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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgtattgtttcattttcttgatgttgacccttcgatctattctaaaaaaaatacaattatatttacgaagattcatctgtgatacttatgtaaagttgtcttgcataacactgcatctgtcaattttggaacagATCCCAGAGGAAGAGAAGAATCTTGGCCCACATGATCGATTGATTCATGTTTACCATTTCATGAAAGACCCTAACCAGAATCAACAAATTCAAAATTTTG

Basic information

species Zea mays
transcript GRMZM2G303655_T01
intron # 17
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G303655_T01 (Zea mays), 3'ss of exon 17
lower sequence: LOC_Os12g30540.1 (Oryza sativa), 3'ss of exon 27
gtttgtattgtttcattttcttgatgttgacccttcgatctattctaaaaaaaatacaattatatttacgaag-attcatctgtgatacttatgtaaagttgtcttgcataacactgcatctgtcaattttggaacagATCCCAGAGGAAGAGAAGAATCTTGGCCCACATGATCGATTGATTCATGTTTACCATTTCATGAAAGACCCTAACCAGAATCAACAAATTCAAAATTTTG
               ||   ||||   |  |  |||   ||      | |   | | ||||  |||||   || || |  |||| ||     | ||   |||  |||||||||| |    ||  |||||  | ||||||| ||||||||||||||||| ||||||||||||||||| ||||||||||||||||||||||||||||| ||||| || |||||                 
--------------gttcgtttgaacat--cttttctgactgac--gatattgacataattccatttagttagtatactactgtcat-----tatattattgatttgcataacatttttgctaccaatt--gaaacagATACCAGAGGAAGAGAAGAACCTTGGCCCACATGATCGGTTGATTCATGTTTACCATTTCATGAAAGATCCTAATCAAAATCAG----------------

upper sequence: GRMZM2G303655_T01 (Zea mays), 3'ss of exon 17
lower sequence: GLYMA20G11330.1 (Glycine max), 3'ss of exon 19
----------------------------------------------gtttgtattgtttcattttcttgatgttgacccttcgatctattctaaaaaaaatacaattatatttacgaagattcatctgtgatacttatgtaaagttgtcttgcataacactgcatct------gtcaattt----tggaacagATCCCAGAGGAAGAGAAGAATCTTGGCCCACATGATCGATTGATTCATGTTTACCATTTCATGAAAGACCCTAACCAGAATCAACAAATTCAAAATTTTG
                                               || || |  | |  | |||||| | ||     ||| |   ||  ||| |       | |  | |  |   | | | || |   ||  || |  ||           ||||   |   |||      ||||  ||    || ||||||| ||||| |||||||| ||||||||  | ||||||||  | |||||||||||||||||||  |||||  |    || || |||                
gtaggaatctctttctgtatgtggggctagatcaagggagatagcatttagtgtaatgttgtattcttgcttttatttgttcaaatgatgataacactgcccgactcttgtaaatatataattatgttctatttttgttcaattcctcacaaaataattgttattcttacatggtcatattcaaatgtaacagATTCCAGAAGAAGAGAAAAATCTTGGTTCTCATGATCGTCTAATTCATGTTTACCATTTCAATAAAGAGACAGCTCAAAACCAAATG-------------

upper sequence: GRMZM2G303655_T01 (Zea mays), 3'ss of exon 17
lower sequence: Vv08s0032g00600.t01 (Vitis vinifera), 3'ss of exon 27
gtttgtattgtttcattttcttgatgttgacccttcgatctattctaaaaaaaatacaattatatttacgaagattcat-ctgtgatacttatgtaaagttgtcttgcataacactgcatctgtcaattttggaacagATCCCAGAGGAAGAGAAGAATCTTGGCCCACATGATCGATTGATTCATGTTTACCATTTCATGAAAGACCCTAACCAGAATCAACAAATTCAAAATTTTG
                                        |  ||    ||   || |   || |  || || ||   | |||   | || ||||    |  ||||   |   |||   |   |||  |      ||||| ||||| ||||||||||||||||| || |||||||| ||||||||||||||||| ||||  || ||  ||   ||||||||                 
---------------------------------------ttgatcattgaactttagatcgatgtacacaaatatctttactggtgttctcatgttggctaatcttatcttgaacttttttaatcatct------cagattccagAAGAAGAGAAGAATCTTGGTCCCCATGATCGCTTGATTCATGTTTACCACTTCACAAAGGAGACTGTACAGAATCAGATG-------------

