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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgcatgcccccaaggtgatgcggttatttacttcccaacagctttgtcgcgtccgttctgttgcattgcatcacctgtttgtatttactgggcttggcagGGTGACGCGGACATCTTCTTCCCAACCGACTTCCGGCTCCTGGAGCAGATCGACCATAACTGCGCTGGCTTCTCAAAGGAGCAGAAGAATCCCGGCGCAT

Basic information

species Zea mays
transcript GRMZM2G101217_T02
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G101217_T08 (Zea mays), 3'ss of exon 11
lower sequence: LOC_Os01g68390.1 (Oryza sativa), 3'ss of exon 11
---tgcatgcccccaaggtgatgcggttatttacttcccaacagctttgtcgcg-tccgttctgttgcattgcatcacctgtttgtatttactgggcttggcagGGTGACGCGGACATCTTCTTCCCAACCGACTTCCGGCTCCTGGAGCAGATCGACCATAACTGCGCTGGCTTCTCAAAGGAGCAGAAGAATCCCGGCGCAT
   |    ||    ||| || |  |  ||| |  ||   ||     |||| | | |  ||  | ||  ||   || |   |       |||     |||| ||||||||||| || || |||||||||||||| ||| ||||  ||||| ||||||||||| ||||| |||| ||||||||  |||| ||||| ||||| ||||
aactttgagcaattaagttgttatg-ctatgtgttt---aattaagttgttgtgctatgtgttattatatattattaaaagaactcggttatgttacttgccagGGTGACGCAGATATTTTCTTCCCAACCGATTTCTGGCTTTTGGAGAAGATCGACCATGACTGCTCTGGTTTCTCAAAACAGCAAAAGAACCCCGGTGCAT
















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|60352980|gb|DN219953.1|DN219953
EST:     AAGGAATGGGAAGACATCAGATCATCGCAACTACTTTGATGCTCAG                         GGTGACGCGGACATCTTCTTCCCAACCGACTTCCGGCTCCTGGAGCAGATC
genomic: AAGG-ATGGGAAGACATCAGATCATCGCAACTACTTTGATGCTCAGgtaaacatat ... ggcttggcagGGTGACGCGGACATCTTCTTCCCAACCGACTTCCGGCTCCTGGAGCAGATC
EST: gi|211301901|gb|FL443563.1|FL443563
EST:     AACGATGGAAAGACATCAGATCATCGCAACTACTTTGATGCTCAG                         GGTGACGCGGACATCTTCTTCCCAACCGATTTCCGGCTCCTGGAGCAGATC
genomic: AAGGATGGGAAGACATCAGATCATCGCAACTACTTTGATGCTCAGgtaaacatat ... ggcttggcagGGTGACGCGGACATCTTCTTCCCAACCGACTTCCGGCTCCTGGAGCAGATC
EST: gi|50337134|gb|CO532260.1|CO532260
EST:     AAGGATGGGAAGACATCAGATCATCGCAACTAC-TTGATGCTCAG                         GGTGACGCGGACATCTTCTTCCCAACCGACTTCCGGCTCCTGGAGCAGATC
genomic: AAGGATGGGAAGACATCAGATCATCGCAACTACTTTGATGCTCAGgtaaacatat ... ggcttggcagGGTGACGCGGACATCTTCTTCCCAACCGACTTCCGGCTCCTGGAGCAGATC
EST: gi|76910426|gb|DV163864.1|DV163864
EST:     AAGGATGGGAAGACATCAGATCATCGCAACTACTTTGATGCTCAG                         GGTGACGCGGACATCTTCTTCCCAACCGACTTCCGGCTCCTGGAGCAGATC
genomic: AAGGATGGGAAGACATCAGATCATCGCAACTACTTTGATGCTCAGgtaaacatat ... ggcttggcagGGTGACGCGGACATCTTCTTCCCAACCGACTTCCGGCTCCTGGAGCAGATC
EST: gi|50325601|gb|CO520727.1|CO520727
EST:     AAGGATGGGAAGACATCAGATCATCGCAACTACTTTGATGCTCAG                         GGTGACGCGGACATCTTCTTCCCAACCGACTTCCGGCTCCTGGAGCAGATC
genomic: AAGGATGGGAAGACATCAGATCATCGCAACTACTTTGATGCTCAGgtaaacatat ... ggcttggcagGGTGACGCGGACATCTTCTTCCCAACCGACTTCCGGCTCCTGGAGCAGATC
EST: gi|50336105|gb|CO531231.1|CO531231
EST:     AAGGATGGGAAGACATCAGATCATCGCAACTACTTTGATGCTCAG                         GGTGACGCGGACATCTTCTTCCCAACCGACTTCCGGCTCCTGGAGCAGATC
genomic: AAGGATGGGAAGACATCAGATCATCGCAACTACTTTGATGCTCAGgtaaacatat ... ggcttggcagGGTGACGCGGACATCTTCTTCCCAACCGACTTCCGGCTCCTGGAGCAGATC
EST: gi|113680102|gb|DW837994.1|DW837994
EST:     GGAAGACATCAGATCATCGCAACTACTTTGATGCTCAG                         GGTGACGCGGACATCTTCTTCCCAACCGACTTCCGGCTCCTGGAGCAAGAT
genomic: GGAAGACATCAGATCATCGCAACTACTTTGATGCTCAGgtaaacatat ... ggcttggcagGGTGACGCGGACATCTTCTTCCCAACCGACTTCCGGCTCCTGGAGCA-GAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtcgcgtccgttctgttgcattgcatcacctgtttgtatttactgggcttggcagGGTGACGCGGACATCTTCTTCCCAACCGACTTCCGGCTCCTGGAGCAGATCGACCATAACTGCGCTGGCTTCTCAAAGGAGCAGAAGAATCCCGGCGCAT
                                tttgtattta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgcatgcccccaaggtgatgcggttatttacttcccaacagctttgtcgcgtccgttctgttgcattgcatcacctgtttgtatttactgggcttggcagGGTGACGCGGACATCTTCTTCCCAACCGACTTCCGGCTCCTGGAGCAGATCGACCATAACTGCGCTGGCTTCTCAAAGGAGCAGAAGAATCCCGGCGCAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG