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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaggtttttttgcttgcctaaattgagttgaataatagcttaaagaactgcatgttaaacttgcagCTGCCATCATGAATTGGAGACTGCACGGATTAATGGGCTGCTTGGAAATATCGATGCAAACACTGGTGATCCTCAAGTTG

Basic information

species Zea mays
transcript GRMZM2G081682_T01
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G081682_T01 (Zea mays), 3'ss of exon 14
lower sequence: LOC_Os07g47290.3 (Oryza sativa), 3'ss of exon 14
gtaaggtttttttgcttgcctaaattgagttgaataatagcttaaag------------aactgcatgttaaacttgcagCTGCCATCATGAATTGGAGACTGCACGGATTAATGGGCTGCTTGGAAATATCGATGCAAACACTGGTGATCCTCAAGTTG
|| ||  ||| |||||| |||||  | | |  |    ||||||| ||            |||| ||||  ||| |||||||||||| |||||  | ||||||||| | |||||||| |||||||| ||||| ||||| |||||||||||||| ||  | |
gttag--tttcttgcttccctaacgtcattcaag--gtagcttacagtggcagtgtcataactccatggaaaatttgcagCTGCCACCATGAGCTTGAGACTGCAAGAATTAATGGTCTGCTTGGGAATATTGATGCCAACACTGGTGATCCCCAGATCG

upper sequence: GRMZM2G081682_T01 (Zea mays), 3'ss of exon 14
lower sequence: GLYMA17G07380.1 (Glycine max), 3'ss of exon 14
------------------------------------------------------gtaaggtttttttgcttg---cctaaattgagttgaata-atagcttaaa---gaactgcatgttaaacttg-cagCTGCCATCATGAATTGGAGACTGCACGGATTAATGGGCTGCTTGGAAATATCGATGCAAACACTGGTGATCCTCAAGTTG
                                                       |||  ||  | | | |    | ||| |  |  || | |  |   ||  |     | |   ||||  || ||  || || ||||||||  | || |||||| |||| |||||  |||| || ||||| ||||||||||||||||||||||||||||
gtgaatcgatcattgtatattgtgtttacatgggctgtccttgatctttcccttttaaatttgatattcataaatcataactgaaactggacacgttctttgtacttacaatttctgttgtacctggtagTTGTCATCATGAGCTCGAAACTGCAAGGATCAATGGATTGCTGGGTAATATTGATGCAAACACTGGTGATCCTCAAGTTG
















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|211073602|gb|FL380705.1|FL380705
EST:     GAGTTCAAGATTAATGTTGAGTGCAACCATGCTACTCTATCTGGACACAG                         CTGCCATCATGAATTGGAGACTGCACGGATTAATGGGCTGCTTGGAAATAT
genomic: GAGTTCAAGATTAATGTTGAGTGCAACCATGCTACTCTATCTGGACACAGgtaaggtttt ... aaacttgcagCTGCCATCATGAATTGGAGACTGCACGGATTAATGGGCTGCTTGGAAATAT
EST: gi|31349785|gb|CD434142.1|CD434142
EST:     GAGTTCAAGATTAATGTTGAGTGCAACCATGCTACTCTATCTGGACACAG                         CTGCCATCATGAA
genomic: GAGTTCAAGATTAATGTTGAGTGCAACCATGCTACTCTATCTGGACACAGgtaaggtttt ... aaacttgcagCTGCCATCATGAA
EST: gi|6194746|gb|AW146850.1|AW146850
EST:     GAGTTCAAGATTAATGTTGAGTGCAACCATGCTACTCTATCTGGACACAG                         CTGCCATCATGAATTGGAGACTGCACGGATTAATGGGCTGCTTGGAAATAT
genomic: GAGTTCAAGATTAATGTTGAGTGCAACCATGCTACTCTATCTGGACACAGgtaaggtttt ... aaacttgcagCTGCCATCATGAATTGGAGACTGCACGGATTAATGGGCTGCTTGGAAATAT
EST: gi|5296207|gb|AI782887.1|AI782887
EST:     GAGTTCAAGATTAATGTTGAGTGCAACCATGCTACTCTATCTGGACACAG                         CTGCCATCATGAATTGGAGACTGCACGGATTAATGGGCTGCTTGGAAATAT
genomic: GAGTTCAAGATTAATGTTGAGTGCAACCATGCTACTCTATCTGGACACAGgtaaggtttt ... aaacttgcagCTGCCATCATGAATTGGAGACTGCACGGATTAATGGGCTGCTTGGAAATAT
EST: gi|33104022|gb|CF063982.1|CF063982
EST:     GAGTTCAAGATTAATGTTGAGTGCAACCATGCTACTCTATCTGGACACAG                         CTGCCATCATGAATTGGAGACTGCACGGATTAATGGGCTGCTTGGAAATAT
genomic: GAGTTCAAGATTAATGTTGAGTGCAACCATGCTACTCTATCTGGACACAGgtaaggtttt ... aaacttgcagCTGCCATCATGAATTGGAGACTGCACGGATTAATGGGCTGCTTGGAAATAT
EST: gi|74232803|gb|DT640717.1|DT640717
EST:     GAGTTCAAGATTAATGTTGAGTGCAACCATGCTACTCTATCTGGACACAG                         CTGCCATCATGAATTGGAGACTGCACGGATTAATGGGCTGCTTGGAAATAT
genomic: GAGTTCAAGATTAATGTTGAGTGCAACCATGCTACTCTATCTGGACACAGgtaaggtttt ... aaacttgcagCTGCCATCATGAATTGGAGACTGCACGGATTAATGGGCTGCTTGGAAATAT
EST: gi|5846747|gb|AI999830.1|AI999830
EST:     GAGTTCAAGATTAATGTTGAGTGCAACCATGCTACTCTATCTGGACACAG                         CTGCCATCATGAATTGGAGACTGCACGGATTAATGGGCTGCTTGGAAATAT
genomic: GAGTTCAAGATTAATGTTGAGTGCAACCATGCTACTCTATCTGGACACAGgtaaggtttt ... aaacttgcagCTGCCATCATGAATTGGAGACTGCACGGATTAATGGGCTGCTTGGAAATAT
EST: gi|60398484|gb|DN231300.1|DN231300
EST:     TAATGTTGAGTGCAACCATGCTACTCTATCTGGACACAG                         CTGCCATCATGAATTGGAGACTGCACGGATTAATGGGCTGCTTGGAAATAT
genomic: TAATGTTGAGTGCAACCATGCTACTCTATCTGGACACAGgtaaggtttt ... aaacttgcagCTGCCATCATGAATTGGAGACTGCACGGATTAATGGGCTGCTTGGAAATAT
EST: gi|211313620|gb|FL416741.1|FL416741
EST:     GAGTTCAAGATTAATGTTGAGTGCAACCATGCTACTCTATCTGGACACAG                         CTGCCATCATGAATTGGAGACTGCACGGATTAATGGGCTGCTTGGAAATAT
genomic: GAGTTCAAGATTAATGTTGAGTGCAACCATGCTACTCTATCTGGACACAGgtaaggtttt ... aaacttgcagCTGCCATCATGAATTGGAGACTGCACGGATTAATGGGCTGCTTGGAAATAT
EST: gi|31250143|gb|CD219167.1|CD219167
EST:     GAGTTCAAGATTAATGTTGAGTGCAACCATGCTACTCTATCTGGACACAG                         CTGCCATCATGAATTGGAGACTGCACGGATTAATGGGCTGCTTGGAAATAT
genomic: GAGTTCAAGATTAATGTTGAGTGCAACCATGCTACTCTATCTGGACACAGgtaaggtttt ... aaacttgcagCTGCCATCATGAATTGGAGACTGCACGGATTAATGGGCTGCTTGGAAATAT
EST: gi|76014001|gb|DT941171.1|DT941171
EST:     TTCAAGATTAATGTTGAGGGCAACCATGCTACTCTATCTGGACACAG                         CTGCCATCATGAATTGGAGACTGCACGGATTAATGGGCTGCTTGGAAATAT
genomic: TTCAAGATTAATGTTGAGTGCAACCATGCTACTCTATCTGGACACAGgtaaggtttt ... aaacttgcagCTGCCATCATGAATTGGAGACTGCACGGATTAATGGGCTGCTTGGAAATAT
EST: gi|211371193|gb|FL385803.1|FL385803
EST:     GAGTTCAAGATTAATGTTGAGTGCAACCATGCTACTCTATCTGGACACAG                         CTGCCATCATGAATTGGAGACTGCACGGATTAATGGGCTGCTTGGAAATAT
genomic: GAGTTCAAGATTAATGTTGAGTGCAACCATGCTACTCTATCTGGACACAGgtaaggtttt ... aaacttgcagCTGCCATCATGAATTGGAGACTGCACGGATTAATGGGCTGCTTGGAAATAT
EST: gi|211434578|gb|FL418942.1|FL418942
EST:     GAGTTCAAGATTAATGTTGAGTGCAACCATGCTACTCTATCTGGACACAG                         CTGCCATCATGAATTGGAGACTGCACGGATTAATGGGCTGCTTGGAAATAT
genomic: GAGTTCAAGATTAATGTTGAGTGCAACCATGCTACTCTATCTGGACACAGgtaaggtttt ... aaacttgcagCTGCCATCATGAATTGGAGACTGCACGGATTAATGGGCTGCTTGGAAATAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcttgcctaaattgagttgaataatagcttaaagaactgcatgttaaacttgcagCTGCCATCATGAATTGGAGACTGCACGGATTAATGGGCTGCTTGGAAATATCGATGCAAACACTGGTGATCCTCAAGTTG
    gcctaaa  putative branch site (score: 3)
                   aataatagcttaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaggtttttttgcttgcctaaattgagttgaataatagcttaaagaactgcatgttaaacttgcagCTGCCATCATGAATTGGAGACTGCACGGATTAATGGGCTGCTTGGAAATATCGATGCAAACACTGGTGATCCTCAAGTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT