Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTTGGCTTGCTGGTTTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACTATTATTTCTTAAGgtgaactgcataccattgtgaaatgtcatatcattaacatctatcatcgtactccttggttactgagtattgacacttccatgtcgatcactgcag

Basic information

species Zea mays
transcript GRMZM2G408989_T03
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G408989_T03 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os05g45310.1 (Oryza sativa), 5'ss of exon 5
CTTGGCTTGCTGGTTTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACTATTATTTCTTAAGgtgaactgcataccattgtgaaatgtcatatcattaacatctatcatcgtactccttggttactgagtattgacacttccatgtcgatcactgcag
||||| ||||||||||||| ||||||||||| ||||| |||||||| ||||| ||||||||||||| ||||| ||||  |||| |||  |||| |                |  ||||  |||       ||| ||||| |||||||||| |   |||||
CTTGGATTGCTGGTTTGGTCCAAACAGCTCTTTATGCGGATTTCTTCTACTACTATTTCTTAAGgtaaactggatactgttgtcaaacctcatttg---------------cagactctctgg-------gtactgacaattccatgtcggttgttgcag

upper sequence: GRMZM2G408989_T03 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA08G12570.1 (Glycine max), 5'ss of exon 5
CTTGGCTTGCTGGTTTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACTATTATTTCTTAAGgtgaactgcataccattgtgaaatgtcatatcattaacatctatcatcgtactccttggttactgagtattgacacttccatgtcgatcactgcag
| ||     | ||| | || || |||||| |||||||||||||||| |||||||||||| | |||| |  |   |  |  ||| ||     || |  ||    | |||  || ||   |     |    | |||    | ||   | | |          
CCTGTGCCTCAGGTGTTGTTCAGACAGCTTTGTATGCAGATTTCTTCTACTATTATTTCATCAGgtaatgttattgtc--tgttaaggtcgatcttgtttttgt-tatgctcatataac--aaatgggtaatataaggagttttgttttgcag-------
















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|18169894|gb|BM339734.1|BM339734
EST:     TTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACTATTATTTCTTAAG                         TTGGAAGAACAACGTGAAGCTCGAGTTGCCTGCTTGAGCATGCTTCGTCGT
genomic: TTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACTATTATTTCTTAAGgtgaactgca ... atcactgcagTTGGAAGAACAACGTGAAGCTCGAGTTGCCTGCTTGAGCATGCTTCGTCGT
EST: gi|16920990|gb|BM074929.1|BM074929
EST:     TTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACTATTATTTCTTAAG                         TTGGAAGAACAACGTGAAGCTCGAGTTGCCTGCTTGAGCATGCTTCGTCGT
genomic: TTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACTATTATTTCTTAAGgtgaactgca ... atcactgcagTTGGAAGAACAACGTGAAGCTCGAGTTGCCTGCTTGAGCATGCTTCGTCGT
EST: gi|18165355|gb|BM335194.1|BM335194
EST:     TTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACTATTATTTCTTAAG                         TTGGAAGAACAACGTGAAGCTCGAGTTGCCTGCTTGAGCATGCTTCGTCGT
genomic: TTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACTATTATTTCTTAAGgtgaactgca ... atcactgcagTTGGAAGAACAACGTGAAGCTCGAGTTGCCTGCTTGAGCATGCTTCGTCGT
EST: gi|91871428|gb|EB401415.1|EB401415
EST:     TTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACTATTATTTCTTAAG                         TTGGAAGAACAACGTGAAGCTCGAGTTGCCTGCTTGAGCATGCTTCGTCGT
genomic: TTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACTATTATTTCTTAAGgtgaactgca ... atcactgcagTTGGAAGAACAACGTGAAGCTCGAGTTGCCTGCTTGAGCATGCTTCGTCGT
EST: gi|78023775|gb|DV492162.1|DV492162
EST:     TTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACTATTATTTCTTAAG                         TTGGAAGAACAACGTGAAGCTCGAGTTGCCTGCTTGAGCATGCTTCGTCGT
genomic: TTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACTATTATTTCTTAAGgtgaactgca ... atcactgcagTTGGAAGAACAACGTGAAGCTCGAGTTGCCTGCTTGAGCATGCTTCGTCGT
EST: gi|78023788|gb|DV492175.1|DV492175
EST:     TTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACTATTATTTCTTAAG                         TTGGAAGAACAACGTGAAGCTCGAGTTGCCTGCTTGAGCATGCTTCGTCGT
genomic: TTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACTATTATTTCTTAAGgtgaactgca ... atcactgcagTTGGAAGAACAACGTGAAGCTCGAGTTGCCTGCTTGAGCATGCTTCGTCGT
EST: gi|16922820|gb|BM075812.1|BM075812
EST:     TTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACTATTATTTCTTAAG                         TTGGAAGAACAACGTGAAGCTCGAGTTGCCTGCTTGAGCATGCTTCGTCGT
genomic: TTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACTATTATTTCTTAAGgtgaactgca ... atcactgcagTTGGAAGAACAACGTGAAGCTCGAGTTGCCTGCTTGAGCATGCTTCGTCGT
EST: gi|6022165|gb|AW067093.1|AW067093
EST:     TTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACTATTATTTCTTAAG                         TTGGAAGAACAACGTGAAGCTCGAGTTGCCTGCTTGAGCATGCTTCGTCGT
genomic: TTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACTATTATTTCTTAAGgtgaactgca ... atcactgcagTTGGAAGAACAACGTGAAGCTCGAGTTGCCTGCTTGAGCATGCTTCGTCGT
EST: gi|32835284|gb|CD974962.1|CD974962
EST:     TTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACTATTATTTCTTAAG                         TTGGAAGAACAACGTGAAGCTCGAGTTGCCTGCTTGAGCATGCTTCGTCGT
genomic: TTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACTATTATTTCTTAAGgtgaactgca ... atcactgcagTTGGAAGAACAACGTGAAGCTCGAGTTGCCTGCTTGAGCATGCTTCGTCGT
EST: gi|14245658|gb|BG874240.1|BG874240
EST:     TTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACTATTATTTCTTAAG                         TTGGAAGAACAACGTGAAGCTCGAGTTGCCTGCTTGAGCATGCTTCGTCGT
genomic: TTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACTATTATTTCTTAAGgtgaactgca ... atcactgcagTTGGAAGAACAACGTGAAGCTCGAGTTGCCTGCTTGAGCATGCTTCGTCGT
EST: gi|78080743|gb|DV509155.1|DV509155
EST:     TTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACTATTATTTCTTAAG                         TTGGAAGAACAACGTGAAGCTCGAGTTGCCTGCTTGAGCATGCTTCGTCGT
genomic: TTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACTATTATTTCTTAAGgtgaactgca ... atcactgcagTTGGAAGAACAACGTGAAGCTCGAGTTGCCTGCTTGAGCATGCTTCGTCGT
EST: gi|211107178|gb|FL251311.1|FL251311
EST:     TTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACTATTATTTCTTAAG                         TTGGAAGAACAACGTGAAGCTCGAGTTGCCTGCTTGAACATGCTTCGTCAT
genomic: TTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACTATTATTTCTTAAGgtgaactgca ... atcactgcagTTGGAAGAACAACGTGAAGCTCGAGTTGCCTGCTTGAGCATGCTTCGTCGT
EST: gi|24769505|gb|CA404634.1|CA404634
EST:     TTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACTATTATTTCTTAAG                         TTGGAAGAACAACGTGAAGCTCGAGTTGCCTGCTTGAGCATGCTTCGTCGT
genomic: TTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACTATTATTTCTTAAGgtgaactgca ... atcactgcagTTGGAAGAACAACGTGAAGCTCGAGTTGCCTGCTTGAGCATGCTTCGTCGT
EST: gi|18169973|gb|BM339813.1|BM339813
EST:     TTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACTATTATTTCTTAAG                         TTGGAAGAACAACGTGAAGCTCGAGTTGCCTGCTTGAGCATGCTTCGTCGT
genomic: TTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACTATTATTTCTTAAGgtgaactgca ... atcactgcagTTGGAAGAACAACGTGAAGCTCGAGTTGCCTGCTTGAGCATGCTTCGTCGT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTTGGCTTGCTGGTTTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACTATTATTTCTTAAGgtgaactgcataccattgtgaaatgtcatatcattaacatctatcatcgtactccttggttactgagtattgacacttccatgtcgatcactgcag

- - - - - - - - - - - - CAGCTC
- - - - - - - - - - - - - - - - -  GCAGAT