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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGATGAAAAACGGATATATTGCAACTGTCACCCTCTTCCAATCATGAGgtacgcaatgtggcttttgcccataatatgcacatctccagagcacggagcatggactaagttaactgtcgaagtcttccattttgacag

Basic information

species Zea mays
transcript GRMZM2G116434_T01
intron # 14
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G116434_T01 (Zea mays), 5'ss of exon 14
lower sequence: LOC_Os06g49990.3 (Oryza sativa), 5'ss of exon 14
GTGATGAAAAACGGATATATTGCAACTGTCACCCTCTTCCAATCATGAGgtacgcaat-gtggcttttgcccataatatgcacatctccagagcacggag-catggacta--agttaactg--tcgaagtcttccattttgacag---------------------------
|| |||||||| ||||||||||||||||| |||||||| ||||||||||||| | | | ||   |  ||| |||| |||||| |  ||   | ||| ||| ||  ||| |  ||| ||  |   | ||   ||| || |                                 
GTCATGAAAAATGGATATATTGCAACTGTTACCCTCTTTCAATCATGAGgtatgtatttgtccttgctgcacatagtatgcaaaa-tctgtaacactgagtcactgaccaacagtgaaacgggacaaaaatttcaatctcagtgctaacagctgatggtgatgcatatccag

upper sequence: GRMZM2G116434_T01 (Zea mays), 5'ss of exon 14
lower sequence: LOC_Os06g49990.2 (Oryza sativa), 5'ss of exon 14
GTGATGAAAAACGGATATATTGCAACTGTCACCCTCTTCCAATCATGAGgtacgcaat-gtggcttttgcccataatatgcacatctccagagcacggag-catggacta--agttaactgt--cgaagtcttccattttgacag
|| |||||||| ||||||||||||||||| |||||||| ||||||||||||| | | | ||   |  ||| |||| |||||| |  ||   | ||| ||| ||  ||| |  ||| ||  |   | ||   ||| || |      
GTCATGAAAAATGGATATATTGCAACTGTTACCCTCTTTCAATCATGAGgtatgtatttgtccttgctgcacatagtatgcaaaa-tctgtaacactgagtcactgaccaacagtgaaacgggacaaaaatttcaatctcag---
















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|37377650|gb|CF625447.1|CF625447
EST:     GTGATGAAAAACGGATATATTGCAACTGTCACCCTCTTCCAATCATGAG                         TGTGCCACTACATGTGCTGCTGCTCTGAGCTCTGGCTGCAACAATGATGGT
genomic: GTGATGAAAAACGGATATATTGCAACTGTCACCCTCTTCCAATCATGAGgtacgcaatg ... attttgacagTGTGCCACTACATGTGCTGCTGCTCTGAGCTCTGGCTGCAACAATGATGGT
EST: gi|6695458|gb|AW288566.1|AW288566
EST:     GTGATGAAAAACGGATATATTGCAACTGTCACCCTCTTCCAATCATGAG                         TGTGCCACTACATGTGCTGCTGCTCTGAGCTCTGGCTGCAACAATGGTGGT
genomic: GTGATGAAAAACGGATATATTGCAACTGTCACCCTCTTCCAATCATGAGgtacgcaatg ... attttgacagTGTGCCACTACATGTGCTGCTGCTCTGAGCTCTGGCTGCAACAATGATGGT
EST: gi|13126006|gb|BG316681.1|BG316681
EST:     GTGATGAAAAACGGATATATTGCAACTGTCACCCTCTTCCAATCATGAG                         TGTGCCACTACATGTGCTGCTGCTCTGAGCTCTGGCTGCAACAATGATG
genomic: GTGATGAAAAACGGATATATTGCAACTGTCACCCTCTTCCAATCATGAGgtacgcaatg ... attttgacagTGTGCCACTACATGTGCTGCTGCTCTGAGCTCTGGCTGCAACAATGATG
EST: gi|67024702|gb|CO453451.1|CO453451
EST:     GTGATGAAAA-CGGATATATTGCAACTGTCACCCTCTTCNA-TCATGAG                         TGTGCCACTACATGTGCTGCTGCTCTGAGCTCTGGCTGCACCA-TGGTGGT
genomic: GTGATGAAAAACGGATATATTGCAACTGTCACCCTCTTCCAATCATGAGgtacgcaatg ... attttgacagTGTGCCACTACATGTGCTGCTGCTCTGAGCTCTGGCTGCAACAATGATGGT
EST: gi|16925040|gb|BM078108.1|BM078108
EST:     GTGATGAAAAACGGATATATTGCAACTGTCACCCTCTTCCAATCATGAG                         TGTGCCACTACATGTGCTGCTGCTCTGAGCTCTGGCTGCAACAATGATGGT
genomic: GTGATGAAAAACGGATATATTGCAACTGTCACCCTCTTCCAATCATGAGgtacgcaatg ... attttgacagTGTGCCACTACATGTGCTGCTGCTCTGAGCTCTGGCTGCAACAATGATGGT
EST: gi|148961880|gb|EE012666.2|EE012666
EST:     GTGATGAAAAACGGATATATTGCAACTGTCACCCTCTTCCAATCATGAG                         TGTGCCACTACATGTGCTGCTGCTTTGAGCTCTGGCTGCAACAATGATGGT
genomic: GTGATGAAAAACGGATATATTGCAACTGTCACCCTCTTCCAATCATGAGgtacgcaatg ... attttgacagTGTGCCACTACATGTGCTGCTGCTCTGAGCTCTGGCTGCAACAATGATGGT
EST: gi|78074282|gb|DV502716.1|DV502716
EST:     GTGATGAAAAACGGATATATTGCAACTGTCACCCTCTTCCAATCATGAG                         TGTGCCACTACATGTGCTGCTGCTTTGAGCTCTGGCTGCAACAATGATGGT
genomic: GTGATGAAAAACGGATATATTGCAACTGTCACCCTCTTCCAATCATGAGgtacgcaatg ... attttgacagTGTGCCACTACATGTGCTGCTGCTCTGAGCTCTGGCTGCAACAATGATGGT
EST: gi|16377490|gb|BI991962.1|BI991962
EST:     GTGATGAAAAACGGATATATTGCAACTGTCACCCTCTTCCAATCATGAG                         TGTGCCACTACATGTGCTGCTGCTCTGAGCTCTGGCTGCAACAATGATGGT
genomic: GTGATGAAAAACGGATATATTGCAACTGTCACCCTCTTCCAATCATGAGgtacgcaatg ... attttgacagTGTGCCACTACATGTGCTGCTGCTCTGAGCTCTGGCTGCAACAATGATGGT
EST: gi|32797638|gb|CD949874.1|CD949874
EST:     GTGATGAAAAACGGATATATTGCAACTGTCACCCTCTTCCAATCATGAG                         TGTGCCACTACATGTGCTGCTGCTCTGAGCTCTGGCTGCAACAATGATGGT
genomic: GTGATGAAAAACGGATATATTGCAACTGTCACCCTCTTCCAATCATGAGgtacgcaatg ... attttgacagTGTGCCACTACATGTGCTGCTGCTCTGAGCTCTGGCTGCAACAATGATGGT
EST: gi|37400992|gb|CF637857.1|CF637857
EST:     GTGATGAAAAACGGATATATTGCAACTGTCACCCTCTTCCAATCATGAG                         TGTGCCACTACATGTGCTGCTGCTCTGAGCTCTGGCTGCAACAATGATGGT
genomic: GTGATGAAAAACGGATATATTGCAACTGTCACCCTCTTCCAATCATGAGgtacgcaatg ... attttgacagTGTGCCACTACATGTGCTGCTGCTCTGAGCTCTGGCTGCAACAATGATGGT
EST: gi|67015496|gb|CO444245.1|CO444245
EST:     GTGATGAAAAACGGATATATTGCAACTGTCACCCTCTTCCA-TCATGAG                         TGTGCCACTACATGTGCTGCTGCTCTGAGCTCTGGCTGC
genomic: GTGATGAAAAACGGATATATTGCAACTGTCACCCTCTTCCAATCATGAGgtacgcaatg ... attttgacagTGTGCCACTACATGTGCTGCTGCTCTGAGCTCTGGCTGC
EST: gi|40334237|gb|CK368307.1|CK368307
EST:     GTGATGAAAAACGGATATATTGCAACTGTCACCCTCTTCCAATCATGAG                         TGTGCCACTACATGTGCTGCTGCTCTGAGCTCTGGCTGCAACAATGATGGT
genomic: GTGATGAAAAACGGATATATTGCAACTGTCACCCTCTTCCAATCATGAGgtacgcaatg ... attttgacagTGTGCCACTACATGTGCTGCTGCTCTGAGCTCTGGCTGCAACAATGATGGT
EST: gi|45568491|gb|CK986089.1|CK986089
EST:     GTGATGAAAAACGGATATATTGCAACTGTCACCCTCTTCCAATCATGAG                         TGTGCCACTACATGTGCTGCTGCTCTGAGCTCTGGCTGCAACATTGATGGT
genomic: GTGATGAAAAACGGATATATTGCAACTGTCACCCTCTTCCAATCATGAGgtacgcaatg ... attttgacagTGTGCCACTACATGTGCTGCTGCTCTGAGCTCTGGCTGCAACAATGATGGT
EST: gi|32787792|gb|CD940028.1|CD940028
EST:     GTGATGAAAAACGGATATATTGCAACTGTCACCCTCTTCCAATCATGAG                         TGTGCCACTACATGTGCTGCTGCTCTGAGCTCTGGCTGCAACAATGGTGGT
genomic: GTGATGAAAAACGGATATATTGCAACTGTCACCCTCTTCCAATCATGAGgtacgcaatg ... attttgacagTGTGCCACTACATGTGCTGCTGCTCTGAGCTCTGGCTGCAACAATGATGGT
EST: gi|32798071|gb|CD950307.1|CD950307
EST:     GTGATGAAAAACGGATATATTGCAACTGTCACCCTCTTCCAATCATGAG                         TGTGCCACTACATGTGCTGCTGCTCTGAGCTCTGGCTGCAACAATGATGGT
genomic: GTGATGAAAAACGGATATATTGCAACTGTCACCCTCTTCCAATCATGAGgtacgcaatg ... attttgacagTGTGCCACTACATGTGCTGCTGCTCTGAGCTCTGGCTGCAACAATGATGGT
EST: gi|33467826|gb|CF244875.1|CF244875
EST:     GTGATGAAAAACGGATATATTGCAACTGTCACCCTCTTCCGATCATGAG                         TGTGCCCCTACATGTGCTGCTGCTTTGAGCTCTGGCTGCAACAATGATGGT
genomic: GTGATGAAAAACGGATATATTGCAACTGTCACCCTCTTCCAATCATGAGgtacgcaatg ... attttgacagTGTGCCACTACATGTGCTGCTGCTCTGAGCTCTGGCTGCAACAATGATGGT
EST: gi|5152761|gb|AI759059.1|AI759059
EST:     GTGATGAAAAACGGATATATTGCAACTGTCACCCTCTTCCAATCATGAG                         TGTGCCACTACATGTGCTGCTGCTCTGAGCTCTGGCTGCAACAATGGTGGT
genomic: GTGATGAAAAACGGATATATTGCAACTGTCACCCTCTTCCAATCATGAGgtacgcaatg ... attttgacagTGTGCCACTACATGTGCTGCTGCTCTGAGCTCTGGCTGCAACAATGATGGT
EST: gi|67014669|gb|CO443418.1|CO443418
EST:     GTGATGAAAAACGGATATATTGCAACTGTCACCCTCTTCCAATCATGAG                         TGTGCCACTACATGTGCTGCTGCTCTGAGCTCTGGCTGCAACAATGGTGGT
genomic: GTGATGAAAAACGGATATATTGCAACTGTCACCCTCTTCCAATCATGAGgtacgcaatg ... attttgacagTGTGCCACTACATGTGCTGCTGCTCTGAGCTCTGGCTGCAACAATGATGGT
EST: gi|60348112|gb|DN215085.1|DN215085
EST:     GTGATGAAAAACGGATATATTGCAACTGTCACCCTCTTCCAATCATGAG                         TGTGCCACTACATGTGCTGCTGCTCTGAGCTCTGGCTGCAACAATGATGGT
genomic: GTGATGAAAAACGGATATATTGCAACTGTCACCCTCTTCCAATCATGAGgtacgcaatg ... attttgacagTGTGCCACTACATGTGCTGCTGCTCTGAGCTCTGGCTGCAACAATGATGGT
EST: gi|12968213|gb|BG265159.1|BG265159
EST:     GTGATGAAAAACGGATATATTGCAACTGTCACCCTCTTCCAATCATGAG                         TGTGCCACTACATGTGCTGCTGCTCTGAGCTCTGGCTGCAACAATGATGGT
genomic: GTGATGAAAAACGGATATATTGCAACTGTCACCCTCTTCCAATCATGAGgtacgcaatg ... attttgacagTGTGCCACTACATGTGCTGCTGCTCTGAGCTCTGGCTGCAACAATGATGGT
EST: gi|71762669|gb|DR960606.1|DR960606
EST:     GTGATGAAAAACGGATATATTGCAACTGTCACCCTCTTCCAATCATGAG                         TGTGCCACTACATGTGCTGCTGCTTTGAGCTCTGGCTGCAACAATGATGGT
genomic: GTGATGAAAAACGGATATATTGCAACTGTCACCCTCTTCCAATCATGAGgtacgcaatg ... attttgacagTGTGCCACTACATGTGCTGCTGCTCTGAGCTCTGGCTGCAACAATGATGGT
EST: gi|78110552|gb|DV528962.1|DV528962
EST:     GTGATGAAAAACGGATATATTGCAACTGTCACCCTCTTCCAATCATGAG                         TGTGCCACTACATGTGCTGCTGCTTTGAGCTCTGGCTGCAACAATGATGGT
genomic: GTGATGAAAAACGGATATATTGCAACTGTCACCCTCTTCCAATCATGAGgtacgcaatg ... attttgacagTGTGCCACTACATGTGCTGCTGCTCTGAGCTCTGGCTGCAACAATGATGGT
EST: gi|76014245|gb|DT941415.1|DT941415
EST:     GTGATGAAAAACGGATATATTGCAACTGTCACCCTCTTCCAATCATGAG                         TGTGCCACTACATGTGCTGCTGCTTTGAGCTCTGGCTGCAACAATGATGGT
genomic: GTGATGAAAAACGGATATATTGCAACTGTCACCCTCTTCCAATCATGAGgtacgcaatg ... attttgacagTGTGCCACTACATGTGCTGCTGCTCTGAGCTCTGGCTGCAACAATGATGGT
EST: gi|84351339|gb|DW245744.1|DW245744
EST:     GTGATGAAAAACGGATATATTGCAACTGTCACCCTCTTCCAATCATGAG                         TGTGCCACTACATGTGCTGCTGCTCTGAGCTCTGGCTGCAACAATGATGGT
genomic: GTGATGAAAAACGGATATATTGCAACTGTCACCCTCTTCCAATCATGAGgtacgcaatg ... attttgacagTGTGCCACTACATGTGCTGCTGCTCTGAGCTCTGGCTGCAACAATGATGGT
EST: gi|101393042|gb|EB818452.1|EB818452
EST:     GTGATGAAAAACGGATATATTGCAACTGTCACCCTCTTCCAATCATGAG                         TGTGCCACTACATGTGCTGTTGTTTTGAGTTCTGGCTGCAACAATGATGGT
genomic: GTGATGAAAAACGGATATATTGCAACTGTCACCCTCTTCCAATCATGAGgtacgcaatg ... attttgacagTGTGCCACTACATGTGCTGCTGCTCTGAGCTCTGGCTGCAACAATGATGGT

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: 45 (upstream exon), 49 (downstream exon)
Score: 78

GTGATGAAAAACGGATATATTGCAACTGTCACCCTCTTCCAATCATGAGgtacgcaatg ... attttgacagTGTGCCACTACATGTGCTGCTGCTCTGAGCTCTGGCTGCAACAATGATGGTTAACCTGCAGAAAGGAAGTATGCCGTACTTTTGTGCTTCAGCAGCAGCA


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 149

GTGATGAAAAACGGATATATTGCAACTGTCACCCTCTTCCAATCATGAGgtacgcaatg ... attttgacagTGTGCCACTACATGTGCTGCTGCTCTGAGCTCTGGCTGCAACAATGATGGTTAACCTGCAGAAAGGAAGTATGCCGTACTTTTGTGCTTCAGCAGCAGCA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 181

GTGATGAAAAACGGATATATTGCAACTGTCACCCTCTTCCAATCATGAGgtacgcaatg ... attttgacagTGTGCCACTACATGTGCTGCTGCTCTGAGCTCTGGCTGCAACAATGATGGTTAACCTGCAGAAAGGAAGTATGCCGTACTTTTGTGCTTCAGCAGCAGCA


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 145

GTGATGAAAAACGGATATATTGCAACTGTCACCCTCTTCCAATCATGAGgtacgcaatg ... attttgacagTGTGCCACTACATGTGCTGCTGCTCTGAGCTCTGGCTGCAACAATGATGGTTAACCTGCAGAAAGGAAGTATGCCGTACTTTTGTGCTTCAGCAGCAGCA