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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgcgataatatctgttccttgcagcagcagcagcctctgttctgccaatgcctgaaatgctagtgacaccatgaatctgtgtgtctgtcttgactcccagGGCTTCGCGTACCTCCCCGGTGGCGTGTGTGTGTCGAGCATGGGGCGGCCGGTGTCGTACGAGCAGGCGGTGGCGTGGAAGGTCCTGAGCGACGACGACA

Basic information

species Zea mays
transcript GRMZM2G423337_T01
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G423337_T01 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os03g43930.2 (Oryza sativa), 3'ss of exon 17
gtatgcgataatatctgttccttgcagcagcagcagcctctgttctgccaatgcctgaaatgctagtgacaccatgaatctgtgtgtctgtcttgactcccagGGCTTCGCGTACCTCCCCGGTGGCGTGTGTGTGTCGAGCATGGGGCGGCCGGTGTCGTACGAGCAGGCGGTGGCGTGGAAGGTCCTGAGCGACGACGACA
        ||    || ||  |   |     |  ||||| ||  |   |  |  |||  ||||| || ||   |             |||| |  ||||| |||| ||||| |||||||| || |||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
-------gtatggactattgttcctaatgctacaagcctttggacaaaccct-tctgtgatgcttgtaaccgaacag---cacaaaactgtttccactcc-agGGTTTCGCCTACCTCCCGGGCGGCGTGTGCGTGTCGAGCATGGGGCGGCCGGTGTCGTACGAGCAGGCGGTGGCGTGGAAGGTCCTGAGCGACGACGACA
















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|60347903|gb|DN214876.1|DN214876
EST:     ACGATGGCAGGAAGGCGCTCTGCACCGAGTACCCTAAGATTATGCAACAG                         GGCTTCGCGTACCTCCCCGGTGGCGTGTGTGTGTCGAGCATGGGACGGCCG
genomic: ACGATGGCAGGAAGGCGCTCTGCACCGAGTACCCTAAGATTATGCAACAGgtatgcgata ... tgactcccagGGCTTCGCGTACCTCCCCGGTGGCGTGTGTGTGTCGAGCATGGGGCGGCCG
EST: gi|76912511|gb|DV164768.1|DV164768
EST:     CGATGGCAGGAAGGCGCTCTGCACCGAGTACCCCTAAGATTATGCAAAAG                         GGCTTCGCGTACCTCCCCGGTG
genomic: CGATGGCAGGAAGGCGCTCTGCACCGAGTACCC-TAAGATTATGCAACAGgtatgcgata ... tgactcccagGGCTTCGCGTACCTCCCCGGTG
EST: gi|211342627|gb|FL344349.1|FL344349
EST:     ACGATGGCAGGAAGGCGCTCTGCACCGAGTACCCTAAGATTATGCAACAG                         GGCTTCGCGTACCTCCCCGGTGGCGTGTGTGTGTCGAGCATGGGGCGGCCG
genomic: ACGATGGCAGGAAGGCGCTCTGCACCGAGTACCCTAAGATTATGCAACAGgtatgcgata ... tgactcccagGGCTTCGCGTACCTCCCCGGTGGCGTGTGTGTGTCGAGCATGGGGCGGCCG
EST: gi|71764261|gb|DR962198.1|DR962198
EST:     ACGATGGCAGGAAGGCGCTCTGCACCGAGTACCCTAAGATTATGCAACAG                         GGCTTCGCGTACCTCCCCGGTGGCGTGTGTGTGTCGAGCATGGGGCGGCCG
genomic: ACGATGGCAGGAAGGCGCTCTGCACCGAGTACCCTAAGATTATGCAACAGgtatgcgata ... tgactcccagGGCTTCGCGTACCTCCCCGGTGGCGTGTGTGTGTCGAGCATGGGGCGGCCG
EST: gi|71298034|gb|DR784986.1|DR784986
EST:     ACGATGGCAGGAAGGCGCTCTGCACCGAGTACCCTAAGATTATGCAACAG                         GGCTTCGCGTACCTCCCCGGTGGCGTGTGTGTGTCGAGCATGGGGCGGCCG
genomic: ACGATGGCAGGAAGGCGCTCTGCACCGAGTACCCTAAGATTATGCAACAGgtatgcgata ... tgactcccagGGCTTCGCGTACCTCCCCGGTGGCGTGTGTGTGTCGAGCATGGGGCGGCCG
EST: gi|4966813|gb|AI691669.1|AI691669
EST:     ACGATGGCAGGAAGGCGCTCTGCACCGAGTACCCTAAGATTATGCAACAG                         GGCTTCGCGTACCTCCCCGGTGGCGTGTGTGTGTCGAGCATGGGGCGGCCG
genomic: ACGATGGCAGGAAGGCGCTCTGCACCGAGTACCCTAAGATTATGCAACAGgtatgcgata ... tgactcccagGGCTTCGCGTACCTCCCCGGTGGCGTGTGTGTGTCGAGCATGGGGCGGCCG
EST: gi|88756793|gb|DY540934.1|DY540934
EST:     ACGATGGCAGGAAGGCGCTCTGCACCGAGTACCCTAAGATTATGCAACAG                         GGCTTCGCGTACCTCCCCGGTGGCGTGTGTGTGTCGAGCATGGGGCGGCCG
genomic: ACGATGGCAGGAAGGCGCTCTGCACCGAGTACCCTAAGATTATGCAACAGgtatgcgata ... tgactcccagGGCTTCGCGTACCTCCCCGGTGGCGTGTGTGTGTCGAGCATGGGGCGGCCG
EST: gi|60400862|gb|DN233669.1|DN233669
EST:     ACGATGGCAGGAAGGCGCTCTGCACCGAGTACCCTAAGATTATGCAACAG                         GGCTTCGCGTACCTCCCCGGTGGCGTGTGTGTGTCGAGCATGGGGCGGCCG
genomic: ACGATGGCAGGAAGGCGCTCTGCACCGAGTACCCTAAGATTATGCAACAGgtatgcgata ... tgactcccagGGCTTCGCGTACCTCCCCGGTGGCGTGTGTGTGTCGAGCATGGGGCGGCCG
EST: gi|71298032|gb|DR784985.1|DR784985
EST:     ACGATGGCAGGAAGGCGCTCTGCACCGAGTACCCTAAGATTATGCAACAG                         GGCTTCGCGTACCTCCCCGGTGGCGTGTGTGTGTCGAGCATGGGGCGGCCG
genomic: ACGATGGCAGGAAGGCGCTCTGCACCGAGTACCCTAAGATTATGCAACAGgtatgcgata ... tgactcccagGGCTTCGCGTACCTCCCCGGTGGCGTGTGTGTGTCGAGCATGGGGCGGCCG
EST: gi|32847407|gb|CD987088.1|CD987088
EST:     CGATGGCAGGAAGGCGCTCTGCACCGAGGTACCCTAAGATTATGCAACAG                         GGCTTCGCGTA
genomic: CGATGGCAGGAAGGCGCTCTGCACCGAG-TACCCTAAGATTATGCAACAGgtatgcgata ... tgactcccagGGCTTCGCGTA
EST: gi|60401652|gb|DN234459.1|DN234459
EST:     ACGATGGCAGGAAGGCGCTCTGCACCGAGTACCCTAAGATTATGCAACAG                         GGCTTCGCGTACCTCCCCGGTGGCGTGTGTGTGTCGAGCATGGGGCGGCCG
genomic: ACGATGGCAGGAAGGCGCTCTGCACCGAGTACCCTAAGATTATGCAACAGgtatgcgata ... tgactcccagGGCTTCGCGTACCTCCCCGGTGGCGTGTGTGTGTCGAGCATGGGGCGGCCG
EST: gi|60396119|gb|DN228988.1|DN228988
EST:     ACGATGGCAGGAAGGCGCTCTGCACCGAGTACCCTAAGATTATGCAACAG                         GGCTTCGCGTACCTCCCCGGTGGCGTGTGTGTGTCGAGCATGGGGCGGCCG
genomic: ACGATGGCAGGAAGGCGCTCTGCACCGAGTACCCTAAGATTATGCAACAGgtatgcgata ... tgactcccagGGCTTCGCGTACCTCCCCGGTGGCGTGTGTGTGTCGAGCATGGGGCGGCCG
EST: gi|60354408|gb|DN221381.1|DN221381
EST:     ACGATGGCAGGAAGGCGCTCTGCACCGAGTACCCTAAGATTATGCAACAG                         GGCTTCGCGTACCTCCCCGGTGGCGTGTGTGTGTCGAGCATGGGGCGGCCG
genomic: ACGATGGCAGGAAGGCGCTCTGCACCGAGTACCCTAAGATTATGCAACAGgtatgcgata ... tgactcccagGGCTTCGCGTACCTCCCCGGTGGCGTGTGTGTGTCGAGCATGGGGCGGCCG
EST: gi|78116184|gb|DV534571.1|DV534571
EST:     ACGATGGCAGGAAGGCGCTCTGCACCGAGTACCCTAAGATTATGCAACAG                         GGCTTCGCGTACCTCCCCGGTGGCGTGTGTGTGTCGAGCATGGGGCGGCCG
genomic: ACGATGGCAGGAAGGCGCTCTGCACCGAGTACCCTAAGATTATGCAACAGgtatgcgata ... tgactcccagGGCTTCGCGTACCTCCCCGGTGGCGTGTGTGTGTCGAGCATGGGGCGGCCG
EST: gi|4804250|gb|AI666116.1|AI666116
EST:     ACGATGGCAGGAAGGCGCTCTGCACCGAGTACCCTAAGATTATGCAACAG                         GGCTTCGCGTACCTCCCCGGTGGCGTGTGTGTGTCGAGCATGGGGCGGCCG
genomic: ACGATGGCAGGAAGGCGCTCTGCACCGAGTACCCTAAGATTATGCAACAGgtatgcgata ... tgactcccagGGCTTCGCGTACCTCCCCGGTGGCGTGTGTGTGTCGAGCATGGGGCGGCCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caatgcctgaaatgctagtgacaccatgaatctgtgtgtctgtcttgactcccagGGCTTCGCGTACCTCCCCGGTGGCGTGTGTGTGTCGAGCATGGGGCGGCCGGTGTCGTACGAGCAGGCGGTGGCGTGGAAGGTCCTGAGCGACGACGACA
                                          tcttgac  putative branch site (score: 3)
                                      tctgtctt  CT-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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgcgataatatctgttccttgcagcagcagcagcctctgttctgccaatgcctgaaatgctagtgacaccatgaatctgtgtgtctgtcttgactcccagGGCTTCGCGTACCTCCCCGGTGGCGTGTGTGTGTCGAGCATGGGGCGGCCGGTGTCGTACGAGCAGGCGGTGGCGTGGAAGGTCCTGAGCGACGACGACA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG