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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctttgaaaactagcctcaaagatttataatttctatttttctcatggatcagtattttttaagagcattgagaaactgaacatgttttctcctgtatcagGTACTTGACGAGATTAGGCCATACCTTGCTGGCACAGGAGGTGGCGAGCTCGAGTTTGTCACAATCGAGGAGCCTATTGTCAAGGTTAGGCTTACAGGCC

Basic information

species Zea mays
transcript GRMZM2G089317_T02
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G089317_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os11g07916.1 (Oryza sativa), 3'ss of exon 3
------------ctttgaaaactagcctcaaagatttataatttctatttttctcatggatcagtattttttaagagcattgagaaactgaacatgttttctcctgtatcagGTACTTGACGAGATTAGGCCATACCTTGCTGGCACAGGAGGTGGCGAGCTCGAGTTTGTCACAATCGAGGAGCCTATTGTCAAGGTTAGGCTTACAGGCC
            ||||  |  |||   |    |    | ||     |||  | | |||||  | ||   |    ||||||       || ||  | ||||  ||| ||| ||||||| || |||||||||||||||||| |||||||||||||||| ||||| || || ||  | |||||||| ||||| ||||||||||||||||| ||||
ataatgttccatcttttgagtctattttggttgggaaaaaa-----attgctgtgatggaa-actaaactgctggagcat------gctaaatttctttttacctttattagGTACTCGATGAGATTAGGCCATACCTTTCTGGCACAGGAGGTGGTGAGCTTGAATTCGTTGCGATCGAGGAACCTATCGTCAAGGTTAGGCTTACGGGCC
















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|108824268|gb|EC278276.1|EC278276
EST:     TTGCTGATGAGGAAACTGGCCTTGAGTTGAACCAAGAGAACATTGAAAAG                         GTACTTGACGAGATTAGGCCATACCTTGCTAGCACAGGAGGTGGCGAGCTC
genomic: TTGCTGATGAGGAAACTGGCCTTGAGTTGAACCAAGAGAACATTGAAAAGgtaaatgttc ... cctgtatcagGTACTTGACGAGATTAGGCCATACCTTGCTGGCACAGGAGGTGGCGAGCTC
EST: gi|13557691|gb|BG549047.1|BG549047
EST:     TTGCTGATGAGGAAACTGGCCTTGAGTTGAACCAAGAGAACATTGAAAAG                         GTACTTGACGAGATTAGGCCATACCTTGCTGGCACAGGAGGTGGCGAGCTC
genomic: TTGCTGATGAGGAAACTGGCCTTGAGTTGAACCAAGAGAACATTGAAAAGgtaaatgttc ... cctgtatcagGTACTTGACGAGATTAGGCCATACCTTGCTGGCACAGGAGGTGGCGAGCTC
EST: gi|45568454|gb|CK986072.1|CK986072
EST:     TTGCTGATGAGGAAACTGGCCTTGAGTTGAACCAAGAGAACATTGAAAAG                         GTACTTGACGAGATTAGGCCATACCTTGCTGGCACAGGAGGTGGCGAGCTC
genomic: TTGCTGATGAGGAAACTGGCCTTGAGTTGAACCAAGAGAACATTGAAAAGgtaaatgttc ... cctgtatcagGTACTTGACGAGATTAGGCCATACCTTGCTGGCACAGGAGGTGGCGAGCTC
EST: gi|6563742|gb|AW231274.1|AW231274
EST:     TTGCTGATGAGGAAACTGGCCTTGAGTTGAACCAAGAGAACATTGAAAAG                         GTACTTGACGAGATTAGGCCATACCTTGCTGGCACAGGAGGTGGCGAGCTC
genomic: TTGCTGATGAGGAAACTGGCCTTGAGTTGAACCAAGAGAACATTGAAAAGgtaaatgttc ... cctgtatcagGTACTTGACGAGATTAGGCCATACCTTGCTGGCACAGGAGGTGGCGAGCTC
EST: gi|211258469|gb|FL134883.1|FL134883
EST:     TTGCTGATGAGGAAACTGGCCTTGAGTTGAACCAAGAGAACATTGAAAAG                         GTACTTGACGAGATTAGGCCATACCTTGCTGGCACAGGAGGTGGCGAGCTC
genomic: TTGCTGATGAGGAAACTGGCCTTGAGTTGAACCAAGAGAACATTGAAAAGgtaaatgttc ... cctgtatcagGTACTTGACGAGATTAGGCCATACCTTGCTGGCACAGGAGGTGGCGAGCTC
EST: gi|29543551|gb|CB603933.1|CB603933
EST:     TTGCTGATGAGGAAACTGGCCTTGAGTTGAACCAAGAGAACATTGAAAAG                         GTACTTGACGAGATTAGGCCATACCTTGCTGGCACAGGAGGTGGCGAGCTC
genomic: TTGCTGATGAGGAAACTGGCCTTGAGTTGAACCAAGAGAACATTGAAAAGgtaaatgttc ... cctgtatcagGTACTTGACGAGATTAGGCCATACCTTGCTGGCACAGGAGGTGGCGAGCTC
EST: gi|211222822|gb|FL455724.1|FL455724
EST:     TTGCTGATGAGGAAACTGGCCTTGAGTTGAACCAAGAGAACATTGAAAAG                         GTACTTGACGAGATTAGGCCATACCTTGCTGGCACAGGAGGTGGCGAGCTC
genomic: TTGCTGATGAGGAAACTGGCCTTGAGTTGAACCAAGAGAACATTGAAAAGgtaaatgttc ... cctgtatcagGTACTTGACGAGATTAGGCCATACCTTGCTGGCACAGGAGGTGGCGAGCTC
EST: gi|60340325|gb|DN207298.1|DN207298
EST:     TTGCTGATGAGGAAACTGGCCTTGAGTTGAACCAAGAGAACATTGAAAAG                         GTACTTGACGAGATTAGGCCATACCTTGCTGGCACAGGAGGTGGCGAGCTC
genomic: TTGCTGATGAGGAAACTGGCCTTGAGTTGAACCAAGAGAACATTGAAAAGgtaaatgttc ... cctgtatcagGTACTTGACGAGATTAGGCCATACCTTGCTGGCACAGGAGGTGGCGAGCTC
EST: gi|76290647|gb|DV030215.1|DV030215
EST:     TTGCTGATGAGGAAACTGGCCTTGAGTTGAACCAAGAGAACATTGAAAAG                         GTACTTGACGAGATTAGGCCATACCTTGCTGGCACAGGAGGTGGCGAGCTC
genomic: TTGCTGATGAGGAAACTGGCCTTGAGTTGAACCAAGAGAACATTGAAAAGgtaaatgttc ... cctgtatcagGTACTTGACGAGATTAGGCCATACCTTGCTGGCACAGGAGGTGGCGAGCTC
EST: gi|12973012|gb|BG268268.1|BG268268
EST:     TTGCTGATGAGGAAACTGGCCTTGAGTTGAACCAAGAGAACATTGAAAAG                         GTACTTGACGAGATTAGGCCATACCTTGCTGGCACAGGAGGTGGCGAGCTC
genomic: TTGCTGATGAGGAAACTGGCCTTGAGTTGAACCAAGAGAACATTGAAAAGgtaaatgttc ... cctgtatcagGTACTTGACGAGATTAGGCCATACCTTGCTGGCACAGGAGGTGGCGAGCTC
EST: gi|37377314|gb|CF625250.1|CF625250
EST:     TTGCTGATGAGGAAACTGGCCTTGAGTTGAACCAAGAGAACATTGAAAAG                         GTACTTGACGAGATTAGGCCATACCTTGCTGGCACAGGAGGTGGCGAGCTC
genomic: TTGCTGATGAGGAAACTGGCCTTGAGTTGAACCAAGAGAACATTGAAAAGgtaaatgttc ... cctgtatcagGTACTTGACGAGATTAGGCCATACCTTGCTGGCACAGGAGGTGGCGAGCTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggatcagtattttttaagagcattgagaaactgaacatgttttctcctgtatcagGTACTTGACGAGATTAGGCCATACCTTGCTGGCACAGGAGGTGGCGAGCTCGAGTTTGTCACAATCGAGGAGCCTATTGTCAAGGTTAGGCTTACAGGCC
                                       ttttctcctgtatc  CT-rich tract
     agtattttttaaga  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctttgaaaactagcctcaaagatttataatttctatttttctcatggatcagtattttttaagagcattgagaaactgaacatgttttctcctgtatcagGTACTTGACGAGATTAGGCCATACCTTGCTGGCACAGGAGGTGGCGAGCTCGAGTTTGTCACAATCGAGGAGCCTATTGTCAAGGTTAGGCTTACAGGCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG