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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTTTCCACCCGAACATCAACAGCAACGGCAGCATTTGCCTTGACATTCTTAAGGAACAGTGGAGTCCTGCTTTAACTATCTCAAAGgtaaattgtctacattgtttatattgtgagttctggctgcactctgatccacctgaatcctccgaggttttgaggccttacttttggctccaccccaaca...

Basic information

species Zea mays
transcript GRMZM2G102471_T04
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G102471_T04 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os04g57220.1 (Oryza sativa), 5'ss of exon 4
-------------GTTTTCCACCCGAACATCAACAGCAACGGCAGCATTTGCCTTGACATTCTTAAGGAACAGTGGAGTCCTGCTTTAACTATCTCAAAGgtaaattgtctacattgtttatattgtgagttctggctgcactctgatccacctgaatcctccgaggttttgaggccttacttttggctccaccccaaca
             ||||||||||||||||| || ||||| |||||||||||||| ||||| || ||||||||||||||||||||  | || || |||||||||| || ||  |||    |   ||     || ||||    || |||  |||||||       ||  | |     | ||| || |  |            
TTTCCGCACCAAGGTTTTCCACCCGAACATTAATAGCAATGGCAGCATTTGCCTCGACATCCTCAAGGAACAGTGGAGTCCTGCACTTACCATATCAAAGgtaa-ttatcagcatgacctgatttcaacattttggcccttctgtga--cacctga------tgaattgtgttatcattaattctaacag----------
















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|71433551|gb|DR814601.1|DR814601
EST:     GCCTTGACATTTTTAAGGAACAGTGGAGTCCTGCTTTAACTATCTCAAAG                         GTTCTCCTGTCAATCTGCTCACTGCTCACGGACCCAAACCCTGATGATCCT
genomic: GCCTTGACATTCTTAAGGAACAGTGGAGTCCTGCTTTAACTATCTCAAAGgtaaattgtc ... gtattaacagGTTCTCCTGTCAATCTGCTCACTGCTCACGGACCCAAACCCTGATGATCCT
EST: gi|30591512|gb|CD052410.1|CD052410
EST:     GCCTTGACATTCTTAAGGAACAGTGGAGCCCTGCTTTAACTATCTCAAAG                         GTTCTCCTGTCAATCTGCTCACTGCTCACGGACCCAAACCCTGATGATCCT
genomic: GCCTTGACATTCTTAAGGAACAGTGGAGTCCTGCTTTAACTATCTCAAAGgtaaattgtc ... gtattaacagGTTCTCCTGTCAATCTGCTCACTGCTCACGGACCCAAACCCTGATGATCCT
EST: gi|9732895|gb|BE511647.1|BE511647
EST:     GCCTTGACATTCTTAAGGAACAGTGGAGTCCTGCTTTAACTATCTCAAAG                         GTTCTCCTGTCAATCTGCTCACTGCTCACGGACCCAAACCCTGATGATCCT
genomic: GCCTTGACATTCTTAAGGAACAGTGGAGTCCTGCTTTAACTATCTCAAAGgtaaattgtc ... gtattaacagGTTCTCCTGTCAATCTGCTCACTGCTCACGGACCCAAACCCTGATGATCCT
EST: gi|32912665|gb|CF017477.1|CF017477
EST:     GCCTTGACATTCTTAAGGAACAGTGGAGCCCTGCTTTAACTATCTCAAAG                         GTTCTCCTGTCAATCTGCTCACTGCTCACGGACCCAAACCCTGATGATCCT
genomic: GCCTTGACATTCTTAAGGAACAGTGGAGTCCTGCTTTAACTATCTCAAAGgtaaattgtc ... gtattaacagGTTCTCCTGTCAATCTGCTCACTGCTCACGGACCCAAACCCTGATGATCCT
EST: gi|33098051|gb|CF058011.1|CF058011
EST:     GCCTTGACATTCTTAAGGAACAGTGGAGCCCTGCTTTAACTATCTCAAAG                         GTTCTCCTGTCAATCTGCTCACTGCTCACGGACCCAAACCCTGATGATCCT
genomic: GCCTTGACATTCTTAAGGAACAGTGGAGTCCTGCTTTAACTATCTCAAAGgtaaattgtc ... gtattaacagGTTCTCCTGTCAATCTGCTCACTGCTCACGGACCCAAACCCTGATGATCCT
EST: gi|13388305|gb|BG462264.1|BG462264
EST:     CCTTGACATTCTTAAGGAACAGTGGAGTCCTGCGTTTAACTATCTCAAAG                         GTTCTCCTGTCAATCTGCTCACTGCTCACGGACCCAAACCCTGATGATCCT
genomic: CCTTGACATTCTTAAGGAACAGTGGAGTCCTGC-TTTAACTATCTCAAAGgtaaattgtc ... gtattaacagGTTCTCCTGTCAATCTGCTCACTGCTCACGGACCCAAACCCTGATGATCCT
EST: gi|76012488|gb|DT939658.1|DT939658
EST:     GCCTTGACATTCTTAAGGAACAGTGGAGTCCTGCTTTAACTATCTCAAAG                         GTTCTCCTGTCAATCTGCTCACTGCTCACGGACCCAAACCCTGATGATCCT
genomic: GCCTTGACATTCTTAAGGAACAGTGGAGTCCTGCTTTAACTATCTCAAAGgtaaattgtc ... gtattaacagGTTCTCCTGTCAATCTGCTCACTGCTCACGGACCCAAACCCTGATGATCCT
EST: gi|166453733|gb|EG146319.1|EG146319
EST:     CCTGCTTTAACTATCTCAAAG                         GTTCTCCTGTCAATCTGCTCACTGCTCACGGACCCAAACCCTGATGATCCT
genomic: CCTGCTTTAACTATCTCAAAGgtaaattgtc ... gtattaacagGTTCTCCTGTCAATCTGCTCACTGCTCACGGACCCAAACCCTGATGATCCT
EST: gi|12968754|gb|BG265700.1|BG265700
EST:     GCCTTGACATTCTTAAGGAACAGTGGAGCCCTGCTTTAACTATCTCAAAG                         GTTCTCCTGTCAATCTGCTCACTGCTCACGGACCCAAGCCCTGATGATCCT
genomic: GCCTTGACATTCTTAAGGAACAGTGGAGTCCTGCTTTAACTATCTCAAAGgtaaattgtc ... gtattaacagGTTCTCCTGTCAATCTGCTCACTGCTCACGGACCCAAACCCTGATGATCCT
EST: gi|31352077|gb|CD436434.1|CD436434
EST:     GCCTTGACATTCTTAAGGAACAGTGGAGCCCTGCTTTAACTATCTCAAAG                         GTTCTCCTGTCAATCTGCTCACTGCTCACGGACCCAAACCCTGATGATCCT
genomic: GCCTTGACATTCTTAAGGAACAGTGGAGTCCTGCTTTAACTATCTCAAAGgtaaattgtc ... gtattaacagGTTCTCCTGTCAATCTGCTCACTGCTCACGGACCCAAACCCTGATGATCCT
EST: gi|30306852|gb|CD001525.1|CD001525
EST:     GCCTTGACATTCTTAAGGAACAGTGGAGTCCTGCTTTAACTATCTCAAAG                         GTTCTCCTGTCAATCTGCTCACTGCTCACGGACCCAAACCCTGATGATCCT
genomic: GCCTTGACATTCTTAAGGAACAGTGGAGTCCTGCTTTAACTATCTCAAAGgtaaattgtc ... gtattaacagGTTCTCCTGTCAATCTGCTCACTGCTCACGGACCCAAACCCTGATGATCCT
EST: gi|31406007|gb|CD484739.1|CD484739
EST:     GTGGAGTCCTGCTTTAACTATCTCAAAG                         GTTCTCCTGTCAATCTGCTCACTGCTCACGGACCCAAACCCTGATGATCCT
genomic: GTGGAGTCCTGCTTTAACTATCTCAAAGgtaaattgtc ... gtattaacagGTTCTCCTGTCAATCTGCTCACTGCTCACGGACCCAAACCCTGATGATCCT
EST: gi|78027527|gb|DV495914.1|DV495914
EST:     GCCTTGACATTCTTAAGGAACAGTGGAGTCCTGCTTTAACTATCTCAAAG                         GTTCTCCTGTCAATCTGCTCACTGCTCACGGACCCAAACCCTGATGATCCT
genomic: GCCTTGACATTCTTAAGGAACAGTGGAGTCCTGCTTTAACTATCTCAAAGgtaaattgtc ... gtattaacagGTTCTCCTGTCAATCTGCTCACTGCTCACGGACCCAAACCCTGATGATCCT
EST: gi|32866835|gb|CF006517.1|CF006517
EST:     TCTTAAGGAACAGTGGAGCCCTGCTTTAACTATCTCAAAG                         GTTCTCCTGTCAATCTGCTCACTGCTCACGGACCCAAACCCTGATGATCCT
genomic: TCTTAAGGAACAGTGGAGTCCTGCTTTAACTATCTCAAAGgtaaattgtc ... gtattaacagGTTCTCCTGTCAATCTGCTCACTGCTCACGGACCCAAACCCTGATGATCCT
EST: gi|78023363|gb|DV491750.1|DV491750
EST:     GCCTTGACGTTCTTAAGGAACAGTGGAGCCCTGCTTTAACTATCTCAAAG                         GTTCTCCTGTCAATCTGCTCACTGCTCACGGACCCAAACCCTGATGATCCT
genomic: GCCTTGACATTCTTAAGGAACAGTGGAGTCCTGCTTTAACTATCTCAAAGgtaaattgtc ... gtattaacagGTTCTCCTGTCAATCTGCTCACTGCTCACGGACCCAAACCCTGATGATCCT
EST: gi|45847235|gb|CN071178.1|CN071178
EST:     GCCTTGACATTCTTAAGGAACAGTGGAGTCCTGCTTTAACTATCTCAAAG                         GTTCTCCTGTCAATCTGCTCACTGCTCACGGACCCAAACCCTGATGATCCT
genomic: GCCTTGACATTCTTAAGGAACAGTGGAGTCCTGCTTTAACTATCTCAAAGgtaaattgtc ... gtattaacagGTTCTCCTGTCAATCTGCTCACTGCTCACGGACCCAAACCCTGATGATCCT
EST: gi|16378742|gb|BI992587.1|BI992587
EST:     GCCTTGACATTCTTAAGGAACAGTGGAGTCCTGCTTTAACTATCTCAAAG                         GTTCTCCTGTCAATCTGCTCACTGCTCACGGACCCAAACCCTGATGATCCT
genomic: GCCTTGACATTCTTAAGGAACAGTGGAGTCCTGCTTTAACTATCTCAAAGgtaaattgtc ... gtattaacagGTTCTCCTGTCAATCTGCTCACTGCTCACGGACCCAAACCCTGATGATCCT
EST: gi|28987117|gb|CB351472.1|CB351472
EST:     GCCTTGACATTCTTAAGGAACAGTGGAGTCCTGCTTTAACTATCTCAAAG                         GTTCTCCTGTCAATCTGCTCACTGCTCACGGACCCAAACCCTGATGATCCT
genomic: GCCTTGACATTCTTAAGGAACAGTGGAGTCCTGCTTTAACTATCTCAAAGgtaaattgtc ... gtattaacagGTTCTCCTGTCAATCTGCTCACTGCTCACGGACCCAAACCCTGATGATCCT
EST: gi|211247150|gb|FL033415.1|FL033415
EST:     GCCTTGACATTCTTAAGGAACAGTGGAGTCCTGCTTTAACTATCTCAAAG                         GTTCTCCTGTCAATCTGCTCACTGYTCACGGACCCAAACCYTGATGATCCT
genomic: GCCTTGACATTCTTAAGGAACAGTGGAGTCCTGCTTTAACTATCTCAAAGgtaaattgtc ... gtattaacagGTTCTCCTGTCAATCTGCTCACTGCTCACGGACCCAAACCCTGATGATCCT
EST: gi|31440868|gb|CD510299.1|CD510299
EST:     GTGGAGTCCTGCTTTAACTATCTCAAAG                         GTTCTCCTGTCAATCTGCTCACTGCTCACGGACCCAAACCCTGATGATCCT
genomic: GTGGAGTCCTGCTTTAACTATCTCAAAGgtaaattgtc ... gtattaacagGTTCTCCTGTCAATCTGCTCACTGCTCACGGACCCAAACCCTGATGATCCT
EST: gi|71433552|gb|DR814602.1|DR814602
EST:     GCCTTGACATTCTTAAGGAACAGTGGAGTCCTGCTTTAACTATCTCAAAG                         GTTCTCCTGTCAATCTGCTCACTGCTCACGGACCCAAACCCTGATGATCCT
genomic: GCCTTGACATTCTTAAGGAACAGTGGAGTCCTGCTTTAACTATCTCAAAGgtaaattgtc ... gtattaacagGTTCTCCTGTCAATCTGCTCACTGCTCACGGACCCAAACCCTGATGATCCT
EST: gi|31406006|gb|CD484738.1|CD484738
EST:     GTGGAGTCCTGCTTTAACTATCTCAAAG                         GTTCTCCTGTCAATCTGCTCACTGCTCACGGACCCAAACCCTGATGATCCT
genomic: GTGGAGTCCTGCTTTAACTATCTCAAAGgtaaattgtc ... gtattaacagGTTCTCCTGTCAATCTGCTCACTGCTCACGGACCCAAACCCTGATGATCCT
EST: gi|18173846|gb|BM349234.1|BM349234
EST:     AGTCCTGCTTTAACTATCTCAAAG                         GTTCTCCGGTCAATCTGCTCACTGCTCACGGACCCAAACCCTGATGATCCT
genomic: AGTCCTGCTTTAACTATCTCAAAGgtaaattgtc ... gtattaacagGTTCTCCTGTCAATCTGCTCACTGCTCACGGACCCAAACCCTGATGATCCT
EST: gi|213171042|gb|FM187361.1|FM187361
EST:     GCCTTGACATTCTTAAGGAACAGTGGAGCCCTGCTTTAACTATCTCAAAG                         GTTCTCCTGTCAATCTGCTCACTGCTCACGGACCCAAACCCTGATGATCCT
genomic: GCCTTGACATTCTTAAGGAACAGTGGAGTCCTGCTTTAACTATCTCAAAGgtaaattgtc ... gtattaacagGTTCTCCTGTCAATCTGCTCACTGCTCACGGACCCAAACCCTGATGATCCT
EST: gi|60354791|gb|DN221764.1|DN221764
EST:     GCCTTGACATTCTTAAGGAACAGTGGAGTCCTGCTTTAACTATCTCAAAG                         GTTCTCCTGTCAATCTGCTCACTGCTCACGGACCCAAACCCTGATGATCCT
genomic: GCCTTGACATTCTTAAGGAACAGTGGAGTCCTGCTTTAACTATCTCAAAGgtaaattgtc ... gtattaacagGTTCTCCTGTCAATCTGCTCACTGCTCACGGACCCAAACCCTGATGATCCT
EST: gi|166533862|gb|EG144300.1|EG144300
EST:     CTTTAACTATCTCAAAG                         GTTCTCCTGTCAATCTGCTCACTGCTCACGGACCCAAACCCTGATGATCCT
genomic: CTTTAACTATCTCAAAGgtaaattgtc ... gtattaacagGTTCTCCTGTCAATCTGCTCACTGCTCACGGACCCAAACCCTGATGATCCT
EST: gi|32945100|gb|CF049919.1|CF049919
EST:     CCTGCTTTAACTATCTCAAAG                         GTTCTCCTGTCAATCTGCTCACTGCTCACGGACCCAAACCCTGATGATCCT
genomic: CCTGCTTTAACTATCTCAAAGgtaaattgtc ... gtattaacagGTTCTCCTGTCAATCTGCTCACTGCTCACGGACCCAAACCCTGATGATCCT
EST: gi|16921434|gb|BM075147.1|BM075147
EST:     GTGGAGTCCTGCTTTAACTATCTCAAAG                         GTTCTCCTGTCAATCTGCTCACTGCTCACGGACCCAAACCCTGATGATCCT
genomic: GTGGAGTCCTGCTTTAACTATCTCAAAGgtaaattgtc ... gtattaacagGTTCTCCTGTCAATCTGCTCACTGCTCACGGACCCAAACCCTGATGATCCT
EST: gi|26557459|gb|CA829694.1|CA829694
EST:     GCCTTGACATTTTTAAGGAACAGTGGAGTCCTGCTTTAACTATCTCAAAG                         GTTCTCCTGTCAATCTGCTCACTGCTCACGGACCCAAACCCTGATGATCCT
genomic: GCCTTGACATTCTTAAGGAACAGTGGAGTCCTGCTTTAACTATCTCAAAGgtaaattgtc ... gtattaacagGTTCTCCTGTCAATCTGCTCACTGCTCACGGACCCAAACCCTGATGATCCT
EST: gi|29167828|gb|CB411088.1|CB411088
EST:     GCCCTGACATTCTTAAGGAACAGCGGAGTCCTGCTTTAACTATCTCAAAG                         GTTCTCCTGTCAATCTGCTCACTGCTCACGGACCCAAACCCTGATGATCCT
genomic: GCCTTGACATTCTTAAGGAACAGTGGAGTCCTGCTTTAACTATCTCAAAGgtaaattgtc ... gtattaacagGTTCTCCTGTCAATCTGCTCACTGCTCACGGACCCAAACCCTGATGATCCT
EST: gi|18167063|gb|BM336902.1|BM336902
EST:     GCCTTGACATTCTTAAGGAACAGTGGAGTCCTGCTTTAACTATCTCAAAG                         GTTCTCCTGTCAATCTGCTCACTGCTCACGGACCCAAACCCTGATGATCCT
genomic: GCCTTGACATTCTTAAGGAACAGTGGAGTCCTGCTTTAACTATCTCAAAGgtaaattgtc ... gtattaacagGTTCTCCTGTCAATCTGCTCACTGCTCACGGACCCAAACCCTGATGATCCT
EST: gi|17931291|gb|BM268251.1|BM268251
EST:     GTGGAGTCCTGCTTTAACTATCTCAAAG                         GTTCTCCTGTCAATCTGCTCACTGCTCACGGACCCAAACCCTGATGATCCT
genomic: GTGGAGTCCTGCTTTAACTATCTCAAAGgtaaattgtc ... gtattaacagGTTCTCCTGTCAATCTGCTCACTGCTCACGGACCCAAACCCTGATGATCCT
EST: gi|9961491|gb|BE644279.1|BE644279
EST:     GCCTTGACATTCTTAAGGAACAGTGGAGTCCTGCTTTAACTATCTCAAAG                         GTTCTCCTGTCAATCTGCTCACTGCTCACGGACCCAAACCCTGATGATCCT
genomic: GCCTTGACATTCTTAAGGAACAGTGGAGTCCTGCTTTAACTATCTCAAAGgtaaattgtc ... gtattaacagGTTCTCCTGTCAATCTGCTCACTGCTCACGGACCCAAACCCTGATGATCCT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTTTCCACCCGAACATCAACAGCAACGGCAGCATTTGCCTTGACATTCTTAAGGAACAGTGGAGTCCTGCTTTAACTATCTCAAAGgtaaattgtctacattgtttatattgtgagttctggctgcactctgatccacctgaatcctccgaggttttgaggccttacttttggctccaccccaaca

- - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccacccc