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'   		18  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTCAAGAACCCATGGCCCAATGTTGACGCTCACAGTGGACTCTTGCTGAACCACTTTGGACTATCTGAAACACGgtatgtttgtgcttgtagtttagataccaattcagtcatgtttttttttttttttactttgcaaagctagttctgaatgagcacagagcactcactcatgtctgggacaccaactgtgcag

Basic information

species Zea mays
transcript GRMZM2G063909_T03
intron # 17
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G063909_T03 (Zea mays), 5'ss of exon 17
lower sequence: LOC_Os11g33240.2 (Oryza sativa), 5'ss of exon 18
GTCAAGAACCCATGGCCCAATGTTGACGCTCACAGTGGACTCTTGCTGAACCACTTTGGACTATCTGAAACACGgtatgtttgtgcttgtagtttagataccaattcagtcatgtttttttttttttttactttgcaaagctagttctgaatgagcacagagcactcactcatgtctgggacaccaactgtgcag
||||| ||||||||||| |||||||| |||||||||||| |  ||||||||||||||||| |||||||| | ||||||||||     |   | ||| |||       |  ||  |||  | ||      |   || ||   ||  | |   | || || ||| ||| | | |   | |  |  | || |  ||||
GTCAAAAACCCATGGCCTAATGTTGATGCTCACAGTGGAGTTCTGCTGAACCACTTTGGATTATCTGAAGCTCGgtatgtttacctgtcctggttaaataatttagtaaccaaatttaatcttgaacccatgatggaatagtaaatgtacttcagaac-gagtacttaataaaagcggccat-ctaattacgcag

upper sequence: GRMZM2G063909_T03 (Zea mays), 5'ss of exon 17
lower sequence: LOC_Os02g10070.1 (Oryza sativa), 5'ss of exon 18
GTCAAGAACCCATGGCCCAATGTTGACGCTCACAGTGGACTCTTGCTGAACCACTTTGGACTATCTGAAACACGgtatgtttgtgcttgtagtttagata--ccaattcagtcatgtttttttttttttttactttgcaaagctagttctgaat--gagcacagagcactcactcatgtctgggacaccaactgtgcag
||||| ||||||||||| |||||||| |||||||| ||| |  | ||||||||||||||| |||||||| | |||||||||| |   | | | ||| | |  | |||   | ||||| |  |||  | || |  ||   |    |||    |||   |    ||| |    ||| | |       | | ||||| ||||
GTCAAAAACCCATGGCCTAATGTTGATGCTCACAGCGGAGTTCTACTGAACCACTTTGGATTATCTGAAGCTCGgtatgtttatctgtattggttaaacaatctaat---gccatgtctaatttaatcttgaacttatgatag-agtagcaaatctaactttagaacgagtacttaagaaaacttctctaactgcgcag

upper sequence: GRMZM2G063909_T03 (Zea mays), 5'ss of exon 17
lower sequence: AT2G44350.2 (Arabidopsis thaliana), 5'ss of exon 18
GTCAAGAACCCATGGCCCAATGTTGACGCTCACAGTGGACTCTTGCTGAACCACTTTGGACTATCTGAAACACGgtatgtt-tgtgcttgtagtttagataccaattcagtcatgtttttttttttttttactttgcaaagctagttctgaatgagcacagagcactcactcatgtctgggacaccaactgtgcag
|| |||||||| ||||| |||||||| |||||||||||  ||||||||||||||| ||| ||| | ||| || |||| |   |   |   |  || |  || || || || | |    |     |    ||   |     |   ||| |  |                                            
GTGAAGAACCCGTGGCCAAATGTTGATGCTCACAGTGGGGTCTTGCTGAACCACTATGGTCTAACCGAAGCAAGgtaagaagtagacacctccttcaagtatca-ttgagccttaggatagcactcaaatataatatct-gtgcgttttatag-------------------------------------------

upper sequence: GRMZM2G063909_T03 (Zea mays), 5'ss of exon 17
lower sequence: Vv13s0156g00180.t01 (Vitis vinifera), 5'ss of exon 18
GTCAAGAACCCATGGCCCAATGTTGACGCTCACAGTGGACTCTTGCTGAACCACTTTGGACTATCTGAAACACGgtatgtttgtgcttgtagtttagataccaattcagtcatgtttttttttttttttactttgcaaagctagttctgaatgagcacagagcactcactcatgtctgggacaccaactgtgcag
|| || ||||||||||||||||| || |||||||||||  ||||||||||||| |||||  ||   ||| |||||||     | | |     | |    | || |  | |   |   ||| ||  |||  || |  ||   || |  ||  |        |  |  |  | |    ||    | |  |  |||||
GTTAAAAACCCATGGCCCAATGTCGATGCTCACAGTGGGGTCTTGCTGAACCATTTTGGTTTACACGAAGCACGgtaaa---gagttctc--tctcacaatcattataattg-gagatttcttaatttggctatttaatagta-tcttgggtagatggtaaaaatcctttaacaattg----atc--ccttgcag

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|211314255|gb|FK994155.1|FK994155
EST:     GACGCTCACAGTGGACTCTTGCTGAACCACTTTGGACTATCTGAAACACG                         GTATCACACTGTCTTGTTCGGTGTTTCGAGAANCATGGGGGTAGGATCCCA
genomic: GACGCTCACAGTGGACTCTTGCTGAACCACTTTGGACTATCTGAAACACGgtatgtttgt ... aactgtgcagGTATCACACTGTCTTGTTCGGTGTTTCGAGAAGCATGGGGGTAGGATCCCA
EST: gi|60357508|gb|DN224481.1|DN224481
EST:     GACGCTCACAGTGGACTCTTGCTGAACCACTTTGGACTATCTGAAACACG                         GTATCACACTGTCTTGTTCGGTGTTTCGAGAAGCATGGGGGTAGGATCCCA
genomic: GACGCTCACAGTGGACTCTTGCTGAACCACTTTGGACTATCTGAAACACGgtatgtttgt ... aactgtgcagGTATCACACTGTCTTGTTCGGTGTTTCGAGAAGCATGGGGGTAGGATCCCA
EST: gi|78076903|gb|DV505337.1|DV505337
EST:     GACGCTCACAGTGGACTCTTGCTGAACCACTTTGGACTATCTGAAACACG                         GTATCACACTGTCTTGTTCGGTGTTTCGAGAAGCATGGGGGTAGGATCCCA
genomic: GACGCTCACAGTGGACTCTTGCTGAACCACTTTGGACTATCTGAAACACGgtatgtttgt ... aactgtgcagGTATCACACTGTCTTGTTCGGTGTTTCGAGAAGCATGGGGGTAGGATCCCA
EST: gi|60354991|gb|DN221964.1|DN221964
EST:     GACGCTCACAGTGGACTCTTGCTGAACCACTTTGGACTATCTGAAACACG                         GTATCACACTGTCTTGTTCGGTGTTTCGAGAAGCATGGGGGTAGGATCCCA
genomic: GACGCTCACAGTGGACTCTTGCTGAACCACTTTGGACTATCTGAAACACGgtatgtttgt ... aactgtgcagGTATCACACTGTCTTGTTCGGTGTTTCGAGAAGCATGGGGGTAGGATCCCA
EST: gi|60345083|gb|DN212056.1|DN212056
EST:     GACGCTCACAGTGGACTCTTGCTGAACCACTTTGGACTATCTGAAACACG                         GTATCACACTGTCTTGTTCGGTGTTTCGAGAAGCATGGGGGTAGGATCCCA
genomic: GACGCTCACAGTGGACTCTTGCTGAACCACTTTGGACTATCTGAAACACGgtatgtttgt ... aactgtgcagGTATCACACTGTCTTGTTCGGTGTTTCGAGAAGCATGGGGGTAGGATCCCA
EST: gi|50331232|gb|CO526358.1|CO526358
EST:     GACGCTCACAGTGGACTCTTGCTGAACCACTTTGGACTATCTGAAACACG                         GTATCACACTGTCTTGTTCGGTGTTTCGAGAAGCATGGGGGTAGGATCCCA
genomic: GACGCTCACAGTGGACTCTTGCTGAACCACTTTGGACTATCTGAAACACGgtatgtttgt ... aactgtgcagGTATCACACTGTCTTGTTCGGTGTTTCGAGAAGCATGGGGGTAGGATCCCA
EST: gi|40334210|gb|CK368280.1|CK368280
EST:     GACGCTCACAGTGGACTCTTGCTGAACCACTTTGGACTATCTGAAACACA                         GTATCACACTGTCTTGTTCGGTGTTTCGAGAAGCATGGGGGTAGGATCCCA
genomic: GACGCTCACAGTGGACTCTTGCTGAACCACTTTGGACTATCTGAAACACGgtatgtttgt ... aactgtgcagGTATCACACTGTCTTGTTCGGTGTTTCGAGAAGCATGGGGGTAGGATCCCA
EST: gi|60400601|gb|DN233408.1|DN233408
EST:     GACGCTCACAGTGGACTCTTGCTGAACCACTTTGGACTATATGAAACACG                         GTATCACACTGTCTTGTTCGGTGTTTCGAGAAGCATGGGGGTAGGATCCCA
genomic: GACGCTCACAGTGGACTCTTGCTGAACCACTTTGGACTATCTGAAACACGgtatgtttgt ... aactgtgcagGTATCACACTGTCTTGTTCGGTGTTTCGAGAAGCATGGGGGTAGGATCCCA
EST: gi|17932431|gb|BM269391.1|BM269391
EST:     GACGCTCACAGTGGACTCTTGCTGAACCACTTTGGACTATCTGAAACACG                         GTATCACACTGTCTTGTTCGGTGTTTCGAGAAGCATGGGGGTAGGATCCCA
genomic: GACGCTCACAGTGGACTCTTGCTGAACCACTTTGGACTATCTGAAACACGgtatgtttgt ... aactgtgcagGTATCACACTGTCTTGTTCGGTGTTTCGAGAAGCATGGGGGTAGGATCCCA
EST: gi|37394364|gb|CF634455.1|CF634455
EST:     CTTTGGACTATCTGAAACACG                         GTATCACACTGTCTTGTTCGGTGTTTCGAGAAGCATGGGGGTAGGATCCCA
genomic: CTTTGGACTATCTGAAACACGgtatgtttgt ... aactgtgcagGTATCACACTGTCTTGTTCGGTGTTTCGAGAAGCATGGGGGTAGGATCCCA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTCAAGAACCCATGGCCCAATGTTGACGCTCACAGTGGACTCTTGCTGAACCACTTTGGACTATCTGAAACACGgtatgtttgtgcttgtagtttagataccaattcagtcatgtttttttttttttttactttgcaaagctagttctgaatgagcacagagcactcactcatgtctgggacaccaactgtgcag

- - - - - - - - - - - - - - - -  AGTGGA