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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttggcttacacccccacccttattacaattcttgtcttaattgtatgttggcaattggttgaaattacccagttctatgtcttcctgagtgtgtcaatagATATGAAGAAGCCAAAGCCAAAGGTACTGATAACTATGACCGTGAATTGGAAGAAACCATTGAAAGACTAATTGTTGAGTGTGAAAGGAAGATTCAGAGA

Basic information

species Zea mays
transcript GRMZM2G028096_T02
intron # 2
splice site 3'
intron type U12 (go to U12 genes for details)

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G028096_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os02g39300.1 (Oryza sativa), 3'ss of exon 2
ttggcttacacccccacccttattaca-attcttgtcttaattgtatgttggcaattggttgaaattacccagttctatgt-cttcctgagtgtgtcaatagATATGAAGAAGCCAAAGCCAAAGGTACTGATAACTATGACCGTGAATTGGAAGAAACCATTGAAAGACTAATTGTTGAGTGTGAAAGGAAGATTCAGAGA
   | |   |     |  | | | ||| || || ||||  | |||||||| || ||||  || ||   | | ||||||| |  |||||||   |   ||||||||||||||||| |||||||||||||  || || ||||||||||||||||||||||| || |||||||||||    ||||||||||||||||||||||||
--tgttcttattggtaaacctgtgacacatgctagtctgtactgtatgtttgctattgagtgcaagagctctgttctatttgtttcctgaacttagtaatagATATGAAGAAGCGAAAGCCAAAGGTATGGACAATTATGACCGTGAATTGGAAGAAACTATAGAAAGACTAATATCGGAGTGTGAAAGGAAGATTCAGAGA
















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|211342903|gb|FL126052.1|FL126052
EST:     ATGGACATGGGCCCGTGCCCGAAGCTGCACTCGCTGCAACTGCGCAAAGA                         ATATGAAGAAGCCAAAGCCAAAGGTATTGATAACTATGACCGT
genomic: ATGGACATGGGCCCGTGCCCGAAGCTGCACTCGCTGCAACTGCGCAAAGAgtatccttcc ... gtgtcaatagATATGAAGAAGCCAAAGCCAAAGGTACTGATAACTATGACCGT
EST: gi|211342904|gb|FL126053.1|FL126053
EST:     ATGGACATGGGCCCGTGCCCGAAGCTGCACTCGCTGCAACTGCGCAAAGA                         ATATGAAGAAGCCAAAGCCAAAGGTACTGATAACTATGACCGKGAATTGGA
genomic: ATGGACATGGGCCCGTGCCCGAAGCTGCACTCGCTGCAACTGCGCAAAGAgtatccttcc ... gtgtcaatagATATGAAGAAGCCAAAGCCAAAGGTACTGATAACTATGACCGTGAATTGGA
EST: gi|211342898|gb|FL126047.1|FL126047
EST:     ATGGACATGGGCCCGTGCCCGAAGCTGCACTCGCTGCAACTGCGCAAAGA                         ATATGAAGAAGC-AAAGCCAAAGGTACTGATAACTATGGACCGTGGAATTG
genomic: ATGGACATGGGCCCGTGCCCGAAGCTGCACTCGCTGCAACTGCGCAAAGAgtatccttcc ... gtgtcaatagATATGAAGAAGCCAAAGCCAAAGGTACTGATAACTATG-ACCGTG-AATTG
EST: gi|211342902|gb|FL126051.1|FL126051
EST:     ATGGACATGGGCCCGTGCCCGAAGCTGCACTCGCTGCAACTGCGCAAAGA                         ATATGAAGAAGCCAAAGCCAAAGGTACTGATAACTATGACCGTGAATTGGA
genomic: ATGGACATGGGCCCGTGCCCGAAGCTGCACTCGCTGCAACTGCGCAAAGAgtatccttcc ... gtgtcaatagATATGAAGAAGCCAAAGCCAAAGGTACTGATAACTATGACCGTGAATTGGA
EST: gi|211340511|gb|FL126040.1|FL126040
EST:     ATGGACATGGGCCCGTGCCCGAAGCTGCACTCGCTGCAACTGCGCAAAGA                         ATATGAAGAAGCCAAAGCCAAAGGTACTGATAACTATGACCGTGAATTGGA
genomic: ATGGACATGGGCCCGTGCCCGAAGCTGCACTCGCTGCAACTGCGCAAAGAgtatccttcc ... gtgtcaatagATATGAAGAAGCCAAAGCCAAAGGTACTGATAACTATGACCGTGAATTGGA
EST: gi|211342905|gb|FL126054.1|FL126054
EST:     ATGGACATGGGCCCGTGCCCGAAGCTGCACTCGCTGCAACTGCGCAAAGA                         ATATGAAGAAGCCAAAGCCAAAGGTACTGATAACTATGACCGTGAATTGGA
genomic: ATGGACATGGGCCCGTGCCCGAAGCTGCACTCGCTGCAACTGCGCAAAGAgtatccttcc ... gtgtcaatagATATGAAGAAGCCAAAGCCAAAGGTACTGATAACTATGACCGTGAATTGGA
EST: gi|211342900|gb|FL126049.1|FL126049
EST:     ATGGACATGGGCCCGTGCCCGAAGCTGCACTCGCTGCAACTGCGCAAAGA                         ATATGAAGAAGCCAAAGCCAAAGGTACTGATAACTATGACCGTGAATTGGA
genomic: ATGGACATGGGCCCGTGCCCGAAGCTGCACTCGCTGCAACTGCGCAAAGAgtatccttcc ... gtgtcaatagATATGAAGAAGCCAAAGCCAAAGGTACTGATAACTATGACCGTGAATTGGA
EST: gi|71764556|gb|DR962493.1|DR962493
EST:     ATGGACATGGGCCCGTGCCCGAAGCTGCACTCGCTGCAACTGCGCAAAGA                         ATATGAAGAAGCCAAAGCCAAAGGTACTGATAACTATGACCGTGAATTGGA
genomic: ATGGACATGGGCCCGTGCCCGAAGCTGCACTCGCTGCAACTGCGCAAAGAgtatccttcc ... gtgtcaatagATATGAAGAAGCCAAAGCCAAAGGTACTGATAACTATGACCGTGAATTGGA
EST: gi|74232160|gb|DT640074.1|DT640074
EST:     ATGGACATGGGCCCGTGCCCGAAGCTGCACTCGCTGCAACTGCGCAAAGA                         ATATGAAGAAGCCAAAGCCAAAGGTACTGATAACTATGACCGTGAATTGGA
genomic: ATGGACATGGGCCCGTGCCCGAAGCTGCACTCGCTGCAACTGCGCAAAGAgtatccttcc ... gtgtcaatagATATGAAGAAGCCAAAGCCAAAGGTACTGATAACTATGACCGTGAATTGGA
EST: gi|211342892|gb|FL126041.1|FL126041
EST:     ATGGACATGGGCCCGTGCCCGAAGCTGCACTCGCTGCAACTGCGCAAAGA                         ATATGAAGAAGC-AAAGCCAAAGGTACTGATAACTATGGACCGGGGAATTG
genomic: ATGGACATGGGCCCGTGCCCGAAGCTGCACTCGCTGCAACTGCGCAAAGAgtatccttcc ... gtgtcaatagATATGAAGAAGCCAAAGCCAAAGGTACTGATAACTATG-ACCGTG-AATTG
EST: gi|211342897|gb|FL126046.1|FL126046
EST:     ATGGACATGGGCCCGTGCCCGAAGCTGCACTCGCTGCAACTGCGCAAAGA                         ATATGAAGAAGCCAAAGCCAAAGGTACTGATAACTATGACCGTGAATTGGA
genomic: ATGGACATGGGCCCGTGCCCGAAGCTGCACTCGCTGCAACTGCGCAAAGAgtatccttcc ... gtgtcaatagATATGAAGAAGCCAAAGCCAAAGGTACTGATAACTATGACCGTGAATTGGA
EST: gi|211342893|gb|FL126042.1|FL126042
EST:     ATGGACATGGGCCCGTGCCCGAAGCTGCACTCGCTGCAACTGCGCAAAGA                         ATATGAAGAAGCCAAAGCCAAAGGTACTGATAACTATGACCGTGAATTGGA
genomic: ATGGACATGGGCCCGTGCCCGAAGCTGCACTCGCTGCAACTGCGCAAAGAgtatccttcc ... gtgtcaatagATATGAAGAAGCCAAAGCCAAAGGTACTGATAACTATGACCGTGAATTGGA
EST: gi|211342896|gb|FL126045.1|FL126045
EST:     ATGGACATGGGCCCGTGCCCGAAGCTGCACTCGCTGCAACTGCGCAAAGA                         ATATGAAGAAGCCAAAGCCAAAGGTACTGATAACTATGACCGTGAATTGGA
genomic: ATGGACATGGGCCCGTGCCCGAAGCTGCACTCGCTGCAACTGCGCAAAGAgtatccttcc ... gtgtcaatagATATGAAGAAGCCAAAGCCAAAGGTACTGATAACTATGACCGTGAATTGGA
EST: gi|211340507|gb|FL126036.1|FL126036
EST:     ATGGACATGGGCCCGTGCCCGAAGCTGCACTCGCTGCAACTGCGCAAAGA                         ATATGAAGAAGCCAAAGCCAAAGGTATTGATAACTATGACCGTGAATTGGA
genomic: ATGGACATGGGCCCGTGCCCGAAGCTGCACTCGCTGCAACTGCGCAAAGAgtatccttcc ... gtgtcaatagATATGAAGAAGCCAAAGCCAAAGGTACTGATAACTATGACCGTGAATTGGA
EST: gi|211340510|gb|FL126039.1|FL126039
EST:     ATGGACATGGGCCCGTGCCCGAAGCTGCACTCGCTGCAACTGCGCAAAGA                         ATATGAAGAAGCCAAAGCCAAAGGTACTGATAACTATGACCGTGAATTG
genomic: ATGGACATGGGCCCGTGCCCGAAGCTGCACTCGCTGCAACTGCGCAAAGAgtatccttcc ... gtgtcaatagATATGAAGAAGCCAAAGCCAAAGGTACTGATAACTATGACCGTGAATTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgttggcaattggttgaaattacccagttctatgtcttcctgagtgtgtcaatagATATGAAGAAGCCAAAGCCAAAGGTACTGATAACTATGACCGTGAATTGGAAGAAACCATTGAAAGACTAATTGTTGAGTGTGAAAGGAAGATTCAGAGA
                                    ttcctgagt  putative branch site 
             ttgaaatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttggcttacacccccacccttattacaattcttgtcttaattgtatgttggcaattggttgaaattacccagttctatgtcttcctgagtgtgtcaatagATATGAAGAAGCCAAAGCCAAAGGTACTGATAACTATGACCGTGAATTGGAAGAAACCATTGAAAGACTAATTGTTGAGTGTGAAAGGAAGATTCAGAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - caccccc
- - - - - - - - - - - - - -attcttg
- - - - - - - - - - - - - - - - - - - - - - -tgttggc
- - - - - - - - - - - - - - - - - - - - - - - - - - - ttggttg