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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAGTACTACGTTTGGTGCATCATCTTCATGCCAACGGAGTACCAATGGCTGTTGCGACAGGgtaagtttctttacacctgatgatccatctggcctttccctcaacggtcaatgcccatcacctttcatgaattatagaacactactaatgttttgttgctgacccactgtgtcttacag

Basic information

species Zea mays
transcript GRMZM2G102231_T02
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G102231_T02 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os08g14580.1 (Oryza sativa), 5'ss of exon 3
GAGTACTACGTTTGGTGCATCATCTTCATGCCAACGGAGTACCAATGGCTGTTGCGACAGGgtaagt--ttctttacacctgatg-atccatctg-gcctttccctcaacggtc--aatgcccatcacctttcatgaattatagaacactactaatgttttgttgctgacccactgtgtcttacag
|||| ||||||||| | |||||||| ||||| || |||||||||||||||||||| ||||||||| |  | | | |   |  ||  ||   |||| | |||   | | | | ||   |||  |        |    ||||| |    |  ||   || || |||  |     | |||| ||| |||
GAGTGCTACGTTTGATCCATCATCTCCATGCAAATGGAGTACCAATGGCTGTTGCAACAGGgtaatttatccatgatgaccaatatattgctctgagtcttgtgcactatgttcctgatgaaccctgtgcctttcaaattaga----atcacgtttgattcgttctttcttta-tgtggctt-cag
















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|50338090|gb|CO533216.1|CO533216
EST:     TTGGTGCATCATCTTCATGCCAACGGAGTACCAATGGCTGTTGCGACAGG                         ATCCCATAAACGCCATTTTGCACTGAAGACCCAGAATCACCAGGAAATGTT
genomic: TTGGTGCATCATCTTCATGCCAACGGAGTACCAATGGCTGTTGCGACAGGgtaagtttct ... tgtcttacagATCCCATAAACGCCATTTTGCACTGAAGACCCAGAATCACCAGGAAATGTT
EST: gi|211004136|gb|FL435012.1|FL435012
EST:     TTGGTGCATCATCTTCATGCCAACGGAGTACCAATGGCTGTTGCGACAGG                         ATCCCATAAACGCCATTTTGCACTGAAGACCCAGAATCACCAGGAAATGTT
genomic: TTGGTGCATCATCTTCATGCCAACGGAGTACCAATGGCTGTTGCGACAGGgtaagtttct ... tgtcttacagATCCCATAAACGCCATTTTGCACTGAAGACCCAGAATCACCAGGAAATGTT
EST: gi|148994252|gb|EE034006.2|EE034006
EST:     TTGGTGCATCATCTTCATGCCAACGGAGTACCAATGGCTGTTGCGACAGG                         ATCCCATAAACGCCATTTTGCACTGAAGACCCAGAATCACCAGGAAATGTT
genomic: TTGGTGCATCATCTTCATGCCAACGGAGTACCAATGGCTGTTGCGACAGGgtaagtttct ... tgtcttacagATCCCATAAACGCCATTTTGCACTGAAGACCCAGAATCACCAGGAAATGTT
EST: gi|211016904|gb|FL048021.1|FL048021
EST:     TTGGTGCATCATCTTCATGCCAACGGAGTACCAATGGCTGTTGCGACAGG                         ATCCCATAAACGCCATTTTGCACTGAAGACCCAGAATCACCAGGAAATGTT
genomic: TTGGTGCATCATCTTCATGCCAACGGAGTACCAATGGCTGTTGCGACAGGgtaagtttct ... tgtcttacagATCCCATAAACGCCATTTTGCACTGAAGACCCAGAATCACCAGGAAATGTT
EST: gi|149013687|gb|EE043137.2|EE043137
EST:     TTGGTGCATCATCTTCATGCCAACGGAGTACCAATGGCTGTTGCGACAGG                         ATCCCATAAACGCCATTTTGCACTGAAGACCCAGAATCACCAGGAAATGTT
genomic: TTGGTGCATCATCTTCATGCCAACGGAGTACCAATGGCTGTTGCGACAGGgtaagtttct ... tgtcttacagATCCCATAAACGCCATTTTGCACTGAAGACCCAGAATCACCAGGAAATGTT
EST: gi|211019679|gb|FL048024.1|FL048024
EST:     TTGGTGCATCATCTTCATGCCAACGGAGTACCAATGGCTGTTGCGACAGG                         ATCCCATAAACGCCATTTTGCACTGAAGACCCAGAATCACCAGGAAATGTT
genomic: TTGGTGCATCATCTTCATGCCAACGGAGTACCAATGGCTGTTGCGACAGGgtaagtttct ... tgtcttacagATCCCATAAACGCCATTTTGCACTGAAGACCCAGAATCACCAGGAAATGTT
EST: gi|148954135|gb|EC899536.2|EC899536
EST:     TGGTGCATCATTCTTCATGCCAACGGAGTAACAATGACTGTTGCGACAGG                         ATCCCATAAACGCCATTTT
genomic: TGGTGCATCAT-CTTCATGCCAACGGAGTACCAATGGCTGTTGCGACAGGgtaagtttct ... tgtcttacagATCCCATAAACGCCATTTT
EST: gi|14245028|gb|BG842966.2|BG842966
EST:     TTGGTGCATCATCTTCATGCCAACGGAGTACCAATGGCTGTTGCGACAGG                         ATCCCATAAACGCCATTTTGCACTGAAGACCCAGAATCACCAGGAAATGTT
genomic: TTGGTGCATCATCTTCATGCCAACGGAGTACCAATGGCTGTTGCGACAGGgtaagtttct ... tgtcttacagATCCCATAAACGCCATTTTGCACTGAAGACCCAGAATCACCAGGAAATGTT
EST: gi|50325634|gb|CO520760.1|CO520760
EST:     TTGGTGCATCATCTTCATGCCAACGGAGTACCAATGGCTGTTGCGACAGG                         ATCCCATAAACGCCATTTTGCACTGAAGACCCAGAATCACCAGGAAATGTT
genomic: TTGGTGCATCATCTTCATGCCAACGGAGTACCAATGGCTGTTGCGACAGGgtaagtttct ... tgtcttacagATCCCATAAACGCCATTTTGCACTGAAGACCCAGAATCACCAGGAAATGTT
EST: gi|71773066|gb|DR970984.1|DR970984
EST:     TTGGTGCATCATCTTCATGCCAACGGAGTACCAATGGCTGTTGCGACAGG                         ATCCCATAAACGCCATTTTGCACTCAAGACCCAGAATCACCAGGAAATGTT
genomic: TTGGTGCATCATCTTCATGCCAACGGAGTACCAATGGCTGTTGCGACAGGgtaagtttct ... tgtcttacagATCCCATAAACGCCATTTTGCACTGAAGACCCAGAATCACCAGGAAATGTT
EST: gi|211016905|gb|FL048022.1|FL048022
EST:     TTGGTGCATCATCTTCATGCCAACGGAGTACCAATGGCTGTTGCGACAGG                         ATCCCATAAACGCCA
genomic: TTGGTGCATCATCTTCATGCCAACGGAGTACCAATGGCTGTTGCGACAGGgtaagtttct ... tgtcttacagATCCCATAAACGCCA
EST: gi|50338089|gb|CO533215.1|CO533215
EST:     TTGGTGCATCATCTTCATGCCAACGGAGTACCAATGGCTGTTGCGACAGG                         ATCCCATAAACGCCATTTTGCACTGAAGACCCAGAATCACCAGGAAATGTT
genomic: TTGGTGCATCATCTTCATGCCAACGGAGTACCAATGGCTGTTGCGACAGGgtaagtttct ... tgtcttacagATCCCATAAACGCCATTTTGCACTGAAGACCCAGAATCACCAGGAAATGTT
EST: gi|44901216|gb|CK827761.1|CK827761
EST:     TTGGTGCATCATCTTCATGCCAACGGAGTACCAATGGCTGTCGCGACAGG                         ATCCCATAAACGCCATTTTGCACTGAAGACCCAGAATCACCAGGAAATGTT
genomic: TTGGTGCATCATCTTCATGCCAACGGAGTACCAATGGCTGTTGCGACAGGgtaagtttct ... tgtcttacagATCCCATAAACGCCATTTTGCACTGAAGACCCAGAATCACCAGGAAATGTT
EST: gi|211019681|gb|FL048026.1|FL048026
EST:     TTGGTGCATCATCTTCATGCCCACGGAGTACCAATGGCTGTTGCGACAGG                         ATCCCATAAACGCCATTTTGCACTGAAGACCCAGAATCACCAGGAA-TGGT
genomic: TTGGTGCATCATCTTCATGCCAACGGAGTACCAATGGCTGTTGCGACAGGgtaagtttct ... tgtcttacagATCCCATAAACGCCATTTTGCACTGAAGACCCAGAATCACCAGGAAATGTT
EST: gi|211016902|gb|FL048019.1|FL048019
EST:     TTGGTGCATCATCTTCATGCCAACGGAGTACCAATGGCTGTTGCGACAGG                         ATCCCATAAACGCCATTTTGCACTGAAGACCCAGAATCACCAGGAAATGTT
genomic: TTGGTGCATCATCTTCATGCCAACGGAGTACCAATGGCTGTTGCGACAGGgtaagtttct ... tgtcttacagATCCCATAAACGCCATTTTGCACTGAAGACCCAGAATCACCAGGAAATGTT
EST: gi|60346823|gb|DN213796.1|DN213796
EST:     TTGGTGCATCATCTTCATGCCAACGGAGTACCAATGGCTGTTGCGACAGG                         ATCCCATAAACGCCATTTTGCACTGAAGACCCAGAATCACCAGGAAATGTT
genomic: TTGGTGCATCATCTTCATGCCAACGGAGTACCAATGGCTGTTGCGACAGGgtaagtttct ... tgtcttacagATCCCATAAACGCCATTTTGCACTGAAGACCCAGAATCACCAGGAAATGTT
EST: gi|5649953|gb|AI920313.1|AI920313
EST:     ATCTT-ATGCCAA-GGAG-ACCAATGGCTGTTGCGACAGG                         ATCCCATAAACGCCATTTTGCACTGAAGACCCAGAATCACCAGGAAATGTT
genomic: ATCTTCATGCCAACGGAGTACCAATGGCTGTTGCGACAGGgtaagtttct ... tgtcttacagATCCCATAAACGCCATTTTGCACTGAAGACCCAGAATCACCAGGAAATGTT
EST: gi|149013686|gb|EE043136.2|EE043136
EST:     TTGGTGCATCATCTTCATGCCAACGGAGTACCAATGGCTGTTGCGACAGG                         ATCCCATAAACGCCATTTTGCACTGAAGACCCAGAATCACCAGGAAATGTT
genomic: TTGGTGCATCATCTTCATGCCAACGGAGTACCAATGGCTGTTGCGACAGGgtaagtttct ... tgtcttacagATCCCATAAACGCCATTTTGCACTGAAGACCCAGAATCACCAGGAAATGTT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAGTACTACGTTTGGTGCATCATCTTCATGCCAACGGAGTACCAATGGCTGTTGCGACAGGgtaagtttctttacacctgatgatccatctggcctttccctcaacggtcaatgcccatcacctttcatgaattatagaacactactaatgttttgttgctgacccactgtgtcttacag

- - - - - - - - - - - - - - - - - - - - - - -  GCTGTT