upper sequence: GRMZM2G303655_T01 (Zea mays), 3'ss of exon 17
lower sequence: Vv13s0073g00610.t01 (Vitis vinifera), 3'ss of exon 27
gtttgtattgtttcattttcttgatgttgacccttcgatctattctaaaaaaaatacaattatatttacgaagattcatc--tgtgatacttatgtaaagttgtcttgcataacactgcatctgtcaattttggaacagATCCCAGAGGAAGAGAAGAATCTTGGCCCACATGATCGATTGATTCATGTTTACCATTTCATGAAAGACCCTAACCAGAATCAACAAATTCAAAATTTTG
                                        ||    |  ||  || || ||  | |    |    | ||   | |   |  |  |||     || |    ||    |  | ||      |||   |||||| || || || ||||| || || || || |||||||| |||||||||||||| ||||| ||||||||| | |  ||||||||                 
---------------------------------------ttaccagatcaaccatccactttgactctttagacctgattgttatagcaaatcagtaggagggtttcaagtagttttttaacttgtttctttactacagATTCCTGAAGAGGAGAAAAACCTAGGTCCTCATGATCGGTTGATTCATGTTTATCATTTTATGAAAGACACAACTCAGAATCAGGTG-------------

upper sequence: GRMZM2G303655_T01 (Zea mays), 3'ss of exon 17
lower sequence: Vv06s0009g00960.t01 (Vitis vinifera), 3'ss of exon 27
gtttgtattgtttcattttcttgatgttgacccttcgatctattctaaaaaaaatacaattatatttacgaagattcatctgtgatacttatgtaaagttgtcttgcataacactgcatctgtcaattttggaacagATCCCAGAGGAAGAGAAGAATCTTGGCCCACATGATCGATTGATTCATGTTTACCATTTCATGAAAGACCCTAACCAGAATCAACAAATTCAAAATTTTG
                ||  || || ||     ||  || |  |||||   | ||  || || | |    | ||| ||  | ||||          | || ||     ||||  |       | ||| |||   ||||| || || |||||||| |||||||| ||||| ||||| ||||||||||| ||||| || |  |||||| |    ||||| |||                
----------------ttagttaatttttcttttttaattt--tctaatttagatgaaagtaaaatgtacatgatccagatttgatc---------aattttccaatttaacttt-------taaatattg---cagATTCCTGAAGAAGAGAAAAATCTTGGACCACAGGATCGCTTGATTCATGTATACCACTTTACAAAAGACACAGCTCAGAACCAAATG-------------

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|67032245|gb|CO460994.1|CO460994
EST:     AGAAGATAGAGAACATAAATGATCAGTACTGGACATTACGAGCTGAGGAG                         ATCCCAGAGGAAGAGAAGAATCTTGGCCCACATGATCGATTGATTCATGTT
genomic: AGAAGATAGAGAACATAAATGATCAGTACTGGACATTACGAGCTGAGGAGgtttgtattg ... tttggaacagATCCCAGAGGAAGAGAAGAATCTTGGCCCACATGATCGATTGATTCATGTT
EST: gi|31354456|gb|CD438813.1|CD438813
EST:     AGAAGATAGAGAACATAAATGATCAGTACTGGACATTACGAGCTGAGGAG                         ATCCCAGAGGAAGAGAAGAATCTTGGCCCACATGATCGATTGATTCATGTT
genomic: AGAAGATAGAGAACATAAATGATCAGTACTGGACATTACGAGCTGAGGAGgtttgtattg ... tttggaacagATCCCAGAGGAAGAGAAGAATCTTGGCCCACATGATCGATTGATTCATGTT
EST: gi|32916706|gb|CF021518.1|CF021518
EST:     AGAAGATAGAGAACATAAATGATCAGTACTGGACATTACGAGCTGAGGAG                         ATCCCAGAGGAAGAGAAGAATCTTGGCCCACATGATCGATTGATTCATGTT
genomic: AGAAGATAGAGAACATAAATGATCAGTACTGGACATTACGAGCTGAGGAGgtttgtattg ... tttggaacagATCCCAGAGGAAGAGAAGAATCTTGGCCCACATGATCGATTGATTCATGTT
EST: gi|47962024|gb|CN844733.1|CN844733
EST:     AGAAGATAGAGAACATAAATGATCAGTACTGGACATTACGAGCTGAGGAG                         ATCCCAGAGGAAGAGAAGAATCTTGGCCCACATGATCGATTGATTCATGTT
genomic: AGAAGATAGAGAACATAAATGATCAGTACTGGACATTACGAGCTGAGGAGgtttgtattg ... tttggaacagATCCCAGAGGAAGAGAAGAATCTTGGCCCACATGATCGATTGATTCATGTT
EST: gi|60359281|gb|DN226254.1|DN226254
EST:     AGAAGATAGAGAACATAAATGATCAGTACTGGACATTACGAGCTGAGGAG                         ATCCCAGAGGAAGAGAAGAATCTTGGCCCACATGATCGATTGATTCATGTT
genomic: AGAAGATAGAGAACATAAATGATCAGTACTGGACATTACGAGCTGAGGAGgtttgtattg ... tttggaacagATCCCAGAGGAAGAGAAGAATCTTGGCCCACATGATCGATTGATTCATGTT

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: 46 (upstream exon), 49 (downstream exon)
Score: 233

ATCTTTCCACCTCATGAGAAGATAGAGAACATAAATGATCAGTACTGGACATTACGAGCTGAGGAGgtttgtattg ... tttggaacagATCCCAGAGGAAGAGAAGAATCTTGGCCCACATGATCGATTGATTCATGTTTACCATTTCATGAAAGACCCTAACCAGAATCAACAAATTCAAAATTTTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 213

ATCTTTCCACCTCATGAGAAGATAGAGAACATAAATGATCAGTACTGGACATTACGAGCTGAGGAGgtttgtattg ... tttggaacagATCCCAGAGGAAGAGAAGAATCTTGGCCCACATGATCGATTGATTCATGTTTACCATTTCATGAAAGACCCTAACCAGAATCAACAAATTCAAAATTTTG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 242

ATCTTTCCACCTCATGAGAAGATAGAGAACATAAATGATCAGTACTGGACATTACGAGCTGAGGAGgtttgtattg ... tttggaacagATCCCAGAGGAAGAGAAGAATCTTGGCCCACATGATCGATTGATTCATGTTTACCATTTCATGAAAGACCCTAACCAGAATCAACAAATTCAAAATTTTG


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 178

ATCTTTCCACCTCATGAGAAGATAGAGAACATAAATGATCAGTACTGGACATTACGAGCTGAGGAGgtttgtattg ... tttggaacagATCCCAGAGGAAGAGAAGAATCTTGGCCCACATGATCGATTGATTCATGTTTACCATTTCATGAAAGACCCTAACCAGAATCAACAAATTCAAAATTTTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgatacttatgtaaagttgtcttgcataacactgcatctgtcaattttggaacagATCCCAGAGGAAGAGAAGAATCTTGGCCCACATGATCGATTGATTCATGTTTACCATTTCATGAAAGACCCTAACCAGAATCAACAAATTCAAAATTTTG
                       gcataac  putative branch site (score: 178)
      ttatgtaaa  TA-rich tract