Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGTGTTGAGAAGCTGGTAACCTCAAAGATGATGCTGGAAGGGTCAAACCGGAGGATCCATTCAGTGCACCGGCACTCTGGCTTGgtaatgcctttacaagtgactcaaagttaatagtggttttcatgcaaaatcatgatgttgatgaataaataaaatagcaggatcgaaattctgctttggt...

Basic information

species Zea mays
transcript GRMZM2G008623_T01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G008623_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os01g59600.1 (Oryza sativa), 5'ss of exon 4
GGTGTTGAGAAGCTGGTAACCTCAAAGATGATGCTGGAAGGGTCAAACCGGAGGATCCATTCAGTGCACCGGCACTCTGGCTTGgtaatgcctt---------tacaagtgactcaaagttaatagtggttttcatgcaaaatcatgatg-ttgatgaataaataaaatagcaggatcgaaattctgctttggt
||||| |||||||| ||||| || |||||||||||||| || || ||  |||||||||||||||||||| ||||||||||||||||||   |||         ||||     |   || |  ||   | |||   || ||||  |  |   ||||||||  ||||||  |  |||||     || |        
GGTGTGGAGAAGCTAGTAACTTCGAAGATGATGCTGGAGGGATCTAATAGGAGGATCCATTCAGTGCACTGGCACTCTGGCTTGgtaacatcttgcttccctgtacatagatcctcaaatgtattacgatttcagtgtaaaaaaagtacaattgatgaa-gaataaagca--aggatgttgtttata-------
















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|22819364|gb|BU499454.1|BU499454
EST:     TGGAAGGGTCAAACCGGAGGATCCATTCAGTGCACCGGCACTCTGGCTTG                         GCTGTTGCTGGTTTAGCAGCAGATGGCAGGCAAATTGTTTCAAGGACGAAG
genomic: TGGAAGGGTCAAACCGGAGGATCCATTCAGTGCACCGGCACTCTGGCTTGgtaatgcctt ... tcatttgcagGCTGTTGCTGGTTTAGCAGCAGATGGCAGGCAAATTGTTTCAAGGACGAAG
EST: gi|91049728|gb|EB160146.1|EB160146
EST:     TGGAAGGGTCAAACCGGAGGATCCATTCAGTGCACCGGCACTCTGGCTTG                         GCTGTTGCTGGTTTAGCAGCAGATGGCAGGCAAATTGTTTCAAGGACGAAG
genomic: TGGAAGGGTCAAACCGGAGGATCCATTCAGTGCACCGGCACTCTGGCTTGgtaatgcctt ... tcatttgcagGCTGTTGCTGGTTTAGCAGCAGATGGCAGGCAAATTGTTTCAAGGACGAAG
EST: gi|211461819|gb|FL074147.1|FL074147
EST:     TGGAAGGGTCAAACCGGAGGATCCATTCAGTGCACCGGCACTCTGGCTTG                         GCTGTTGCTGGT
genomic: TGGAAGGGTCAAACCGGAGGATCCATTCAGTGCACCGGCACTCTGGCTTGgtaatgcctt ... tcatttgcagGCTGTTGCTGGT
EST: gi|93284362|gb|EB676626.1|EB676626
EST:     TGGAAGGGTCAAACCGGAGGATCCATTCAGTGCACCGGCACTCTGGCTTG                         GCTGTTGCTGGT
genomic: TGGAAGGGTCAAACCGGAGGATCCATTCAGTGCACCGGCACTCTGGCTTGgtaatgcctt ... tcatttgcagGCTGTTGCTGGT
EST: gi|22819362|gb|BU499452.1|BU499452
EST:     TGGAAGGGTCAAACCGGAGGATCCATTCAGTGCACCGGCACTCTGGCTTG                         GCTGTTGCTGGTTTAGCAGCAGATGGCAGGCAAATTGTTTCAAGGACGAAG
genomic: TGGAAGGGTCAAACCGGAGGATCCATTCAGTGCACCGGCACTCTGGCTTGgtaatgcctt ... tcatttgcagGCTGTTGCTGGTTTAGCAGCAGATGGCAGGCAAATTGTTTCAAGGACGAAG
EST: gi|78106192|gb|DV524610.1|DV524610
EST:     TGGAAGGGTCAAACCGGAGGATCCATTCAGTGCACCGGCACTCTGGCTTG                         GCTGTTGCTGGTTTAGCAGCAGATGGCAGGCAAATTGTTTCAAGGACGAAG
genomic: TGGAAGGGTCAAACCGGAGGATCCATTCAGTGCACCGGCACTCTGGCTTGgtaatgcctt ... tcatttgcagGCTGTTGCTGGTTTAGCAGCAGATGGCAGGCAAATTGTTTCAAGGACGAAG
EST: gi|211064278|gb|FK983495.1|FK983495
EST:     TGGAAGGTTCAAACCGGAGGATCCATTCAGTGCACCGGCACTCTGGCTTG                         GCTGTTGCTGGTTTAGCAGCAGATGGCAGGCAAATTGTTTCAAGGACAAAG
genomic: TGGAAGGGTCAAACCGGAGGATCCATTCAGTGCACCGGCACTCTGGCTTGgtaatgcctt ... tcatttgcagGCTGTTGCTGGTTTAGCAGCAGATGGCAGGCAAATTGTTTCAAGGACGAAG
EST: gi|211461823|gb|FL074151.1|FL074151
EST:     TGGAAGGGTCAAACCGGAG-ATCCATTCAGTGCACCGGCACTCTGGCTTG                         GCTGTTGCTGGTTTAGCAGCAGATGGCAGGCAA
genomic: TGGAAGGGTCAAACCGGAGGATCCATTCAGTGCACCGGCACTCTGGCTTGgtaatgcctt ... tcatttgcagGCTGTTGCTGGTTTAGCAGCAGATGGCAGGCAA
EST: gi|211064280|gb|FK983497.1|FK983497
EST:     TGGAAGGGTCAAACCGGAGGATCCATTCAGTGCACCGGCACTCTGGCTTG                         GCTGTTGCTGGTTTAGCARCAGATGGCAGGCAAATTGTTTCMAGGACGAAG
genomic: TGGAAGGGTCAAACCGGAGGATCCATTCAGTGCACCGGCACTCTGGCTTGgtaatgcctt ... tcatttgcagGCTGTTGCTGGTTTAGCAGCAGATGGCAGGCAAATTGTTTCAAGGACGAAG
EST: gi|78106193|gb|DV524611.1|DV524611
EST:     TGGAAGGGTCAAACCGGAGGATCCATTCAGTGCACCGGCACTCTGGCTTG                         GCTGTTGCTGGTTTAGCAGCAGATGGCAGGCAAATTGTTTCAAGGACGAAG
genomic: TGGAAGGGTCAAACCGGAGGATCCATTCAGTGCACCGGCACTCTGGCTTGgtaatgcctt ... tcatttgcagGCTGTTGCTGGTTTAGCAGCAGATGGCAGGCAAATTGTTTCAAGGACGAAG
EST: gi|22819430|gb|BU499520.1|BU499520
EST:     TGGAAGGGTCAAACCGGAGGATCCATTCAGTGCACCGGCACTCTGGCTTG                         GCTGTTGCTGGTTTAGCAGCAGATGGCAGGCAAATTGTTTCAAGGACGAAG
genomic: TGGAAGGGTCAAACCGGAGGATCCATTCAGTGCACCGGCACTCTGGCTTGgtaatgcctt ... tcatttgcagGCTGTTGCTGGTTTAGCAGCAGATGGCAGGCAAATTGTTTCAAGGACGAAG
EST: gi|71431491|gb|DR812541.1|DR812541
EST:     TGGAAGGGTCAAACCGGAGGATCCATTCAGTGCACCGGCACTCTGGCTTG                         GCTGTTGCTGGTTTAGCAGCAGATGGCAGGCAAATTGTTTCAAGGACGAAG
genomic: TGGAAGGGTCAAACCGGAGGATCCATTCAGTGCACCGGCACTCTGGCTTGgtaatgcctt ... tcatttgcagGCTGTTGCTGGTTTAGCAGCAGATGGCAGGCAAATTGTTTCAAGGACGAAG
EST: gi|21843523|gb|BQ704104.1|BQ704104
EST:     TGGAAGGGTCAAACCGGAGGATCCATTCAGTGCACCGGCACTCTGGCTTG                         GCTGTTGCTGGTTTAGCAGCAGATGGCAGGCAAATTGTTTCAAGGACGAAG
genomic: TGGAAGGGTCAAACCGGAGGATCCATTCAGTGCACCGGCACTCTGGCTTGgtaatgcctt ... tcatttgcagGCTGTTGCTGGTTTAGCAGCAGATGGCAGGCAAATTGTTTCAAGGACGAAG
EST: gi|148931430|gb|EC874390.2|EC874390
EST:     TGGAAGGGTCAAACCGGAGGATCCATTCAGTGCACCGGCACTCTGGCTTG                         GCTGTTGCTGGTTTAGCAGCAGATGGCAGGCAAATTGTTTCAAGGACGAAG
genomic: TGGAAGGGTCAAACCGGAGGATCCATTCAGTGCACCGGCACTCTGGCTTGgtaatgcctt ... tcatttgcagGCTGTTGCTGGTTTAGCAGCAGATGGCAGGCAAATTGTTTCAAGGACGAAG
EST: gi|211064283|gb|FK983500.1|FK983500
EST:     TGGAAGGGTCAAACCGGAG-ATCCATTCAGTGCACCGGCACTCTGGCTTG                         GCTGTTGCTGGTTTAGCAGCAGATGGCAGGCAAATTGTTTCAAGGACGAAG
genomic: TGGAAGGGTCAAACCGGAGGATCCATTCAGTGCACCGGCACTCTGGCTTGgtaatgcctt ... tcatttgcagGCTGTTGCTGGTTTAGCAGCAGATGGCAGGCAAATTGTTTCAAGGACGAAG
EST: gi|50333782|gb|CO528908.1|CO528908
EST:     TGGAAGGGTCAAACCGGAGGATCCATTCAGTGCACCGGCACTCTGGCTTG                         GCTGTTGCTGGTTTAGCAGCAGATGGCAGGCAAATTGTTTCAAGGACGAAG
genomic: TGGAAGGGTCAAACCGGAGGATCCATTCAGTGCACCGGCACTCTGGCTTGgtaatgcctt ... tcatttgcagGCTGTTGCTGGTTTAGCAGCAGATGGCAGGCAAATTGTTTCAAGGACGAAG
EST: gi|211064277|gb|FK983494.1|FK983494
EST:     TGGAAGGGTCAAACCGGAG-ATCCATTCAGTGCACCGGCACTCTGGCTTG                         GCTGTTGCTGGTTTAGCAGCAGATGGCAGGCAAATTGTTTCAAGGACGA
genomic: TGGAAGGGTCAAACCGGAGGATCCATTCAGTGCACCGGCACTCTGGCTTGgtaatgcctt ... tcatttgcagGCTGTTGCTGGTTTAGCAGCAGATGGCAGGCAAATTGTTTCAAGGACGA
EST: gi|26456267|gb|CA827850.1|CA827850
EST:     TGGAAGGGTCAAACCGGAGGATCCATTCAGTGCACCGGCACTCTGGCTTG                         GCTGTTGCTGGTTTAGCAGCAGATGGCAGGCAAATTGTTTCAAGGACGA
genomic: TGGAAGGGTCAAACCGGAGGATCCATTCAGTGCACCGGCACTCTGGCTTGgtaatgcctt ... tcatttgcagGCTGTTGCTGGTTTAGCAGCAGATGGCAGGCAAATTGTTTCAAGGACGA
EST: gi|148981882|gb|EE027956.2|EE027956
EST:     TGGAAGGGTCAAACCGGAGGATCCATTCAGTGCACCGGCACTCTGGCTTG                         GCTGTTGCTGGTTTAGCAGCAGATGGCAGGCAAATTGTTTCAAGGACGAAG
genomic: TGGAAGGGTCAAACCGGAGGATCCATTCAGTGCACCGGCACTCTGGCTTGgtaatgcctt ... tcatttgcagGCTGTTGCTGGTTTAGCAGCAGATGGCAGGCAAATTGTTTCAAGGACGAAG
EST: gi|211464348|gb|FL074165.1|FL074165
EST:     TGGAAGGGTCAAACCGGAG-ATCCATTCAGTGCACCGGCACTCTGGCTTG                         GCTGTTGCTGGTTTAGCAGCAGATGGCAGGCAAATTGTTTCAAGG
genomic: TGGAAGGGTCAAACCGGAGGATCCATTCAGTGCACCGGCACTCTGGCTTGgtaatgcctt ... tcatttgcagGCTGTTGCTGGTTTAGCAGCAGATGGCAGGCAAATTGTTTCAAGG
EST: gi|5566922|gb|AI881833.1|AI881833
EST:     TGGAAGGGTCAAACCGGAGGATCCATTCAGTGCACCGGCACTCTGGCTTG                         GCTGTTGCTGGTTTAGCAGCAGATGGCAGGCAAATTGTTTCAAGGACGAAG
genomic: TGGAAGGGTCAAACCGGAGGATCCATTCAGTGCACCGGCACTCTGGCTTGgtaatgcctt ... tcatttgcagGCTGTTGCTGGTTTAGCAGCAGATGGCAGGCAAATTGTTTCAAGGACGAAG
EST: gi|149084419|gb|EE173874.2|EE173874
EST:     TGGAAGGGTCAAACCGGAGGATCCATTCAGTGCACCGGCACTCTGGCTTG                         GCTGTTGCTGGTTTAGCAGCAGATGGCAGGCAAATTGTTTCAAGGACGAAG
genomic: TGGAAGGGTCAAACCGGAGGATCCATTCAGTGCACCGGCACTCTGGCTTGgtaatgcctt ... tcatttgcagGCTGTTGCTGGTTTAGCAGCAGATGGCAGGCAAATTGTTTCAAGGACGAAG
EST: gi|148949932|gb|EC895439.2|EC895439
EST:     TGGAAGGGTCAAACCGGAGGATCCATTCAGTGCACCGGCACTCTGGCTTG                         GCTGTTGCTGGTTTAGCAGCAGATGGCAGGCAAATTGTTTCAAGGACGAAG
genomic: TGGAAGGGTCAAACCGGAGGATCCATTCAGTGCACCGGCACTCTGGCTTGgtaatgcctt ... tcatttgcagGCTGTTGCTGGTTTAGCAGCAGATGGCAGGCAAATTGTTTCAAGGACGAAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGTGTTGAGAAGCTGGTAACCTCAAAGATGATGCTGGAAGGGTCAAACCGGAGGATCCATTCAGTGCACCGGCACTCTGGCTTGgtaatgcctttacaagtgactcaaagttaatagtggttttcatgcaaaatcatgatgttgatgaataaataaaatagcaggatcgaaattctgctttggt

- - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT