||   |   || ||  ||||||| || ||||||||||| |||||||| ||||| ||    |||||||||||||||||  |||      
gtacgttcttcttcgatttg-------------atccccttttgtgggcacgtcgtggggttttcgatttgcgtgtgacggttagcatgccgctgtgcagA------AAAAGGAGGATGCATCGGCTCTGATTCAGAGCACGGAAGAAATTAAGAAGAGGTTGGCTGCCAAGGAGACGGAGGTGCAGGAGGCCAAAGGCACGCTGG
















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|211021857|gb|FL368551.1|FL368551
EST:     TCCGGCAGGAGCTCAACGCTACCAGCAAGAAGATTGGCAAGCTCAAAGCC                         AGCAAGCAAGAAGAGGAAGCGAAGAAGCTCATGGAGAGCACAGACGAAATT
genomic: TCCGGCAGGAGCTCAACGCTACCAGCAAGAAGATTGGCAAGCTCAAAGCCgtacgttctg ... ttctttgcagAGCAAGCAAGAAGAGGAAGCGAAGAAGCTCATGGAGAGCACAGACGAAATT
EST: gi|211054847|gb|FL421737.1|FL421737
EST:     TCCGGCAGGAGCTCAACGCTACCAGCAAGAAGATTGGCAAGCTCAAAGCC                         AGCAAGCAAGAAGAGGAAGCGAAGAAGCTCATGGAGAGCACAGACGAAATT
genomic: TCCGGCAGGAGCTCAACGCTACCAGCAAGAAGATTGGCAAGCTCAAAGCCgtacgttctg ... ttctttgcagAGCAAGCAAGAAGAGGAAGCGAAGAAGCTCATGGAGAGCACAGACGAAATT
EST: gi|18171951|gb|BM347339.1|BM347339
EST:     TCCGGCAGGAGCTCAACGCTACCAGCAAGAAGATTGGCAAGCTCAAAGCC                         AGCAAGCAAGAAGAGGAAGCGAAGAAGCTCATGGAGAGCACAGACGAAATT
genomic: TCCGGCAGGAGCTCAACGCTACCAGCAAGAAGATTGGCAAGCTCAAAGCCgtacgttctg ... ttctttgcagAGCAAGCAAGAAGAGGAAGCGAAGAAGCTCATGGAGAGCACAGACGAAATT
EST: gi|148937654|gb|EC881846.2|EC881846
EST:     TCCGGCAGGAGCTCAACGCTACCAGCAAGAAGATTGGCAAGCTCAAAGCC                         AGCAAGCAAGAAGAGGAAGCGAAGAAGCTCATGGAGAGCACAGACGAAATT
genomic: TCCGGCAGGAGCTCAACGCTACCAGCAAGAAGATTGGCAAGCTCAAAGCCgtacgttctg ... ttctttgcagAGCAAGCAAGAAGAGGAAGCGAAGAAGCTCATGGAGAGCACAGACGAAATT
EST: gi|32805473|gb|CD957707.1|CD957707
EST:     TCCGGCAGGAGCTCAACGCTACCAGCAAGAAGATCGGCAAGCTCAAAGCC                         AGCAAGCAAGAAGAGGAAGCGAAGAAGCTCATGGAGAGCACAGACGAAATT
genomic: TCCGGCAGGAGCTCAACGCTACCAGCAAGAAGATTGGCAAGCTCAAAGCCgtacgttctg ... ttctttgcagAGCAAGCAAGAAGAGGAAGCGAAGAAGCTCATGGAGAGCACAGACGAAATT
EST: gi|37421408|gb|CF648402.1|CF648402
EST:     TCCGGCAGGAGCTCAACGCTACCAGCAAGAAGATTGGCAAGCTCAAAGCC                         AGCAAGCAAGAAGAGGAAGCGAAGAAGCTCATGGAGAGCACAGACGAAATT
genomic: TCCGGCAGGAGCTCAACGCTACCAGCAAGAAGATTGGCAAGCTCAAAGCCgtacgttctg ... ttctttgcagAGCAAGCAAGAAGAGGAAGCGAAGAAGCTCATGGAGAGCACAGACGAAATT
EST: gi|18174283|gb|BM349671.1|BM349671
EST:     TCCGGCAGGAGCTCAACGCTACCAGCAAGAAGATTGGCAAGCTCAAAGCC                         AGCAAGCAAGAAGAGGAAGCGAAGAAGCTCATGGAAAGCACAGACGAAATT
genomic: TCCGGCAGGAGCTCAACGCTACCAGCAAGAAGATTGGCAAGCTCAAAGCCgtacgttctg ... ttctttgcagAGCAAGCAAGAAGAGGAAGCGAAGAAGCTCATGGAGAGCACAGACGAAATT
EST: gi|32803008|gb|CD955244.1|CD955244
EST:     TCCGGCAGGAGCTCAACGCTACCAGCAAGAAGATCGGCAAGCTCAAAGCC                         AGCAAGCAAGAAGAGGAAGCGAAGAAGCTCATGGAGAGCACAGACGAGATT
genomic: TCCGGCAGGAGCTCAACGCTACCAGCAAGAAGATTGGCAAGCTCAAAGCCgtacgttctg ... ttctttgcagAGCAAGCAAGAAGAGGAAGCGAAGAAGCTCATGGAGAGCACAGACGAAATT
EST: gi|148931370|gb|EC874280.2|EC874280
EST:     TCCGGCAGGAGCTCAACGCTACCAGCAAGAAGATTGGCAAGCTCAAAGCC                         AGCAAGCAAGAAGAGGAAGCGAAGAAGCTCATGGAGAGCACAGACGAAATT
genomic: TCCGGCAGGAGCTCAACGCTACCAGCAAGAAGATTGGCAAGCTCAAAGCCgtacgttctg ... ttctttgcagAGCAAGCAAGAAGAGGAAGCGAAGAAGCTCATGGAGAGCACAGACGAAATT
EST: gi|28985482|gb|CB350662.1|CB350662
EST:     TCCGGCAGGAGCTCAACGCTACCAGCAAGAAGATTGGCAAGCTCAAAGCC                         AGCAAGCAAGAAGAGGAAGCGAAGAAGCTCATGGAGAGCACAGACGAAATT
genomic: TCCGGCAGGAGCTCAACGCTACCAGCAAGAAGATTGGCAAGCTCAAAGCCgtacgttctg ... ttctttgcagAGCAAGCAAGAAGAGGAAGCGAAGAAGCTCATGGAGAGCACAGACGAAATT
EST: gi|32790625|gb|CD942861.1|CD942861
EST:     TCCGGCAGGAGCTCACCGCTACCAGCAAGAAGATCGGCAAGCTCAAAGCC                         AGCAAGCAAGAAGAGGAAGCGAAGAAGCTCATGGAGAGCACAGACGAA
genomic: TCCGGCAGGAGCTCAACGCTACCAGCAAGAAGATTGGCAAGCTCAAAGCCgtacgttctg ... ttctttgcagAGCAAGCAAGAAGAGGAAGCGAAGAAGCTCATGGAGAGCACAGACGAA
EST: gi|18164364|gb|BM334203.1|BM334203
EST:     TCCGGCAGGAGCTCAACGCTACCAGCAAGAAGATTGGCAAGCTCAAAGCC                         AGCAAGCAAGAAGAGGAAGCGAAGAAGCTCATGGAGAGCACAGACGAAATT
genomic: TCCGGCAGGAGCTCAACGCTACCAGCAAGAAGATTGGCAAGCTCAAAGCCgtacgttctg ... ttctttgcagAGCAAGCAAGAAGAGGAAGCGAAGAAGCTCATGGAGAGCACAGACGAAATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctcggggttctgggttttgtgtgagtatgtgttcggtggcgtgtttctttgcagAGCAAGCAAGAAGAGGAAGCGAAGAAGCTCATGGAGAGCACAGACGAAATTAAGAAAAGGTTGGCAGCCAAAGAAGTTGAGGTGCAGGAGGCCAAGAGCA
                                          tgtttcttt  CT-rich tract
                                            tttcttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacgttctgtctcgaattgcgatgcactcatcatcccttttccttctcggggttctgggttttgtgtgagtatgtgttcggtggcgtgtttctttgcagAGCAAGCAAGAAGAGGAAGCGAAGAAGCTCATGGAGAGCACAGACGAAATTAAGAAAAGGTTGGCAGCCAAAGAAGTTGAGGTGCAGGAGGCCAAGAGCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA