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'   		11  
 5'  3'   		12  
 5'  3'   		13  
 5'  3'   		14  
 5'  3'   		15  
 5'  3'   		16  
 5'  3'   		17  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtattattaattgtctcccctccctttctatctcttcttcatctacgcatttccaagccttccatctctccgtggactcgctgcaggactaggatcgaaggcattccataactcaaaagttgtttacacctgtagtttgctccatacagGAAAGATCTGAAAATCAATGCACCAGTCAATTAAAGTCCTTGATCGATCAAGTCAGCATGCAGCAGGAGAAGATTGTAGCATTGGAAG

Basic information

species Zea mays
transcript GRMZM2G426275_T04
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G426275_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os02g58590.1 (Oryza sativa), 3'ss of exon 2
gtaagtattattaattgtctcccctccctttctatctcttcttcatctacgcatttccaagccttccatctctccgtggact-cgctgcaggactaggatcgaaggcattccataactcaaaagttgtttacacctgtagtttgctccatacagGAAAGATCTGAAAATCAATGCACCAGTCAATTAAAGTCCTTGATCGATCAAGTCAGCATGCAGCAGGAGAAGATTGTAGCATTGGAAG
                                                  | |    ||| | |           ||  |||  |    |    | | | || ||| | |  |||  |       || | | ||       ||||   ||  |||||| ||| ||||| ||||||||||||||| |    |||||||||||||||||||||   ||||||||||||||||| || |||||||
--------------------------------------------------gaacggtcaaacatgt-gctaaaaagtcaactgtgtcaaacattttgaaacggagggagtatatatttttggt-ctgctcaaactcactaattgca--atttagGAAAAATCCGAAAACCAATGCACCAGTCAACTCCGCTCCTTGATCGATCAAGTCAGCTCTCAGCAGGAGAAGATTGTCGCGTTGGAAG
















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|211529742|gb|FL258568.1|FL258568
EST:     TGCGCCTCTTTGCTACTCAGTCCCATTATGCGGACCGTCTTGCGGAAGCA                         GAAAGATCTGAAAATCAATGCACCAGTCAATTAAAGTCCTTGATCGATCAA
genomic: TGCGCCTCTTTGCTACTCAGTCCCATTATGCGGACCGTCTTGCGGAAGCAgtaagtatta ... ctccatacagGAAAGATCTGAAAATCAATGCACCAGTCAATTAAAGTCCTTGATCGATCAA
EST: gi|148986617|gb|EE030388.2|EE030388
EST:     TGCGCCTCTTTGCTACTCAGTCCCATTATGCGGACCGTCTTGCGGAAGCA                         GAAAGATCTGAAAATCAATGCACCAGTCAATTAAAGTCCTTGATCGATCAA
genomic: TGCGCCTCTTTGCTACTCAGTCCCATTATGCGGACCGTCTTGCGGAAGCAgtaagtatta ... ctccatacagGAAAGATCTGAAAATCAATGCACCAGTCAATTAAAGTCCTTGATCGATCAA
EST: gi|211526749|gb|FL258558.1|FL258558
EST:     TGCGCCTCTTTGCTACTCAGTCCCATTATGCGGACCGTCTTGCGGAACCA                         GAAAGATCTGAAAATCAATGCACCAGTCAATTAAAGTCCTTGATCGATCAA
genomic: TGCGCCTCTTTGCTACTCAGTCCCATTATGCGGACCGTCTTGCGGAAGCAgtaagtatta ... ctccatacagGAAAGATCTGAAAATCAATGCACCAGTCAATTAAAGTCCTTGATCGATCAA
EST: gi|211529739|gb|FL258565.1|FL258565
EST:     TGCGCCTCTTTGCTACTCAGTCCCATTATGCGGACCGTCTTGCGGAAGCA                         GAAAGATCTGAAAATCAATGCACCAGTCAATTAAAGTCCTTGATCGATCAA
genomic: TGCGCCTCTTTGCTACTCAGTCCCATTATGCGGACCGTCTTGCGGAAGCAgtaagtatta ... ctccatacagGAAAGATCTGAAAATCAATGCACCAGTCAATTAAAGTCCTTGATCGATCAA
EST: gi|211526751|gb|FL258560.1|FL258560
EST:     TGCGCCTCTTTGCTACTCAGTCCCATTATGCGGACCGTCTTGCGGAAGCA                         GAAAGATCTGAAAATCAATGCACCAGTCAATTAAAGTCCTTGATCGATCAA
genomic: TGCGCCTCTTTGCTACTCAGTCCCATTATGCGGACCGTCTTGCGGAAGCAgtaagtatta ... ctccatacagGAAAGATCTGAAAATCAATGCACCAGTCAATTAAAGTCCTTGATCGATCAA
EST: gi|211529740|gb|FL258566.1|FL258566
EST:     TGCGCCTCTTTGCTACTCAGTCCCATTATGCGGACCGTCTTGCGGAACCA                         GAAAGATCTGAAAATCAATGCACCAGTCAATTAAAGTCCTTGATCG
genomic: TGCGCCTCTTTGCTACTCAGTCCCATTATGCGGACCGTCTTGCGGAAGCAgtaagtatta ... ctccatacagGAAAGATCTGAAAATCAATGCACCAGTCAATTAAAGTCCTTGATCG
EST: gi|211529737|gb|FL258563.1|FL258563
EST:     TGCGCCTCTTTGCTACTCAGTCCCATTATGCGGACCGTCTTGCGGAAGCA                         GAAAGATCTGAAAATCAATGCACCAGTCAATTAAAGTCCTTGATCGATCAA
genomic: TGCGCCTCTTTGCTACTCAGTCCCATTATGCGGACCGTCTTGCGGAAGCAgtaagtatta ... ctccatacagGAAAGATCTGAAAATCAATGCACCAGTCAATTAAAGTCCTTGATCGATCAA
EST: gi|149082839|gb|EE172063.2|EE172063
EST:     TGCGCCTCTTTGCTACTCAGTCCCATTATGCGGACCGTCTTGCGGAAGCA                         GAAAGATCTGAAAATCAATGCACCAGTCAATTAAAGTCCTTGATCGATCAA
genomic: TGCGCCTCTTTGCTACTCAGTCCCATTATGCGGACCGTCTTGCGGAAGCAgtaagtatta ... ctccatacagGAAAGATCTGAAAATCAATGCACCAGTCAATTAAAGTCCTTGATCGATCAA
EST: gi|211526747|gb|FL258556.1|FL258556
EST:     TGCGCCTCTTTGCTACTCAGTCCCATTATGCGGACCGTCTTGCSGAASSA                         GAAAGATCTGAAAATCAATGCACCAGTCAATTAAAGTCCTTGATCGATCAA
genomic: TGCGCCTCTTTGCTACTCAGTCCCATTATGCGGACCGTCTTGCGGAAGCAgtaagtatta ... ctccatacagGAAAGATCTGAAAATCAATGCACCAGTCAATTAAAGTCCTTGATCGATCAA
EST: gi|211529741|gb|FL258567.1|FL258567
EST:     TGCGCCTCTTTGCTACTCAGTCCCATTATGCGGACCGTCTTGCGGAAGCA                         GAAAGATCTGAAAATCAATGCACCAGTCAATTAAAGTCCTTGATCGATCAA
genomic: TGCGCCTCTTTGCTACTCAGTCCCATTATGCGGACCGTCTTGCGGAAGCAgtaagtatta ... ctccatacagGAAAGATCTGAAAATCAATGCACCAGTCAATTAAAGTCCTTGATCGATCAA
EST: gi|211526748|gb|FL258557.1|FL258557
EST:     TGCGCCTCTTTGCTACTCAGTCCCATTATGCGGACCGTCTTGCGGAAGCA                         GAAAGATCTGAAAATCAATGCACCAGTCAATTAAAGTCCTTGATCGATCAA
genomic: TGCGCCTCTTTGCTACTCAGTCCCATTATGCGGACCGTCTTGCGGAAGCAgtaagtatta ... ctccatacagGAAAGATCTGAAAATCAATGCACCAGTCAATTAAAGTCCTTGATCGATCAA
EST: gi|211526752|gb|FL258561.1|FL258561
EST:     GCGCCTCTTTGCTAGCTCAGTCCCATTATGCGGACCGTCTTGCGGAAGCA                         GAAAGATCTGAAAAT
genomic: GCGCCTCTTTGCTA-CTCAGTCCCATTATGCGGACCGTCTTGCGGAAGCAgtaagtatta ... ctccatacagGAAAGATCTGAAAAT
EST: gi|211526745|gb|FL258554.1|FL258554
EST:     TGCGCCTCTTTGCTACTCAGTCCCATTATGCGGACCGTCTTGCGGAAGCA                         GAAAGATCTGAAAATCAATGCACCAGTCAATTAAAGTCCTTGATCGATCAA
genomic: TGCGCCTCTTTGCTACTCAGTCCCATTATGCGGACCGTCTTGCGGAAGCAgtaagtatta ... ctccatacagGAAAGATCTGAAAATCAATGCACCAGTCAATTAAAGTCCTTGATCGATCAA
EST: gi|211529736|gb|FL258562.1|FL258562
EST:     TGCGCCTCTTTGCTACTCAGTCCCATTATGCGGACCGTCTTGCGGAAGCA                         GAAAGATCTGAAAATCAATGCACCAGTCAATTAAAGTCCTTGATCGATCAA
genomic: TGCGCCTCTTTGCTACTCAGTCCCATTATGCGGACCGTCTTGCGGAAGCAgtaagtatta ... ctccatacagGAAAGATCTGAAAATCAATGCACCAGTCAATTAAAGTCCTTGATCGATCAA
EST: gi|211526750|gb|FL258559.1|FL258559
EST:     TGCGCCTCTTTGCTACTCAGTCCCATTATGCGGACCGTCTTGCGGAAGCA                         GAAAGATCTGAAAATCAATGCACCAGTCAATTAAAGTCCTTGATCGATCAA
genomic: TGCGCCTCTTTGCTACTCAGTCCCATTATGCGGACCGTCTTGCGGAAGCAgtaagtatta ... ctccatacagGAAAGATCTGAAAATCAATGCACCAGTCAATTAAAGTCCTTGATCGATCAA
EST: gi|71439957|gb|DR821007.1|DR821007
EST:     TGCGCCTCTTTGCTACTCAGTCCCATTATGCGGACCGTCTTGCGGAAGCA                         GAAAGATCTGAAAATCAATGCACCAGTCAATTAAAGTCCTTGATCGATCAA
genomic: TGCGCCTCTTTGCTACTCAGTCCCATTATGCGGACCGTCTTGCGGAAGCAgtaagtatta ... ctccatacagGAAAGATCTGAAAATCAATGCACCAGTCAATTAAAGTCCTTGATCGATCAA
EST: gi|211526744|gb|FL258553.1|FL258553
EST:     TGCGCCTCTTTGCTACTCAGTCCCATTATGCGGACCGTCTTGCGGAAGCA                         GAAAGATCTGAAAATCAATGCACCAGTCAATTAAAGTCCTTGATCGATCAA
genomic: TGCGCCTCTTTGCTACTCAGTCCCATTATGCGGACCGTCTTGCGGAAGCAgtaagtatta ... ctccatacagGAAAGATCTGAAAATCAATGCACCAGTCAATTAAAGTCCTTGATCGATCAA
EST: gi|211529738|gb|FL258564.1|FL258564
EST:     TGCGCCTCTTTGCTACTCAGTCCCATTATGCGGACCGTCTTGCGGAAGCA                         GAAAGATCTGAAAATCAATGCACCAGTCAATTAAAGTCCTTGATCGATCAA
genomic: TGCGCCTCTTTGCTACTCAGTCCCATTATGCGGACCGTCTTGCGGAAGCAgtaagtatta ... ctccatacagGAAAGATCTGAAAATCAATGCACCAGTCAATTAAAGTCCTTGATCGATCAA
EST: gi|76285204|gb|DV024772.1|DV024772
EST:     TGCGCCTCTTTGCTACTCAGTCCCATTATGCGGACCGTCTTGCGGAAGCA                         GAAAGATCTGAAAATCAATGCACCAGTCAATTAAAGTCCTTGATCGATCAA
genomic: TGCGCCTCTTTGCTACTCAGTCCCATTATGCGGACCGTCTTGCGGAAGCAgtaagtatta ... ctccatacagGAAAGATCTGAAAATCAATGCACCAGTCAATTAAAGTCCTTGATCGATCAA
EST: gi|74244431|gb|DT652345.1|DT652345
EST:     TGCGCCTCTTTGCTACTCAGTCCCATTATGCGGACCGTCTTGCGGAAGCA                         GAAAGATCTGAAAATCAATGCACCAGTCAATTAAAGTCCTTGATCGATCAA
genomic: TGCGCCTCTTTGCTACTCAGTCCCATTATGCGGACCGTCTTGCGGAAGCAgtaagtatta ... ctccatacagGAAAGATCTGAAAATCAATGCACCAGTCAATTAAAGTCCTTGATCGATCAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcgaaggcattccataactcaaaagttgtttacacctgtagtttgctccatacagGAAAGATCTGAAAATCAATGCACCAGTCAATTAAAGTCCTTGATCGATCAAGTCAGCATGCAGCAGGAGAAGATTGTAGCATTGGAAG
           ccataac  putative branch site (score: 3)
                                         tttgctcc  putative PPT
                    aaaagtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtattattaattgtctcccctccctttctatctcttcttcatctacgcatttccaagccttccatctctccgtggactcgctgcaggactaggatcgaaggcattccataactcaaaagttgtttacacctgtagtttgctccatacagGAAAGATCTGAAAATCAATGCACCAGTCAATTAAAGTCCTTGATCGATCAAGTCAGCATGCAGCAGGAGAAGATTGTAGCATTGGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG