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

...tggcaccgctatatacttcaataaagctgacattggcctttcagttgaaattgaagcaatcgtcgtttaatactctattgtttgcatcttctatgtacagGCAAAAGGGATGAACTATCTTCATAAGCGTAATCCTCCAATAGTCCACCGGGATCTTAAGTCACCAAACCTGTTGGTTGACAAAAAGTACACTGTGAAA

Basic information

species Zea mays
transcript GRMZM2G059671_T04
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G059671_T01 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os02g32610.2 (Oryza sativa), 3'ss of exon 11
------------------------------------------------tggcaccgctatatacttca-ataaagctgacattggcctttcagttgaaattgaagcaatcgtcgtttaatactct---attgtttgcatcttctatgtacagGCAAAAGGGATGAACTATCTTCATAAGCGTAATCCTCCAATAGTCCACCGGGATCTTAAGTCACCAAACCTGTTGGTTGACAAAAAGTACACTGTGAAA
                                                || |   |  |||| ||| | ||||||   |  ||| || |  | |  |||||| ||         | ||| | ||    ||| | || | ||||  | | ||||| || |||||||| || ||||| ||||| |||||||| ||||||||||||||||| ||||||||||| ||||||||||| ||||||||||||||||| 
gtaaaatcatatatacttatctcaatacagaatttaggtctaacagaatgac-tggacatatgctttatataaagtaaaggttgaccgtagaatcaaaattgtaggtgcttctttataaaaatcattgattttgtgtaccttc-gtatccagGCTAAGGGGATGAATTACCTTCACAAGCGCAATCCTCCTATAGTCCACCGGGATCTAAAGTCACCAAATCTGTTGGTTGATAAAAAGTACACTGTGAAG

upper sequence: GRMZM2G059671_T01 (Zea mays), 3'ss of exon 9
lower sequence: GLYMA13G21480.1 (Glycine max), 3'ss of exon 10
----------tggcaccgctatatacttcaataaagctgacattggcctttcagttgaaat--tgaagcaatcgtcgtttaatactctattgtttgc-atcttct-atgtacagGCAAAAGGGATGAACTATCTTCATAAGCGTAATCCTCCAATAGTCCACCGGGATCTTAAGTCACCAAACCTGTTGGTTGACAAAAAGTACACTGTGAAA
              |      ||||||          |   | |    ||| | ||  |||     |    | ||  |||  || |  |   | ||  || || | || | |||||||| |||||||| ||||||||||| |||||||| || || || ||  | ||||| || || ||||||||  | |||||||| || || || ||||| 
gtatgtatttaaaaaataaactatactgtttcttcttttttagtattttttgaattataatgtcataatctttgtatttttttaattaaccatgtgttattttatcatttgcagGCAAAGGGGATGAATTATCTTCATAAACGTAATCCCCCCATTGTTCATAGAGATCTGAAATCTCCAAACCTTCTTGTTGACAAGAAATATACAGTGAAG

upper sequence: GRMZM2G059671_T01 (Zea mays), 3'ss of exon 9
lower sequence: GLYMA10G07610.1 (Glycine max), 3'ss of exon 12
--tggcaccgcta-tatacttcaataaagctgacattggcctttcagttgaaattgaagcaatcgtcgtttaatactctattgtttgcatcttctatgtacagGCAAAAGGGATGAACTATCTTCATAAGCGTAATCCTCCAATAGTCCACCGGGATCTTAAGTCACCAAACCTGTTGGTTGACAAAAAGTACACTGTGAAA
      || | |  |    || | ||    |||  |||   | |||  | ||| | |        |  ||| ||   | || || |   | |   || | |||||||| |||||||| ||||||||||| |||||||| || || || ||  | ||||| || || ||||||||  | |||||||| || || || ||||| 
aactctactgtttctgctttttagtatttttgaatttgtattgtca--taaaaataatctttgtattctttgattaaccat-gtgttattttatcatttgcagGCAAAGGGGATGAATTATCTTCATAAACGTAATCCCCCCATTGTTCATAGAGATCTGAAATCTCCAAACCTTCTTGTTGACAAGAAATATACAGTGAAG

upper sequence: GRMZM2G059671_T01 (Zea mays), 3'ss of exon 9
lower sequence: Vv08s0007g03910.t01 (Vitis vinifera), 3'ss of exon 10
tggcaccgctatatacttcaataaagctgacattggccttt---cagttgaaat---tgaagcaatcgtcgtttaatactctattgtttgcatcttctatgtacagGCAAAAGGGATGAACTATCTTCATAAGCGTAATCCTCCAATAGTCCACCGGGATCTTAAGTCACCAAACCTGTTGGTTGACAAAAAGTACACTGTGAAA
         | | |   | | |     |   ||   |||||   ||| | ||||   |      ||  || |||       | || |||   | |   |   |||||| || || ||||| ||||||||||| || |||||||| || || || || ||| | ||||| |||||||| |||||||||||||| ||||| ||||| 
------tatttttttagtgattgttatttggatgcaccttttaccagctaaaataacttgttttattatcatttccgtgctttttttttttttttaaaacaaacagGCCAAGGGCATGAATTATCTTCATAAACGCAATCCTCCCATTGTTCATCGAGATTTGAAGTCTCCAAACCTTTTGGTTGACAAAAAATACACCGTGAAG

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|20802940|gb|BQ293990.1|BQ293990
EST:     CAAGGGAAAATCTGGAGGAGCGCCGCCGCTTGAGTATGGCTTTCGACGTG                         GCAAAAGGGATGAACTATCTTCATAAGCGTAATCCTCCAATAGTCCACCGG
genomic: CAAGGGAAAATCTGGAGGAGCGCCGCCGCTTGAGTATGGCTTTCGACGTGgtaaaaaact ... ctatgtacagGCAAAAGGGATGAACTATCTTCATAAGCGTAATCCTCCAATAGTCCACCGG
EST: gi|76284240|gb|DV023808.1|DV023808
EST:     CAAGGGAAAATCTGGAGGAGCGCCGCCGCTTGAGTATGGCTTTTGACGTG                         GCAAAAGGGATGAACTATCTTCATAAGCGTAATCCTCCAATAGTCCACCGG
genomic: CAAGGGAAAATCTGGAGGAGCGCCGCCGCTTGAGTATGGCTTTCGACGTGgtaaaaaact ... ctatgtacagGCAAAAGGGATGAACTATCTTCATAAGCGTAATCCTCCAATAGTCCACCGG
EST: gi|67042437|gb|CO468692.1|CO468692
EST:     CAAGGGAAAATCTGGAGGAGCGCCGCCGCTTGAGTATGGCTTTCGACGTG                         GTAAAAGGGATGAACTATCTTCATAAGCGTAATCCTCCAATAGTCCACCGG
genomic: CAAGGGAAAATCTGGAGGAGCGCCGCCGCTTGAGTATGGCTTTCGACGTGgtaaaaaact ... ctatgtacagGCAAAAGGGATGAACTATCTTCATAAGCGTAATCCTCCAATAGTCCACCGG
EST: gi|149096725|gb|EE182499.2|EE182499
EST:     GAGTATGGCTTTCGACGTG                         GCAAAAGGGATGAACTATCTTCATAAGCGTAATCCTCCAATAGTCCACCGG
genomic: GAGTATGGCTTTCGACGTGgtaaaaaact ... ctatgtacagGCAAAAGGGATGAACTATCTTCATAAGCGTAATCCTCCAATAGTCCACCGG
EST: gi|32836824|gb|CD976502.1|CD976502
EST:     CAAGGGAAAATCTGGAGGAGCGCCGCCGCTTGAGTATGGCTTTCGACGTG                         GCAAAAGGGATGAACTATCTTCATAAGCGTAATCCTCCAATAGTCCACCGG
genomic: CAAGGGAAAATCTGGAGGAGCGCCGCCGCTTGAGTATGGCTTTCGACGTGgtaaaaaact ... ctatgtacagGCAAAAGGGATGAACTATCTTCATAAGCGTAATCCTCCAATAGTCCACCGG
EST: gi|26456437|gb|CA828020.1|CA828020
EST:     CAAGGGAAAATCTGGAGGAGCGCCGCCGCTTGAGTATGGCTTTCGACGTG                         GCAAAAGGGATGAACTATCTTCATAAGCGTAATCCTCCAATAGTCCACCGG
genomic: CAAGGGAAAATCTGGAGGAGCGCCGCCGCTTGAGTATGGCTTTCGACGTGgtaaaaaact ... ctatgtacagGCAAAAGGGATGAACTATCTTCATAAGCGTAATCCTCCAATAGTCCACCGG
EST: gi|32839244|gb|CD978925.1|CD978925
EST:     CAAGGGAAAATCTGGAGGAGCGCCGCCGCTTGAGTATGGCTTTCGACGTG                         GCAAAAGGGATGAACTATCTTCATAAGCGTAATCCTCCAATAGTCCACCGG
genomic: CAAGGGAAAATCTGGAGGAGCGCCGCCGCTTGAGTATGGCTTTCGACGTGgtaaaaaact ... ctatgtacagGCAAAAGGGATGAACTATCTTCATAAGCGTAATCCTCCAATAGTCCACCGG
EST: gi|32837172|gb|CD976850.1|CD976850
EST:     CAAGGGAAAATCTGGAGGAGCGCCGCCGCTTGAGTATGGCTTTCGACGTG                         GCAAAAGGGATGAACTATCTTCATAAGCGTAATCCTCCAATAGTCCACCGG
genomic: CAAGGGAAAATCTGGAGGAGCGCCGCCGCTTGAGTATGGCTTTCGACGTGgtaaaaaact ... ctatgtacagGCAAAAGGGATGAACTATCTTCATAAGCGTAATCCTCCAATAGTCCACCGG
EST: gi|60358265|gb|DN225238.1|DN225238
EST:     CAAGGGAAAATCTGGAGGAGCGCCGCCGCTTGAGTATGGCTTTCGACGTG                         GCAAAAGGGATGAACTATCTTCATAAGCGTAATCCTCCAATAGTCCACCGG
genomic: CAAGGGAAAATCTGGAGGAGCGCCGCCGCTTGAGTATGGCTTTCGACGTGgtaaaaaact ... ctatgtacagGCAAAAGGGATGAACTATCTTCATAAGCGTAATCCTCCAATAGTCCACCGG
EST: gi|60357002|gb|DN223975.1|DN223975
EST:     CAAGGGAAAATCTGGAGGAGCGCCGCCGCTTGAGTATGGCTTTCGACGTG                         GCAAAAGGGATGAACTATCTTCATAAGCGTAATCCTCCAATAGTCCACCGG
genomic: CAAGGGAAAATCTGGAGGAGCGCCGCCGCTTGAGTATGGCTTTCGACGTGgtaaaaaact ... ctatgtacagGCAAAAGGGATGAACTATCTTCATAAGCGTAATCCTCCAATAGTCCACCGG
EST: gi|60337361|gb|DN204334.1|DN204334
EST:     CAAGGGAAAATCTGGAGGAGCGCCGCCGCTTGAGTATGGCTTTCGACGTG                         GCAAAAGGGATGAACTATCTTCATAAGCGTAATCCTCCAATAGTCCACCGG
genomic: CAAGGGAAAATCTGGAGGAGCGCCGCCGCTTGAGTATGGCTTTCGACGTGgtaaaaaact ... ctatgtacagGCAAAAGGGATGAACTATCTTCATAAGCGTAATCCTCCAATAGTCCACCGG
EST: gi|32838830|gb|CD978511.1|CD978511
EST:     CAAGGGAAAATCTGGAGGAGCGCCGCCGCTTGAGTATGGCTTTCGACGTG                         GCAAAAGGGATGAACTATCTTCATAAGCGTAATCCTCCAATAGTCCACCGG
genomic: CAAGGGAAAATCTGGAGGAGCGCCGCCGCTTGAGTATGGCTTTCGACGTGgtaaaaaact ... ctatgtacagGCAAAAGGGATGAACTATCTTCATAAGCGTAATCCTCCAATAGTCCACCGG
EST: gi|32836743|gb|CD976421.1|CD976421
EST:     CAAGGGAAAATCTGGAGGAGCGCCGCCGCTTGAGTATGGCTTTCGACGTG                         GCAAAAGGGATGAACTATCTTCATAAGCGTAATCCTCCAATAGTCCACCGG
genomic: CAAGGGAAAATCTGGAGGAGCGCCGCCGCTTGAGTATGGCTTTCGACGTGgtaaaaaact ... ctatgtacagGCAAAAGGGATGAACTATCTTCATAAGCGTAATCCTCCAATAGTCCACCGG
EST: gi|78544345|gb|DV621843.1|DV621843
EST:     CAA-GGAAAATCTGGAGGAGCGCCGCCGCTTGAGTATGGCTTTCGACGTG                         GCAAAAGGGATGAACTATCTTCATAAGCGTAATCCTCCAATAGTCCACCGG
genomic: CAAGGGAAAATCTGGAGGAGCGCCGCCGCTTGAGTATGGCTTTCGACGTGgtaaaaaact ... ctatgtacagGCAAAAGGGATGAACTATCTTCATAAGCGTAATCCTCCAATAGTCCACCGG

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: 48 (upstream exon), 49 (downstream exon)
Score: 67

AGGTAGCTTATACAGACTTTTACACAGGCATGCTGCAAGGGAAAATCTGGAGGAGCGCCGCCGCTTGAGTATGGCTTTCGACGTGgtaaaaaact ... ctatgtacagGCAAAAGGGATGAACTATCTTCATAAGCGTAATCCTCCAATAGTCCACCGGGATCTTAAGTCACCAAACCTGTTGGTTGACAAAAAGTACACTGTGAAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 72

AGGTAGCTTATACAGACTTTTACACAGGCATGCTGCAAGGGAAAATCTGGAGGAGCGCCGCCGCTTGAGTATGGCTTTCGACGTGgtaaaaaact ... ctatgtacagGCAAAAGGGATGAACTATCTTCATAAGCGTAATCCTCCAATAGTCCACCGGGATCTTAAGTCACCAAACCTGTTGGTTGACAAAAAGTACACTGTGAAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 96

AGGTAGCTTATACAGACTTTTACACAGGCATGCTGCAAGGGAAAATCTGGAGGAGCGCCGCCGCTTGAGTATGGCTTTCGACGTGgtaaaaaact ... ctatgtacagGCAAAAGGGATGAACTATCTTCATAAGCGTAATCCTCCAATAGTCCACCGGGATCTTAAGTCACCAAACCTGTTGGTTGACAAAAAGTACACTGTGAAA


Block sizes: 31 (upstream exon), 42 (downstream exon)
Score: 17

AGGTAGCTTATACAGACTTTTACACAGGCATGCTGCAAGGGAAAATCTGGAGGAGCGCCGCCGCTTGAGTATGGCTTTCGACGTGgtaaaaaact ... ctatgtacagGCAAAAGGGATGAACTATCTTCATAAGCGTAATCCTCCAATAGTCCACCGGGATCTTAAGTCACCAAACCTGTTGGTTGACAAAAAGTACACTGTGAAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgaaattgaagcaatcgtcgtttaatactctattgtttgcatcttctatgtacagGCAAAAGGGATGAACTATCTTCATAAGCGTAATCCTCCAATAGTCCACCGGGATCTTAAGTCACCAAACCTGTTGGTTGACAAAAAGTACACTGTGAAA
                   gtttaat  putative branch site (score: 17)
                                       catcttct  putative PPT
                    tttaatactctatt  TA-rich tract