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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcaactcctacaacttatgtttaagacagagggttctagatttgtgcatcgattttcttgtcataacaaagctttcaattcatatttctggaacttttagactgacatgctttccaatctaccttttggaatagCTCTGGAAGAGGTTTAGAGGGGAAGACAAGCCCCCAGCACATCTAGGTGCAAGCAGAGACTACAATGTGGACATGGTGCCAAAG

Basic information

species Zea mays
transcript GRMZM2G117507_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G117507_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os05g34540.1 (Oryza sativa), 3'ss of exon 2
gtaagcaactcctacaacttatgttt-aagacagagggttctagatttgtgcatcgattttct---------------tgtcataacaaag----------ctttcaattcatatttctggaacttttagactgacat-gctttccaatctaccttttggaatagCTCTGGAAGAGGTTTAGAGGGGAAGACAAGCCCCCAGCACATCTAGGTGCAAGCAGAGACTACAATGTGGACATGGTGCCAAAG
|||||||||||| |  |  ||  ||| || |     ||||  | ||| | |     ||||  |               ||| || ||  ||          | ||  ||| ||  |        || |  |||||||| | |||  |||   | ||| |    |||| |||||||||||||||||||||||||| |||||||| ||||| |||||||||||||| |||||||| || ||||| ||||||
gtaagcaactccaatgaactaaatttgaatagtagaggtttcatattcgcgtgcttatttcttgcgaagggatgcttatgttattacggagtacattatatcctttgattaattctatctttgtttgtttactgacattggttttgaattcgcttttggattaagCTGTGGAAGAGGTTTAGAGGGGAAGACAAACCCCCAGCTCATCTGGGTGCAAGCAGAGATTACAATGTAGATATGGTCCCAAAG

upper sequence: GRMZM2G117507_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os05g23860.1 (Oryza sativa), 3'ss of exon 2
gtaagcaa-ctcctac-aacttatgtttaagacagagggttctagatttgtgcatcg--------------attttcttgtcataacaaagctttcaattcat----atttctggaacttttagactgacat-gctttccaatctaccttttggaatagCTCTGGAAGAGGTTTAGAGGGGAAGACAAGCCCCCAGCACATCTAGGTGCAAGCAGAGACTACAATGTGGACATGGTGCCAAAG
|||||||| || | |  ||||||  || |  |     || |||| || |   | ||               ||  |  ||| || ||| ||      |||  |    |||| | |  ||| |  |||||||| | |||||| |   | ||||||||||||| |||||||||||||||||||||||||| ||||| || ||||| ||  |||||| ||| |||||||| || ||||| ||||||
gtaagcaaactgcaatgaacttaatttgaccagtacagggtctatatcttgtcgtcatatcatgtcaaggaatgcttatgttattacagagtacattatttcttttaattttttgtccttgttcactgacattgttttccacttcgctttttggaatagCTGTGGAAGAGGTTTAGAGGGGAAGACAAACCCCCGGCTCATCTGGGCTCAAGCAAAGATTACAATGTAGATATGGTCCCAAAG
















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|211472425|gb|FL096495.1|FL096495
EST:     ACAGAAATGACTACTATGGAGGAGATTCCACCTCGCTCAACCTTAATCAG                         CTCTGGAAGAGGTTTAGAGGGGAAGACAAGCCCCCAGCACATCTAGGTGCA
genomic: ACAGAAATGACTACTATGGAGGAGATTCCACCTCACTCAACCTTAATCAGgtaagcaact ... tttggaatagCTCTGGAAGAGGTTTAGAGGGGAAGACAAGCCCCCAGCACATCTAGGTGCA
EST: gi|211472428|gb|FL096498.1|FL096498
EST:     ACAGAAATGACTACTATGGAGGAGATTCCACCTCGCTCAACCTTAATCAG                         CTCTGGAAGAGGTTTAGAGGGGAAGACAAGCCCCCAGCACATCTAGGTGCA
genomic: ACAGAAATGACTACTATGGAGGAGATTCCACCTCACTCAACCTTAATCAGgtaagcaact ... tttggaatagCTCTGGAAGAGGTTTAGAGGGGAAGACAAGCCCCCAGCACATCTAGGTGCA
EST: gi|33101206|gb|CF061166.1|CF061166
EST:     ACAGAAATGACTACTATGGAGGAGATTCCACCTCACTCAACCTTAATCAG                         CTCTGGAAGAGGTTTAGAGGGGAAGACAAGCCCCCAGCACATCTAGGTGCA
genomic: ACAGAAATGACTACTATGGAGGAGATTCCACCTCACTCAACCTTAATCAGgtaagcaact ... tttggaatagCTCTGGAAGAGGTTTAGAGGGGAAGACAAGCCCCCAGCACATCTAGGTGCA
EST: gi|15590140|gb|BI674756.1|BI674756
EST:     ACAGAAATGACTACTATGGAGGAGATTCCACCTCACTCAACCTTAATCAG                         CTCTGGAAGAGGTTTAGAGGGGAAGACAAGCCCCCAGCACATCTAGGTGCA
genomic: ACAGAAATGACTACTATGGAGGAGATTCCACCTCACTCAACCTTAATCAGgtaagcaact ... tttggaatagCTCTGGAAGAGGTTTAGAGGGGAAGACAAGCCCCCAGCACATCTAGGTGCA
EST: gi|211474937|gb|FL096500.1|FL096500
EST:     ACAGAAATGACTACTATGGAGGAGATTCCACCTCACTCAACCTTAATCAG                         CTCTGGAAGAGGTTTAGAGGGGAAGACAAGCCCCCAGCACATCTAGGTGCA
genomic: ACAGAAATGACTACTATGGAGGAGATTCCACCTCACTCAACCTTAATCAGgtaagcaact ... tttggaatagCTCTGGAAGAGGTTTAGAGGGGAAGACAAGCCCCCAGCACATCTAGGTGCA
EST: gi|211474947|gb|FL096510.1|FL096510
EST:     ACAGAAATGACTACTATGGAGGAGATTCCACCTCGCTCAACCTTAATCAG                         CTCTGGAAGAGGTTTAGAGGGGAAGACAAGCCCCCAGCACATCTAGGTGCA
genomic: ACAGAAATGACTACTATGGAGGAGATTCCACCTCACTCAACCTTAATCAGgtaagcaact ... tttggaatagCTCTGGAAGAGGTTTAGAGGGGAAGACAAGCCCCCAGCACATCTAGGTGCA
EST: gi|211474946|gb|FL096509.1|FL096509
EST:     ACAGAAATGACTACTATGGAGGAGATTCCACCTCGCTCAACCTTAATCAG                         CTCTGGAAGAGGTTTAGAGGGGAAGACAAGCCCCCAGCACATCTAGGTGCA
genomic: ACAGAAATGACTACTATGGAGGAGATTCCACCTCACTCAACCTTAATCAGgtaagcaact ... tttggaatagCTCTGGAAGAGGTTTAGAGGGGAAGACAAGCCCCCAGCACATCTAGGTGCA
EST: gi|60396978|gb|DN229797.1|DN229797
EST:     ACAGAAATGACTACTATGGAGGAGATTCCACCTCACTCAACCTTAATCAG                         CTCTGGAAGAGGTTTAGAGGGGAAGACAAGCCCCCAGCACATCTAGGTGCA
genomic: ACAGAAATGACTACTATGGAGGAGATTCCACCTCACTCAACCTTAATCAGgtaagcaact ... tttggaatagCTCTGGAAGAGGTTTAGAGGGGAAGACAAGCCCCCAGCACATCTAGGTGCA
EST: gi|29544525|gb|CB604905.1|CB604905
EST:     ACAGAAATGACTACTATGGAGGAGATTCCACCTCACTCAACCTTAATCAG                         CTCTGGAAGAGGTTTAGAGGGGAAGACAAGCCCCCAGCACATCTAGGTGCA
genomic: ACAGAAATGACTACTATGGAGGAGATTCCACCTCACTCAACCTTAATCAGgtaagcaact ... tttggaatagCTCTGGAAGAGGTTTAGAGGGGAAGACAAGCCCCCAGCACATCTAGGTGCA
EST: gi|211472424|gb|FL096494.1|FL096494
EST:     ACAGAAATGACTACTATGGAGGAGATTCCACCTCGCTCAACCTTAATCAG                         CTCTGGAAGAGGTTTAGAGGGGAAGACAAGCCCCCAGCACATCTAGGTGCA
genomic: ACAGAAATGACTACTATGGAGGAGATTCCACCTCACTCAACCTTAATCAGgtaagcaact ... tttggaatagCTCTGGAAGAGGTTTAGAGGGGAAGACAAGCCCCCAGCACATCTAGGTGCA
EST: gi|211472420|gb|FL096490.1|FL096490
EST:     ACAGAAATGACTACTATGGAGGAGATTCCACCTCGCTCAACCTTAATCAG                         CTCTGGAAGAGGTTTAGAGGGGAAGACAAGCCCCCAGCACATCTAGGTGCA
genomic: ACAGAAATGACTACTATGGAGGAGATTCCACCTCACTCAACCTTAATCAGgtaagcaact ... tttggaatagCTCTGGAAGAGGTTTAGAGGGGAAGACAAGCCCCCAGCACATCTAGGTGCA
EST: gi|31351669|gb|CD436026.1|CD436026
EST:     ACAGAAATGACTACTATGGAGGAGATTCCACCTCACTCAACCTTAATCAG                         CTCTGGAAGAGGTTTAGAGGGGAAGACAAGCCCCCAGCACATCTAGGTGCA
genomic: ACAGAAATGACTACTATGGAGGAGATTCCACCTCACTCAACCTTAATCAGgtaagcaact ... tttggaatagCTCTGGAAGAGGTTTAGAGGGGAAGACAAGCCCCCAGCACATCTAGGTGCA
EST: gi|33101002|gb|CF060962.1|CF060962
EST:     ACAGAAATGACTACTATGGAGGAGATTCCACCTCACTCAACCTTAATCAG                         CTCTGGAAGAGGTTTAGAGGGGAAGACAAGCCCCCAGCACATCTAGGTACA
genomic: ACAGAAATGACTACTATGGAGGAGATTCCACCTCACTCAACCTTAATCAGgtaagcaact ... tttggaatagCTCTGGAAGAGGTTTAGAGGGGAAGACAAGCCCCCAGCACATCTAGGTGCA
EST: gi|211474939|gb|FL096502.1|FL096502
EST:     ACAGAAATGACTACTATGGAGGAGATTCCACCTCACTCAACCTTAATCAG                         CTCTGGAAGAGGTTTAGAGGGGAAGACAAGCCCCCAGCACATCTAGGTGCA
genomic: ACAGAAATGACTACTATGGAGGAGATTCCACCTCACTCAACCTTAATCAGgtaagcaact ... tttggaatagCTCTGGAAGAGGTTTAGAGGGGAAGACAAGCCCCCAGCACATCTAGGTGCA
EST: gi|211474948|gb|FL096511.1|FL096511
EST:     ACAGAAATGACTACTATGGAGGAGATTCCACCTCGCTCAACCTTAATCAG                         CTCTGGAAGAGGTTTAGAGGGGAAGACAAGCCCCCAGCACATCTAGGTGCA
genomic: ACAGAAATGACTACTATGGAGGAGATTCCACCTCACTCAACCTTAATCAGgtaagcaact ... tttggaatagCTCTGGAAGAGGTTTAGAGGGGAAGACAAGCCCCCAGCACATCTAGGTGCA
EST: gi|211474938|gb|FL096501.1|FL096501
EST:     ACAGAAATGACTACTATGGAGGAGATTCCACCTCACTCAACCTTAATCAG                         CTCTGGAAGAGGTTTAGAGGGGAAGACAAGCCCCCAGCACATCTAGGTGCA
genomic: ACAGAAATGACTACTATGGAGGAGATTCCACCTCACTCAACCTTAATCAGgtaagcaact ... tttggaatagCTCTGGAAGAGGTTTAGAGGGGAAGACAAGCCCCCAGCACATCTAGGTGCA
EST: gi|211474941|gb|FL096504.1|FL096504
EST:     ACAGAAATGACTACTATGGAGGAGATTCCACCTCACTCAACCTTAATCAG                         CTCTGGAAGAGGTTTAGAGGGGAAGACAAGCCCCCAGCACATCTAGGTGCA
genomic: ACAGAAATGACTACTATGGAGGAGATTCCACCTCACTCAACCTTAATCAGgtaagcaact ... tttggaatagCTCTGGAAGAGGTTTAGAGGGGAAGACAAGCCCCCAGCACATCTAGGTGCA
EST: gi|31360108|gb|CD444465.1|CD444465
EST:     ACAGAAATGACTACTATGGAGGAGATTCCACCTCACTCAACCTTAATCAG                         CTCTGGAAGAGGTTTAGAGGGGAAGACAAGCCCCCAGCACATCTAGGTGCA
genomic: ACAGAAATGACTACTATGGAGGAGATTCCACCTCACTCAACCTTAATCAGgtaagcaact ... tttggaatagCTCTGGAAGAGGTTTAGAGGGGAAGACAAGCCCCCAGCACATCTAGGTGCA
EST: gi|211472423|gb|FL096493.1|FL096493
EST:     ACAGAAATGACTACTATGGAGGAGATTCCACCTCGCTCAACCTTAATCAG                         CTCTGGAAGAGGTTTAGAGGGGAAGACAAGCCCCCAGCACATCTAGGTGCA
genomic: ACAGAAATGACTACTATGGAGGAGATTCCACCTCACTCAACCTTAATCAGgtaagcaact ... tttggaatagCTCTGGAAGAGGTTTAGAGGGGAAGACAAGCCCCCAGCACATCTAGGTGCA
EST: gi|211472427|gb|FL096497.1|FL096497
EST:     ACAGAAATGACTACTATGGAGGAGATTCCACCTCACTCAACCTTAATCAG                         CTCTGGAAGAGGTTTAGAGGGGAAGACAAGCCCCCAGCACATCTAGGTGCA
genomic: ACAGAAATGACTACTATGGAGGAGATTCCACCTCACTCAACCTTAATCAGgtaagcaact ... tttggaatagCTCTGGAAGAGGTTTAGAGGGGAAGACAAGCCCCCAGCACATCTAGGTGCA
EST: gi|211472426|gb|FL096496.1|FL096496
EST:     ACAGAAATGACTACTATGGAGGAGATTCCACCTCACTCAACCTTAATCAG                         CTCTGGAAGAGGTTTAGAGGGGAAGACAAGCCCCCAGCACATCTAGGTGCA
genomic: ACAGAAATGACTACTATGGAGGAGATTCCACCTCACTCAACCTTAATCAGgtaagcaact ... tttggaatagCTCTGGAAGAGGTTTAGAGGGGAAGACAAGCCCCCAGCACATCTAGGTGCA
EST: gi|211474943|gb|FL096506.1|FL096506
EST:     ACAGAAATGACTACTATGGAGGAGATTCCACCTCACTCAACCTTAATCAG                         CTCTGGAAGAGGTTTAGAGGGGAAGACAAGCCCCCAGCACATCTAGGTGCA
genomic: ACAGAAATGACTACTATGGAGGAGATTCCACCTCACTCAACCTTAATCAGgtaagcaact ... tttggaatagCTCTGGAAGAGGTTTAGAGGGGAAGACAAGCCCCCAGCACATCTAGGTGCA
EST: gi|211472429|gb|FL096499.1|FL096499
EST:     ACAGAAATGACTACTATGGAGGAGATTCCACCTCGCTCAACCTTAATCAG                         CTCTGGAAGAGGTTTAGAGGGGAAGACAAGCCCCCAGCACATCTAGGTGCA
genomic: ACAGAAATGACTACTATGGAGGAGATTCCACCTCACTCAACCTTAATCAGgtaagcaact ... tttggaatagCTCTGGAAGAGGTTTAGAGGGGAAGACAAGCCCCCAGCACATCTAGGTGCA
EST: gi|24773930|gb|CA409184.1|CA409184
EST:     TGGAGGAGATTCCACCTCGCTCAACCTTAATCAG                         CTCTGGAAGAGGTTTAGAGGGGAAGACAAGCCCCCAGCACATCTAGGTGCA
genomic: TGGAGGAGATTCCACCTCACTCAACCTTAATCAGgtaagcaact ... tttggaatagCTCTGGAAGAGGTTTAGAGGGGAAGACAAGCCCCCAGCACATCTAGGTGCA
EST: gi|29946002|gb|CB815929.1|CB815929
EST:     ACAGAAATGACTACTATGGAGGAGATTCCACCTCACTCAACCTTAATCAG                         CTCTGGAAGAGGTTTAGAGGGGAAGACAAGCCCCCAGCACATCTAGGTGCA
genomic: ACAGAAATGACTACTATGGAGGAGATTCCACCTCACTCAACCTTAATCAGgtaagcaact ... tttggaatagCTCTGGAAGAGGTTTAGAGGGGAAGACAAGCCCCCAGCACATCTAGGTGCA
EST: gi|26557597|gb|CA829832.1|CA829832
EST:     ACAGAAATGACTACTATGGAGGAGATTCCACCTCACTCAACCTTAATCAG                         CTCTGGAAGAGGTTTAGAGGGGAAGACAAGCCCCCAGCACATCTAGGTGCA
genomic: ACAGAAATGACTACTATGGAGGAGATTCCACCTCACTCAACCTTAATCAGgtaagcaact ... tttggaatagCTCTGGAAGAGGTTTAGAGGGGAAGACAAGCCCCCAGCACATCTAGGTGCA
EST: gi|211113229|gb|FL096514.1|FL096514
EST:     ACAGAAATGACTACTATGGAGGAGATTCCACCTCGCTCAACCTTAATCAG                         CTCTGGAAGAGGTTTAGAGGGGAAGACAAGCCCCCAGCACATCTAGGTGCA
genomic: ACAGAAATGACTACTATGGAGGAGATTCCACCTCACTCAACCTTAATCAGgtaagcaact ... tttggaatagCTCTGGAAGAGGTTTAGAGGGGAAGACAAGCCCCCAGCACATCTAGGTGCA

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: 280

GTTTTGCATATGGACAGAAATGACTACTATGGAGGAGATTCCACCTCACTCAACCTTAATCAGgtaagcaact ... tttggaatagCTCTGGAAGAGGTTTAGAGGGGAAGACAAGCCCCCAGCACATCTAGGTGCAAGCAGAGACTACAATGTGGACATGGTGCCAAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 399

GTTTTGCATATGGACAGAAATGACTACTATGGAGGAGATTCCACCTCACTCAACCTTAATCAGgtaagcaact ... tttggaatagCTCTGGAAGAGGTTTAGAGGGGAAGACAAGCCCCCAGCACATCTAGGTGCAAGCAGAGACTACAATGTGGACATGGTGCCAAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 453

GTTTTGCATATGGACAGAAATGACTACTATGGAGGAGATTCCACCTCACTCAACCTTAATCAGgtaagcaact ... tttggaatagCTCTGGAAGAGGTTTAGAGGGGAAGACAAGCCCCCAGCACATCTAGGTGCAAGCAGAGACTACAATGTGGACATGGTGCCAAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 194

GTTTTGCATATGGACAGAAATGACTACTATGGAGGAGATTCCACCTCACTCAACCTTAATCAGgtaagcaact ... tttggaatagCTCTGGAAGAGGTTTAGAGGGGAAGACAAGCCCCCAGCACATCTAGGTGCAAGCAGAGACTACAATGTGGACATGGTGCCAAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcatatttctggaacttttagactgacatgctttccaatctaccttttggaatagCTCTGGAAGAGGTTTAGAGGGGAAGACAAGCCCCCAGCACATCTAGGTGCAAGCAGAGACTACAATGTGGACATGGTGCCAAAG
                    gactgac  putative branch site (score: 194)
                                      tctacctttt  putative PPT
            aactttta  TA-rich tract