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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgaaggcctaaatcctaatttcttcattatatgctcttcaattcatctgaatactgagtatatttttatgcttgctttgttaacagGATGTTGATGAGAAGCTCCTCTATGATACCTTCAGTGCATTTGGAGTGATTGTAACTAATCCTAAG

Basic information

species Zea mays
transcript GRMZM2G102639_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G102639_T02 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os10g31900.1 (Oryza sativa), 3'ss of exon 5
gtgaaggcctaaatcctaatttcttcattatatgctcttcaattcatctgaatactgagtatatttttatgcttgctttgttaacagGATGTTGATGAGAAGCTCCTCTATGATACCTTCAGTGCATTTGGAGTGATTGTAACTAATCCTAAG
|| ||  | |     |||  || ||| ||||  |||| |   | |||  ||| | ||  || ||   | ||  | || ||||  ||||||||||| || |||||||| || |||||||||||||| |||||||||||||| |||||||| |||
gtaaaaacttgtggtctagctt-ttctttatcagctcgtt--tgcatgcgaagagtggcta-atggctttgtgttctgtgtt--cagGATGTTGACGAAAAGCTCCTGTACGATACCTTCAGTGCGTTTGGAGTGATTGTGACTAATCCCAAG

upper sequence: GRMZM2G102639_T02 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA12G36950.1 (Glycine max), 3'ss of exon 5
gtgaaggcctaaatccta-atttcttcatta----tatgc--tcttcaattcatctgaatactgagtatatttttatgcttgctttgttaacagGATGTTGATGAGAAGCTCCTCTATGATACCTTCAGTGCATTTGGAGTGATTGTAACTAATCCTAAG
|| |    | ||||  |  |  | || || |     ||||  |  |  ||| |  | || ||| |  | ||   | | | |  | |  |  |||||||| || ||||||||| | |||||||| ||||||||||||||||| ||||| |||||||| |||
gtaagtaaccaaattatgcaagtgttaatcagactcatgcagttatgcattgaattcaagacttaa-acatgagtgttcctaatgttgttgcagGATGTAGACGAGAAGCTCTTGTATGATACTTTCAGTGCATTTGGAGTTATTGTTACTAATCCAAAG

upper sequence: GRMZM2G102639_T02 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA09G00310.1 (Glycine max), 3'ss of exon 5
gtgaaggcctaaatcctaatttcttca-------ttatatgctcttcaattcatctgaatactgagtatatttttatgcttgctttgttaacagGATGTTGATGAGAAGCTCCTCTATGATACCTTCAGTGCATTTGGAGTGATTGTAACTAATCCTAAG
|| |    | ||||  |       | |       | ||    |  |  ||| |  | || ||| | || ||   | | | |  | |  |  |||||||| |||||||||||| | ||||| || ||||||||||||||||| ||||| |||||||| |||
gtaagtcaccaaattatggaagtgttaaacagactcatgcagttatgcattgaattcaagactta-tacatgagtgttcctaatgttgttgcagGATGTAGATGAGAAGCTCTTGTATGACACTTTCAGTGCATTTGGAGTTATTGTTACTAATCCAAAG

upper sequence: GRMZM2G102639_T02 (Zea mays), 3'ss of exon 3
lower sequence: AT2G18510.1 (Arabidopsis thaliana), 3'ss of exon 5
gtgaaggcctaa-atcctaatttcttcattatatgctcttcaat--tcatctgaatactgagtatatttttatgcttgctttgttaacagGATGTTGATGAGAAGCTCCTCTATGATACCTTCAGTGCATTTGGAGTGATTGTAACTAATCCTAAG
|| |    ||    |  ||   |||   ||  || |||| |||   |||| | |   || ||  |       |  |   ||  || | ||||||| |||||||||||| | |||||||| |||||||||||||| |||||||   |||||||||||
gtaagtatcttttgtggtagactctgattttgatactctacaaaggtcatttaatctcttagc-tgaccaggttttgttttcttttatagGATGTGGATGAGAAGCTCTTGTATGATACTTTCAGTGCATTTGGTGTGATTGCTTCTAATCCTAAG

upper sequence: GRMZM2G102639_T02 (Zea mays), 3'ss of exon 3
lower sequence: Vv04s0023g01470.t01 (Vitis vinifera), 3'ss of exon 5
----------------------------------------------gtgaaggcctaaatcctaatttcttcattatatgctcttcaat--tcatctgaatactgagtatatttttatgcttgct--------ttgttaacagGATGTTGATGAGAAGCTCCTCTATGATACCTTCAGTGCATTTGGAGTGATTGTAACTAATCCTAAG
                                              ||   |    ||| |||  | |     | |    ||| |  |   |  |   |  |||   |  | |||||   |||          || ||  |||||||| |||||||| || || |||||||| ||||||||||||||||| ||||| || ||||| |||
gtaagtagttcaattccttatttttatttatttttattgggaagttgtattgtatcaaaacctt-tgtgggtgtgaaggactcatggacagttgttgtatcactagtttcaattttaaagttgaccctggatgttctttgcagGATGTGGATGAGAAACTTCTGTATGATACTTTCAGTGCATTTGGAGTCATTGTCACAAATCCCAAG

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|26558877|gb|CA831112.1|CA831112
EST:     AGAAGAGCTTGGACGTTGGAGCAAATCTGTTTATTGGCAATCTTGATCCG                         GATGTTGATGAGAAGCTCCTCTATGATACCTTCAGTGCATTTGGAGTGATT
genomic: AGAAGAGCTTGGACGTTGGAGCAAATCTGTTTATTGGCAATCTTGATCCGgtgaaggcct ... ttgttaacagGATGTTGATGAGAAGCTCCTCTATGATACCTTCAGTGCATTTGGAGTGATT
EST: gi|78090866|gb|DV519240.1|DV519240
EST:     AGAAGAGCTTGGACGTTGGAGCAAATCTGTTTATTGGCAATCTTGATCCG                         GATGTTGATGAGAAGCTCCTCTATGATACCTTCAGTGCATTTGGAGTGATT
genomic: AGAAGAGCTTGGACGTTGGAGCAAATCTGTTTATTGGCAATCTTGATCCGgtgaaggcct ... ttgttaacagGATGTTGATGAGAAGCTCCTCTATGATACCTTCAGTGCATTTGGAGTGATT
EST: gi|91056510|gb|EB166928.1|EB166928
EST:     AGAAGAGCTTGGACGTTGGAGCAAATCTGTTTATTGGCAATCTTGATCCG                         GATGTTGATGAGAAGCTCCTCTATGATACCTTCAGTGCATTTGGAGTGATT
genomic: AGAAGAGCTTGGACGTTGGAGCAAATCTGTTTATTGGCAATCTTGATCCGgtgaaggcct ... ttgttaacagGATGTTGATGAGAAGCTCCTCTATGATACCTTCAGTGCATTTGGAGTGATT
EST: gi|148943004|gb|EC888052.2|EC888052
EST:     AGAAGAGCTTGGACGTTGGAGCAAATCTGTTTATTGGCAATCTTGATCCG                         GATGTTGATGAGAAGCTCCTCTATGATACCTTCAGTGCATTTGGAGTGATT
genomic: AGAAGAGCTTGGACGTTGGAGCAAATCTGTTTATTGGCAATCTTGATCCGgtgaaggcct ... ttgttaacagGATGTTGATGAGAAGCTCCTCTATGATACCTTCAGTGCATTTGGAGTGATT
EST: gi|87157489|gb|DY402278.1|DY402278
EST:     AGAAGAGCTTGGACGTTGGAGCAAATCTGTTTATTGGCAATCTTGATCCG                         GATGTTGATGAGAAGCTCCTCTATGATACCTTCAGTGCATTTGGAGTGATT
genomic: AGAAGAGCTTGGACGTTGGAGCAAATCTGTTTATTGGCAATCTTGATCCGgtgaaggcct ... ttgttaacagGATGTTGATGAGAAGCTCCTCTATGATACCTTCAGTGCATTTGGAGTGATT
EST: gi|33467168|gb|CF244217.1|CF244217
EST:     AGAAGAGCTTGGACGTTGGAGCAAATCTGTTTATTGGCAATCTTGATCCG                         GATGTTGATGAGAAGCTCCTCTATGATACCTTCAGTGCATTTGGAGTGATT
genomic: AGAAGAGCTTGGACGTTGGAGCAAATCTGTTTATTGGCAATCTTGATCCGgtgaaggcct ... ttgttaacagGATGTTGATGAGAAGCTCCTCTATGATACCTTCAGTGCATTTGGAGTGATT
EST: gi|148956981|gb|EC902927.2|EC902927
EST:     AGAAGAGCTTGGACGTTGGAGCAAATCTGTTTATTGGCAATCTTGATCCG                         GATGTTGATGAGAAGCTCCTCTATGATACCTTCAGTGCATTTGGAGTGATT
genomic: AGAAGAGCTTGGACGTTGGAGCAAATCTGTTTATTGGCAATCTTGATCCGgtgaaggcct ... ttgttaacagGATGTTGATGAGAAGCTCCTCTATGATACCTTCAGTGCATTTGGAGTGATT
EST: gi|148933043|gb|EE285938.2|EE285938
EST:     AGAAGAGCTTGGACGTTGGAGCAAATCTGTTTATTGGCAATCTTGATCCG                         GATGTTGATGAGAAGCTCCTCTATGATACCTTCAGTGCATTTGGAGTGATT
genomic: AGAAGAGCTTGGACGTTGGAGCAAATCTGTTTATTGGCAATCTTGATCCGgtgaaggcct ... ttgttaacagGATGTTGATGAGAAGCTCCTCTATGATACCTTCAGTGCATTTGGAGTGATT
EST: gi|78124664|gb|DV543048.1|DV543048
EST:     AAAAGAGCTTGGACGTTGGAGCAAATCTGTTTATTGGCAATCTTGATCCG                         GATGTTGATGAAAAGCTCCTCTATGATACCTTCAGTGCATTTGGAGTGATT
genomic: AGAAGAGCTTGGACGTTGGAGCAAATCTGTTTATTGGCAATCTTGATCCGgtgaaggcct ... ttgttaacagGATGTTGATGAGAAGCTCCTCTATGATACCTTCAGTGCATTTGGAGTGATT
EST: gi|50322326|gb|CO517452.1|CO517452
EST:     AGAAGAGCTTGGACGTTGGAGCAAATCTGTTTATTGGCAATCTTGATCCG                         GATGTTGATGAGAAGCTCCTCTATGATACCTTCAGTGCATTTGGAGTGATT
genomic: AGAAGAGCTTGGACGTTGGAGCAAATCTGTTTATTGGCAATCTTGATCCGgtgaaggcct ... ttgttaacagGATGTTGATGAGAAGCTCCTCTATGATACCTTCAGTGCATTTGGAGTGATT
EST: gi|89762379|gb|DY689990.1|DY689990
EST:     AGAAGAGCTTGGACGTTGGAGCAAATCTGTTTATTGGCAATCTTGATCCG                         GATGTTGATGAGAAGCTCCTCTATGATACCTTCAGTGCATTTGGAGTGATT
genomic: AGAAGAGCTTGGACGTTGGAGCAAATCTGTTTATTGGCAATCTTGATCCGgtgaaggcct ... ttgttaacagGATGTTGATGAGAAGCTCCTCTATGATACCTTCAGTGCATTTGGAGTGATT
EST: gi|94477767|gb|EB706725.1|EB706725
EST:     AGAAGAGCTTGGACGTTGGAGCAAATCTGTTTATTGGCAATCTTGATCCG                         GATGTTGATGAGAAGCTCCTCTATGATACCTTCAGTGCATTTGGAGTGATT
genomic: AGAAGAGCTTGGACGTTGGAGCAAATCTGTTTATTGGCAATCTTGATCCGgtgaaggcct ... ttgttaacagGATGTTGATGAGAAGCTCCTCTATGATACCTTCAGTGCATTTGGAGTGATT
EST: gi|76288123|gb|DV027691.1|DV027691
EST:     AGAAGAGCTTGGACGTTGGAGCAAATCTGTTTATTGGCAATCTTGATCCG                         GATGTTGATGAGAAGCTCCTCTATGATACCTTCAGTGCATTTGGAGTGATT
genomic: AGAAGAGCTTGGACGTTGGAGCAAATCTGTTTATTGGCAATCTTGATCCGgtgaaggcct ... ttgttaacagGATGTTGATGAGAAGCTCCTCTATGATACCTTCAGTGCATTTGGAGTGATT
EST: gi|71425499|gb|DR806709.1|DR806709
EST:     AGAAGAGCTTGGACGTTGGAGCAAATCTGTTTATTGGCAATCTTGATCCG                         GATGTTGATGAGAAGCTCCTCTATGATACCTTCAGTGCATTTGGAGTGATT
genomic: AGAAGAGCTTGGACGTTGGAGCAAATCTGTTTATTGGCAATCTTGATCCGgtgaaggcct ... ttgttaacagGATGTTGATGAGAAGCTCCTCTATGATACCTTCAGTGCATTTGGAGTGATT
EST: gi|31355533|gb|CD439890.1|CD439890
EST:     AGAAGAGCTTGGACGTTGGAGCAAATCTGTTTATTGGCAATCTTGATCCG                         GATGTTGATGAGAAGCTCCTCTATGATACCTTCAGTGCATTTGGAGTGATT
genomic: AGAAGAGCTTGGACGTTGGAGCAAATCTGTTTATTGGCAATCTTGATCCGgtgaaggcct ... ttgttaacagGATGTTGATGAGAAGCTCCTCTATGATACCTTCAGTGCATTTGGAGTGATT
EST: gi|76291455|gb|DV031023.1|DV031023
EST:     AGAAGAGCTTGGACGTTGGAGCAAATCTGTTTATTGGCAATCTTGATCCG                         GATGTTGATGAGAAGCTCCTCTATGATACCTTCAGTGCATTTGGAGTGATT
genomic: AGAAGAGCTTGGACGTTGGAGCAAATCTGTTTATTGGCAATCTTGATCCGgtgaaggcct ... ttgttaacagGATGTTGATGAGAAGCTCCTCTATGATACCTTCAGTGCATTTGGAGTGATT
EST: gi|76015742|gb|DT942912.1|DT942912
EST:     AGAAGAGCTTGGACGTTGGAGCAAATCTGTTTATTGGCAATCTTGATCCG                         GATGTTGATGAGAAGCTCCTCTATGATACCTTCAGTGCATTTGGAGTGATT
genomic: AGAAGAGCTTGGACGTTGGAGCAAATCTGTTTATTGGCAATCTTGATCCGgtgaaggcct ... ttgttaacagGATGTTGATGAGAAGCTCCTCTATGATACCTTCAGTGCATTTGGAGTGATT
EST: gi|76290093|gb|DV029661.1|DV029661
EST:     AGAAGAGCTTGGACGTTGGAGCAAATCTGTTTATTGGCAATCTTGATCCG                         GATGTTGATGAGAAGCTCCTCTATGATACCTTCAGTGCATTTGGAGTGATT
genomic: AGAAGAGCTTGGACGTTGGAGCAAATCTGTTTATTGGCAATCTTGATCCGgtgaaggcct ... ttgttaacagGATGTTGATGAGAAGCTCCTCTATGATACCTTCAGTGCATTTGGAGTGATT
EST: gi|148961210|gb|EE011925.2|EE011925
EST:     AAGAGCTTGGACGTTTGGAGCAAATCCTGTTTATTGGCAATCTTGATCCG                         GATGTTGATGAGAAGCTCCTCTATGATACCTTCCGTGCATTTGGGAGTGAT
genomic: AAGAGCTTGGACGTT-GGAGCAAATC-TGTTTATTGGCAATCTTGATCCGgtgaaggcct ... ttgttaacagGATGTTGATGAGAAGCTCCTCTATGATACCTTCAGTGCATTTGG-AGTGAT
EST: gi|86472905|gb|DY239275.1|DY239275
EST:     AGAAGAGCTTGGACGTTGGAGCAAATCTGTTTATTGGCAATCTTGATCCG                         GATGTTGAAGAAAAGCTCCTCTATGATACCTTCAGTGCATTTGGAG
genomic: AGAAGAGCTTGGACGTTGGAGCAAATCTGTTTATTGGCAATCTTGATCCGgtgaaggcct ... ttgttaacagGATGTTGATGAGAAGCTCCTCTATGATACCTTCAGTGCATTTGGAG
EST: gi|78124734|gb|DV543118.1|DV543118
EST:     AAAAGAGCTTGGACGTTGGAGCAAATCTGTTTATTGGCAATCTTGATCCG                         GATGTTGATGAGAAGCTCCTCTATGATACCTTCAGTGCATTTGGAGTGATT
genomic: AGAAGAGCTTGGACGTTGGAGCAAATCTGTTTATTGGCAATCTTGATCCGgtgaaggcct ... ttgttaacagGATGTTGATGAGAAGCTCCTCTATGATACCTTCAGTGCATTTGGAGTGATT
EST: gi|148938096|gb|EC882358.2|EC882358
EST:     AGAAGAGCTTGGACGTTGGAGCAAATCTGTTTATTGGCAATCTTGATCCG                         GATGTTGATGAGAAGCTCCTCTATGATACCTTCAGTGCATTTGGAGTGATT
genomic: AGAAGAGCTTGGACGTTGGAGCAAATCTGTTTATTGGCAATCTTGATCCGgtgaaggcct ... ttgttaacagGATGTTGATGAGAAGCTCCTCTATGATACCTTCAGTGCATTTGGAGTGATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgctcttcaattcatctgaatactgagtatatttttatgcttgctttgttaacagGATGTTGATGAGAAGCTCCTCTATGATACCTTCAGTGCATTTGGAGTGATTGTAACTAATCCTAAG
                                       cttgcttt  CT-rich tract
                       tgagtatatttttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgaaggcctaaatcctaatttcttcattatatgctcttcaattcatctgaatactgagtatatttttatgcttgctttgttaacagGATGTTGATGAGAAGCTCCTCTATGATACCTTCAGTGCATTTGGAGTGATTGTAACTAATCCTAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG