Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTAACTTGGCAAATGAGGGCAATACGAGTGCTACCTATGTTCATTCTTCCTGCTGTATCCTCTGTCATATATTCAACAGTTGTTAACTTCACAAGGATGTgtaagtactcagaaagccctgttaggaaacactgtttctaatataacttgtagaatataccaggttttgaattttcatttatttttgcagttttataaga...

Basic information

species Zea mays
transcript GRMZM2G074436_T01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G074436_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os02g41990.1 (Oryza sativa), 5'ss of exon 2
CTAACTTGGCAAATGAGGGCAATACGAGTGCTACCTATGTTCATTCTTCCTGCTGTATCCTCTGTCATATATTCAACAGTTGTTAACTTCACAAGGATGTgtaagtactcagaaagccctgttaggaaacactgtttctaatataacttgtagaatataccaggttttga--attttcatttatttttgcagttttataaga--
 |||| ||| ||||||||||||| |||||||| || |||||  |  | ||||||||||| ||||| ||||||||||||||||| || |||||||||||| |||||||     || ||  | || | |   ||  || ||  |  |  |||   ||||| | |  ||   |  |||| | |    |||| | ||||| ||     
ATAACATGGGAAATGAGGGCAATCCGAGTGCTGCCGATGTTTGTCTTGCCTGCTGTATCTTCTGTGATATATTCAACAGTTGTAAAATTCACAAGGATGCgtaagtaactc-aatgctgttttggaacgtaccattactgtt-catattgactaatatgc-atattcaaactatttccgtgagattttactgtttt-tactctt
















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|32921707|gb|CF026519.1|CF026519
EST:     TGCTGTATCCTCTGTCATATATTCAGCAGTTGTTAACTTCACAAGGATGT                         TTGAGCAGAAAGACCAGAAGACCCTTGAAAAATTGAGGGCTGAGAGGAAAG
genomic: TGCTGTATCCTCTGTCATATATTCAACAGTTGTTAACTTCACAAGGATGTgtaagtactc ... ctgtttccagTTGAGCAGAAAGACCAGAAGACCCTTGAAAAATTGAGGGCTGAGAGGAAAG
EST: gi|149089324|gb|EE178549.2|EE178549
EST:     TGCTGTATCCTCTGTCATATATTCAACAGTTGTTAACTTCACAAGGATGT                         TTGAGCAGAAAGACCAGAAGACCCTTGAAAAATTGAGGGCTGAGAGGAAAG
genomic: TGCTGTATCCTCTGTCATATATTCAACAGTTGTTAACTTCACAAGGATGTgtaagtactc ... ctgtttccagTTGAGCAGAAAGACCAGAAGACCCTTGAAAAATTGAGGGCTGAGAGGAAAG
EST: gi|4730506|gb|AI649672.1|AI649672
EST:     TGCTGTATCCTCTGTCATATATTCAACAGTTGTTAACTTCACAAGGATGT                         TTGAGCAGAAAGACCAGAAGACCCTTGAAAAATTGGAGGGGCTGAGGAGGA
genomic: TGCTGTATCCTCTGTCATATATTCAACAGTTGTTAACTTCACAAGGATGTgtaagtactc ... ctgtttccagTTGAGCAGAAAGACCAGAAGACCCTTGAAAAATT-GA-GGGCTGA-GAGGA
EST: gi|148955777|gb|EC901479.2|EC901479
EST:     TGCTGTATCCTCTGTCATATATTCAACAGTTGTTAACTTCACAAGGATGT                         TTGAGCAGAAAGACCAGAAGACCCTTGAAAAATTGAGGGCTGAGAGGAAAG
genomic: TGCTGTATCCTCTGTCATATATTCAACAGTTGTTAACTTCACAAGGATGTgtaagtactc ... ctgtttccagTTGAGCAGAAAGACCAGAAGACCCTTGAAAAATTGAGGGCTGAGAGGAAAG
EST: gi|149010193|gb|EE042010.2|EE042010
EST:     TGCTGTATCCTCTGTCATATATTCAACAGTTGTTAACTTCACAAGGATGT                         TTGAGCAGAAAGACCAGAAGACCCTTGAAAAATTGAGGGCTGAGAGGAAAG
genomic: TGCTGTATCCTCTGTCATATATTCAACAGTTGTTAACTTCACAAGGATGTgtaagtactc ... ctgtttccagTTGAGCAGAAAGACCAGAAGACCCTTGAAAAATTGAGGGCTGAGAGGAAAG
EST: gi|149075912|gb|EE164472.2|EE164472
EST:     TGCTGTATCCTCTGTCATATATTCAACAGTTGTTAACTTCACAAGGATGT                         TTGAGCAGAAAGACCAGAAGACCCTTGAAAAATTGAGGGCTGAGAGGAAAG
genomic: TGCTGTATCCTCTGTCATATATTCAACAGTTGTTAACTTCACAAGGATGTgtaagtactc ... ctgtttccagTTGAGCAGAAAGACCAGAAGACCCTTGAAAAATTGAGGGCTGAGAGGAAAG
EST: gi|148999505|gb|EE036470.2|EE036470
EST:     TGCTGTATCCTCTGTCATATATTCAACAGTTGTTAACTTCACAAGGATGT                         TTGAGCAGAAAGACCAGAAGACCCTTGAAAAATTGAGGGCTGAGAGGAAAG
genomic: TGCTGTATCCTCTGTCATATATTCAACAGTTGTTAACTTCACAAGGATGTgtaagtactc ... ctgtttccagTTGAGCAGAAAGACCAGAAGACCCTTGAAAAATTGAGGGCTGAGAGGAAAG
EST: gi|101397837|gb|EB820795.1|EB820795
EST:     TGCTGTATCCTCTGTCATATATTCAACAGTTGTTAACTTCACAAGGATGT                         TTGAGCAGAAAGACCAGAAGACCCTTGAAAAATTGAGGGCTGAGAGGAAAG
genomic: TGCTGTATCCTCTGTCATATATTCAACAGTTGTTAACTTCACAAGGATGTgtaagtactc ... ctgtttccagTTGAGCAGAAAGACCAGAAGACCCTTGAAAAATTGAGGGCTGAGAGGAAAG
EST: gi|32843641|gb|CD983322.1|CD983322
EST:     TGCTGTATCCTCTGTCATATATTCAACAGTTGTTAACTTCACAAGGATGT                         TTGAGCAGAAAGACCAGAAGACCCTTGAAAAATTGAGGGCTGAGAGGAAAG
genomic: TGCTGTATCCTCTGTCATATATTCAACAGTTGTTAACTTCACAAGGATGTgtaagtactc ... ctgtttccagTTGAGCAGAAAGACCAGAAGACCCTTGAAAAATTGAGGGCTGAGAGGAAAG
EST: gi|71439041|gb|DR820091.1|DR820091
EST:     TGCTGTATCCTCTGTCATATATTCAACAGTTGTTAACTTCACAAGGATGT                         TTGAGCAGAAAGACCAGAAGACCCTTGAAAAATTGAGGGCTGAGAGGAAAG
genomic: TGCTGTATCCTCTGTCATATATTCAACAGTTGTTAACTTCACAAGGATGTgtaagtactc ... ctgtttccagTTGAGCAGAAAGACCAGAAGACCCTTGAAAAATTGAGGGCTGAGAGGAAAG
EST: gi|5928783|gb|AW056075.1|AW056075
EST:     TGCTGTATCCTCTGTCATATATTCAACAGTTGTTAACTTCACAAGGATGT                         TTGAGCAGAAAGACCAGAAGACCCTTGAAAAATTGAGGGCTGAGAGGAAAG
genomic: TGCTGTATCCTCTGTCATATATTCAACAGTTGTTAACTTCACAAGGATGTgtaagtactc ... ctgtttccagTTGAGCAGAAAGACCAGAAGACCCTTGAAAAATTGAGGGCTGAGAGGAAAG
EST: gi|76933107|gb|DV173324.1|DV173324
EST:     TGCTGTATCCTCTGTCATATATTCAACAGTTGTTAACTTCACAAGGATGT                         TTGAGCAGAAAGACCAGAAGACCCTTGAAAAATTGAGGGCTGAGAGGAAAG
genomic: TGCTGTATCCTCTGTCATATATTCAACAGTTGTTAACTTCACAAGGATGTgtaagtactc ... ctgtttccagTTGAGCAGAAAGACCAGAAGACCCTTGAAAAATTGAGGGCTGAGAGGAAAG
EST: gi|71427128|gb|DR808178.1|DR808178
EST:     TGCTGTATCCTCTGTCATATATTCAACAGTTGTTAACTTCACAAGGATGT                         TTGAGCAGAAAGACCAGAAGACCCTTGAAAAATTGAGGGCTGAGAGGAAAG
genomic: TGCTGTATCCTCTGTCATATATTCAACAGTTGTTAACTTCACAAGGATGTgtaagtactc ... ctgtttccagTTGAGCAGAAAGACCAGAAGACCCTTGAAAAATTGAGGGCTGAGAGGAAAG
EST: gi|67031507|gb|CO460256.1|CO460256
EST:     TGCTGTATCCTCTGTCATATATTCAACAGTTGTTAACTTCACAAGGATGT                         TTGAGCAGAAAGACCAGAAGACCCTTGAAAAATTGAGGGCTGAGAGAAAAG
genomic: TGCTGTATCCTCTGTCATATATTCAACAGTTGTTAACTTCACAAGGATGTgtaagtactc ... ctgtttccagTTGAGCAGAAAGACCAGAAGACCCTTGAAAAATTGAGGGCTGAGAGGAAAG
EST: gi|93282520|gb|EB674784.1|EB674784
EST:     TGCTGTATCCTCTGTCATATATTCAACAGTTGTTAACTTCACAAGGATGT                         TTGAGCAGAAAGACCAGAAGACCCTTGAAAAATTGAGGGCTGAGAGGAAAG
genomic: TGCTGTATCCTCTGTCATATATTCAACAGTTGTTAACTTCACAAGGATGTgtaagtactc ... ctgtttccagTTGAGCAGAAAGACCAGAAGACCCTTGAAAAATTGAGGGCTGAGAGGAAAG
EST: gi|74239243|gb|DT647157.1|DT647157
EST:     TGCTGTATCCTCTGTCATATATTCAACAGTTGTTAACTTCACAAGGATGT                         TTGAGCAGAAAGACCAGAAGACCCTTGAAAAATTGAGGGCTGAGAGGAAAG
genomic: TGCTGTATCCTCTGTCATATATTCAACAGTTGTTAACTTCACAAGGATGTgtaagtactc ... ctgtttccagTTGAGCAGAAAGACCAGAAGACCCTTGAAAAATTGAGGGCTGAGAGGAAAG
EST: gi|211168737|gb|FL336589.1|FL336589
EST:     TGCTGTATCCTCTGTCATATATTCAACAGTTGTTAACTTCACAAGGATGT                         TTGAGCAGAAAGACCAGAAGACCCTTGAAAAA
genomic: TGCTGTATCCTCTGTCATATATTCAACAGTTGTTAACTTCACAAGGATGTgtaagtactc ... ctgtttccagTTGAGCAGAAAGACCAGAAGACCCTTGAAAAA
EST: gi|33100226|gb|CF060186.1|CF060186
EST:     TGCTGTATCCTCTGTCATATATTCAACAGTTGTTAACTTCACAAGGATGT                         TTGAGCAGAAAGACCAGAAGACCCTTGAAAAATTGAGGGCTGAGAGGAAAG
genomic: TGCTGTATCCTCTGTCATATATTCAACAGTTGTTAACTTCACAAGGATGTgtaagtactc ... ctgtttccagTTGAGCAGAAAGACCAGAAGACCCTTGAAAAATTGAGGGCTGAGAGGAAAG
EST: gi|71436211|gb|DR817261.1|DR817261
EST:     TGCTGTATCCTCTGTCATATATTCAACAGTTGTTAACTTCACAAGGATGT                         TTGAGCAGAAAGACCAGAAGACCCTTGAAAAATTGAGGGCTGAGAGGAAAG
genomic: TGCTGTATCCTCTGTCATATATTCAACAGTTGTTAACTTCACAAGGATGTgtaagtactc ... ctgtttccagTTGAGCAGAAAGACCAGAAGACCCTTGAAAAATTGAGGGCTGAGAGGAAAG
EST: gi|149015075|gb|EE044828.2|EE044828
EST:     TGCTGTATCCTCTGTCATATATTCAACAGTTGTTAACTTCACAAGGATGT                         TTGAGCAGAAAGACCAGAAGACCCTTGAAAAATTGAGGGCTGAGAGGAAAG
genomic: TGCTGTATCCTCTGTCATATATTCAACAGTTGTTAACTTCACAAGGATGTgtaagtactc ... ctgtttccagTTGAGCAGAAAGACCAGAAGACCCTTGAAAAATTGAGGGCTGAGAGGAAAG
EST: gi|78091242|gb|DV519616.1|DV519616
EST:     TGCTGTATCCTCTGTCATATATTCAACAGTTGTTAACTTCACAAGGATGT                         TTGAGCAGAAAGACCAGAAGACCCTTGAAAAATTGAGGGCTGAGAGGAAAG
genomic: TGCTGTATCCTCTGTCATATATTCAACAGTTGTTAACTTCACAAGGATGTgtaagtactc ... ctgtttccagTTGAGCAGAAAGACCAGAAGACCCTTGAAAAATTGAGGGCTGAGAGGAAAG
EST: gi|148970214|gb|EE021148.2|EE021148
EST:     TGCTGTATCCTCTGTCATATATTCAACAGTTGTTAACTTCACAAGGATGT                         TTGAGCAGAAAGACCAGAAGACCCTTGAAAAATTGAGGGCTGAGAGGAAAG
genomic: TGCTGTATCCTCTGTCATATATTCAACAGTTGTTAACTTCACAAGGATGTgtaagtactc ... ctgtttccagTTGAGCAGAAAGACCAGAAGACCCTTGAAAAATTGAGGGCTGAGAGGAAAG
EST: gi|32833079|gb|CD972757.1|CD972757
EST:     GTCATATATTCAACAGTTGTTAACTTCACAAGGATGT                         TTGAGCAGAAAGACCAGAAGACCCTTGAAAAATTGAGGGCTGAGAGGAAAG
genomic: GTCATATATTCAACAGTTGTTAACTTCACAAGGATGTgtaagtactc ... ctgtttccagTTGAGCAGAAAGACCAGAAGACCCTTGAAAAATTGAGGGCTGAGAGGAAAG
EST: gi|78115258|gb|DV533646.1|DV533646
EST:     TGCTGTATCCTCTGTCATATATTCAACAGTTGTTAACTTCACAAGGATGT                         TTGAGCAGAAAGACCAGAAGACCCTTGAAAAATTGAGGGCTGAGAGGAAAG
genomic: TGCTGTATCCTCTGTCATATATTCAACAGTTGTTAACTTCACAAGGATGTgtaagtactc ... ctgtttccagTTGAGCAGAAAGACCAGAAGACCCTTGAAAAATTGAGGGCTGAGAGGAAAG
EST: gi|74240884|gb|DT648798.1|DT648798
EST:     TGCTGTATCCTCTGTCATATATTCAACAGTTGTTAACTTCACAAGGATGT                         TTGAGCAGAAAGACCAGAAGACCCTTGAAAAATTGAGGGCTGAGAGGAAAG
genomic: TGCTGTATCCTCTGTCATATATTCAACAGTTGTTAACTTCACAAGGATGTgtaagtactc ... ctgtttccagTTGAGCAGAAAGACCAGAAGACCCTTGAAAAATTGAGGGCTGAGAGGAAAG
EST: gi|101399969|gb|EB821831.1|EB821831
EST:     TGCTGTATCCTCTGTCATATATTCAACAGTTGTTAACTTCACAAGGATGT                         TTGAGCAGAAAGACCAGAAGACCCTTGAAAAATTGAGGGCTGAGAGGAAAG
genomic: TGCTGTATCCTCTGTCATATATTCAACAGTTGTTAACTTCACAAGGATGTgtaagtactc ... ctgtttccagTTGAGCAGAAAGACCAGAAGACCCTTGAAAAATTGAGGGCTGAGAGGAAAG
EST: gi|149084452|gb|EE173910.2|EE173910
EST:     TGCTGTATCCTCTGTCATATATTCAACAGTTGTTAACTTCACAAGGATGT                         TTGAGCAGAAAGACCAGAAGACCCTTGAAAAATTGAGGGCTGAGAGGAAAG
genomic: TGCTGTATCCTCTGTCATATATTCAACAGTTGTTAACTTCACAAGGATGTgtaagtactc ... ctgtttccagTTGAGCAGAAAGACCAGAAGACCCTTGAAAAATTGAGGGCTGAGAGGAAAG
EST: gi|71431983|gb|DR813033.1|DR813033
EST:     TGCTGTATCCTCTGTCATATATTCAACAGTTGTTAACTTCACAAGGATGT                         TTGAGCAGAAAGACCAGAAGACCCTTGAAAAATTGAGGGCTGAGAGGAAAG
genomic: TGCTGTATCCTCTGTCATATATTCAACAGTTGTTAACTTCACAAGGATGTgtaagtactc ... ctgtttccagTTGAGCAGAAAGACCAGAAGACCCTTGAAAAATTGAGGGCTGAGAGGAAAG
EST: gi|211519332|gb|FL321899.1|FL321899
EST:     TGCTGTATCCTCTGTCATATATTCAACAGTTGTTAACTTCACAAGGATGT                         TTGAGCAGAAAGACC
genomic: TGCTGTATCCTCTGTCATATATTCAACAGTTGTTAACTTCACAAGGATGTgtaagtactc ... ctgtttccagTTGAGCAGAAAGACC
EST: gi|32832044|gb|CD971722.1|CD971722
EST:     TGCTGTATCCTCTGTCATATATTCAACAGTTGTTAACTTCACAAGGATGT                         TTGAGCAGAAAGACCAGAAGACCCTTGAAAAATTGAGGGCTGAGAGGAAAG
genomic: TGCTGTATCCTCTGTCATATATTCAACAGTTGTTAACTTCACAAGGATGTgtaagtactc ... ctgtttccagTTGAGCAGAAAGACCAGAAGACCCTTGAAAAATTGAGGGCTGAGAGGAAAG
EST: gi|91053445|gb|EB163863.1|EB163863
EST:     TGCTGTATCCTCTGTCATATATTCAACAGTTGTTAACTTCACAAGGATGT                         TTGAGCAGAAAGACCAGAAGACCCTTGAAAAATTGAGGGCTGAGAGGAAAG
genomic: TGCTGTATCCTCTGTCATATATTCAACAGTTGTTAACTTCACAAGGATGTgtaagtactc ... ctgtttccagTTGAGCAGAAAGACCAGAAGACCCTTGAAAAATTGAGGGCTGAGAGGAAAG
EST: gi|32833441|gb|CD973119.1|CD973119
EST:     TGCTGTATCCTCTGTCATATATTCAACAGTTGTTAACTTCACAAGGATGT                         TTGAGCAGAAAGACCAGAAGACCCTTGAAAAATTGAGGGCTGAGAGGAAAG
genomic: TGCTGTATCCTCTGTCATATATTCAACAGTTGTTAACTTCACAAGGATGTgtaagtactc ... ctgtttccagTTGAGCAGAAAGACCAGAAGACCCTTGAAAAATTGAGGGCTGAGAGGAAAG
EST: gi|211136977|gb|FL317636.1|FL317636
EST:     TGCTGTATCCTCTGTCATATATTCAACAGTTGTTAACTTCACAAGGATGT                         TTGAGCAGAAAGACCAGAAGACCCTTGAAAAATTGAGGGCTGAGAGGAAAG
genomic: TGCTGTATCCTCTGTCATATATTCAACAGTTGTTAACTTCACAAGGATGTgtaagtactc ... ctgtttccagTTGAGCAGAAAGACCAGAAGACCCTTGAAAAATTGAGGGCTGAGAGGAAAG
EST: gi|94476107|gb|EB705065.1|EB705065
EST:     TGCTGTATCCTCTGTCATATATTCAACAGTTGTTAACTTCACAAGGATGT                         TTGAGCAAAAAGACCAGAAGAACCCTTGAAAAATTGAGGGCTGAAAGGAAA
genomic: TGCTGTATCCTCTGTCATATATTCAACAGTTGTTAACTTCACAAGGATGTgtaagtactc ... ctgtttccagTTGAGCAGAAAGACCAGAAGA-CCCTTGAAAAATTGAGGGCTGAGAGGAAA

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 106

CTAACTTGGCAAATGAGGGCAATACGAGTGCTACCTATGTTCATTCTTCCTGCTGTATCCTCTGTCATATATTCAACAGTTGTTAACTTCACAAGGATGTgtaagtactc ... ctgtttccagTTGAGCAGAAAGACCAGAAGACCCTTGAAAAATTGAGGGCTGAGAGGAAAGCCAAGATTGATGAGCTTAAAGAGAGAACAAATTATTATCTAACACAGCA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 143

CTAACTTGGCAAATGAGGGCAATACGAGTGCTACCTATGTTCATTCTTCCTGCTGTATCCTCTGTCATATATTCAACAGTTGTTAACTTCACAAGGATGTgtaagtactc ... ctgtttccagTTGAGCAGAAAGACCAGAAGACCCTTGAAAAATTGAGGGCTGAGAGGAAAGCCAAGATTGATGAGCTTAAAGAGAGAACAAATTATTATCTAACACAGCA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 120

CTAACTTGGCAAATGAGGGCAATACGAGTGCTACCTATGTTCATTCTTCCTGCTGTATCCTCTGTCATATATTCAACAGTTGTTAACTTCACAAGGATGTgtaagtactc ... ctgtttccagTTGAGCAGAAAGACCAGAAGACCCTTGAAAAATTGAGGGCTGAGAGGAAAGCCAAGATTGATGAGCTTAAAGAGAGAACAAATTATTATCTAACACAGCA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 169

CTAACTTGGCAAATGAGGGCAATACGAGTGCTACCTATGTTCATTCTTCCTGCTGTATCCTCTGTCATATATTCAACAGTTGTTAACTTCACAAGGATGTgtaagtactc ... ctgtttccagTTGAGCAGAAAGACCAGAAGACCCTTGAAAAATTGAGGGCTGAGAGGAAAGCCAAGATTGATGAGCTTAAAGAGAGAACAAATTATTATCTAACACAGCA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTAACTTGGCAAATGAGGGCAATACGAGTGCTACCTATGTTCATTCTTCCTGCTGTATCCTCTGTCATATATTCAACAGTTGTTAACTTCACAAGGATGTgtaagtactcagaaagccctgttaggaaacactgtttctaatataacttgtagaatataccaggttttgaattttcatttatttttgcagttttataaga

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG