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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtttttccgcttaacttagagatatgttcactcacccccccttttttatttgttctcatgccatgctgacaatcttagGTATCCAAAAGATTCTGAAAAGCTAATGTTATCGAGACAAACTGGGTTGACAAGAAGTCAG

Basic information

species Zea mays
transcript GRMZM2G011588_T03
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G011588_T03 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os03g47740.2 (Oryza sativa), 3'ss of exon 4
gtaagtttttccgcttaacttagagatatgttcactcacccccccttttttatttgttctcatgccatgctg--acaatcttagGTATCCAAAAGATTCTGAAAAGCTAATGTTATCGAGACAAACTGGGTTGACAAGAAGTCAG
||||||   |    |||   || |   || |||| |  ||     ||| ||  ||||| ||||| |||  ||   |  ||||||||||||||||||||| |||||||| ||| || ||||||||||||| || ||||||||||||
gtaagtgactttcttta---tacactcattttcatttgcctgttttttctt--ttgttgtcatgacattttgttgctttcttagGTATCCAAAAGATTCAGAAAAGCTGATGCTAGCGAGACAAACTGGCTTAACAAGAAGTCAG
















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|211185591|gb|FL318526.1|FL318526
EST:     AATTCAGTCTCGATTCTCCGGGCTTGGCTTTTTGAACACTTCCTTCACCC                         GTATCCAAAAGATTCTGAAAAGCTAATGTTATCGAGACAAACTGGGTTGAC
genomic: AATTCAGTCTCGATTCTCCGGGCTTGGCTTTTTGAACATTTCCTTCACCCgtaagttttt ... acaatcttagGTATCCAAAAGATTCTGAAAAGCTAATGTTATCGAGACAAACTGGGTTGAC
EST: gi|211335472|gb|FL342536.1|FL342536
EST:     AATTCAGTCTCGATTCTCCGGGCTTGGCTTTTTGAACATTTCCTTCACCC                         GTATCCAAAAGATTCTGAAAAGCTAATGTTATCGAGACAAACTGGGTTGAC
genomic: AATTCAGTCTCGATTCTCCGGGCTTGGCTTTTTGAACATTTCCTTCACCCgtaagttttt ... acaatcttagGTATCCAAAAGATTCTGAAAAGCTAATGTTATCGAGACAAACTGGGTTGAC
EST: gi|211093605|gb|FL328986.1|FL328986
EST:     AATTCAGTCTCGATTCTCCGGGCTTGGCTTTTTGAACACTTCCTTCACCC                         GTATCCAAAAGATTCTGAAAAGCTAATGTTATCGAGACAAACTGGGTTGAC
genomic: AATTCAGTCTCGATTCTCCGGGCTTGGCTTTTTGAACATTTCCTTCACCCgtaagttttt ... acaatcttagGTATCCAAAAGATTCTGAAAAGCTAATGTTATCGAGACAAACTGGGTTGAC
EST: gi|91872093|gb|EB402050.1|EB402050
EST:     AATTCAGTCTCGATTCTCCGGGCTTGGCTTTTTGAACATTTCCTTCACCC                         GTATCCAAAAGATTCTGAAAAGCTAATGTTATCGAGACAAACTGGGTTGAC
genomic: AATTCAGTCTCGATTCTCCGGGCTTGGCTTTTTGAACATTTCCTTCACCCgtaagttttt ... acaatcttagGTATCCAAAAGATTCTGAAAAGCTAATGTTATCGAGACAAACTGGGTTGAC
EST: gi|211016399|gb|FL363405.1|FL363405
EST:     AATTCAGTCTCGATTCTCCGGGCTTGGCTTTTTGAACATTTCCTTCACCC                         GTATCCAAAAGATTCTGAAAAGCTAATGTTATCGAGACAAACTGGGTTGAC
genomic: AATTCAGTCTCGATTCTCCGGGCTTGGCTTTTTGAACATTTCCTTCACCCgtaagttttt ... acaatcttagGTATCCAAAAGATTCTGAAAAGCTAATGTTATCGAGACAAACTGGGTTGAC
EST: gi|6626604|gb|AW258136.1|AW258136
EST:     AATTCAGTCTCGATTCTCCGGGCTTGGCTTTTTGAACACTTCCTTCACCC                         GTATCCAAAAGATTCTGAAAAGCTAATGTTATCGAGACAAACTGGGTTGAC
genomic: AATTCAGTCTCGATTCTCCGGGCTTGGCTTTTTGAACATTTCCTTCACCCgtaagttttt ... acaatcttagGTATCCAAAAGATTCTGAAAAGCTAATGTTATCGAGACAAACTGGGTTGAC
EST: gi|91049857|gb|EB160275.1|EB160275
EST:     AATTCAGTCTCGATTCTCCGGGCTTGGCTTTTTGAACATTTCCTTCACCC                         GTATCCAAAAGATTCTGAAAAGCTAATGTTATCGAGACAAACTGGGTTGAC
genomic: AATTCAGTCTCGATTCTCCGGGCTTGGCTTTTTGAACATTTCCTTCACCCgtaagttttt ... acaatcttagGTATCCAAAAGATTCTGAAAAGCTAATGTTATCGAGACAAACTGGGTTGAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgttcactcacccccccttttttatttgttctcatgccatgctgacaatcttagGTATCCAAAAGATTCTGAAAAGCTAATGTTATCGAGACAAACTGGGTTGACAAGAAGTCAG
                                        tgctgac  putative branch site (score: 2)
                  ttttttatttgttct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtttttccgcttaacttagagatatgttcactcacccccccttttttatttgttctcatgccatgctgacaatcttagGTATCCAAAAGATTCTGAAAAGCTAATGTTATCGAGACAAACTGGGTTGACAAGAAGTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT