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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgcattgagtttcttttactcacattttttgtaagccttttgttatgcattgagagtttattttacttattactttttttgtaataatgtcttttttacttgtcaatatagGCTGTTGCGCTTGCAAATCAAAAACTTCTTGGAATTCCTTCA

Basic information

species Zea mays
transcript GRMZM5G866758_T01
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G866758_T02 (Zea mays), 3'ss of exon 11
lower sequence: LOC_Os09g07830.2 (Oryza sativa), 3'ss of exon 11
gtatgcattgagtttcttttactcacattttttgtaagccttttgttatgcattgagagtttattttacttattactttttttgtaataatgtcttttttacttgtcaatatagGCTGTTGCGCTTGCAAATCAAAAACTTCTTGGAATTCCTTCA
||||| |||||   ||| | | |||  || ||    ||  |||| || || | | | | ||| ||  |   |  | | |  | ||| | ||    |||| |||| |||||| |||||||||| |||||||||||||| ||||||||||||||||||
gtatg-attgatcatctgt-attcaacttatt----agtttttttttttgtaatcataatttgttcca---aaaattctaatggtatttat----ttttgacttatcaatacagGCTGTTGCACTTGCAAATCAAAAGCTTCTTGGAATTCCTTCA
















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|17931054|gb|BM268014.1|BM268014
EST:     GATTAGAGTCATCCCGTGTTGATTTCTATGAGATTAATGAAGCCTTTTCG                         GCTGTTGCGCTTGCAAATCAAAAACTTCTTGGAATTCCTTCA
genomic: GATTAGAGTCATCCCGTGTTGATTTCTATGAGATTAATGAAGCCTTTTCGgtatgcattg ... gtcaatatagGCTGTTGCGCTTGCAAATCAAAAACTTCTTGGAATTCCTTCA
EST: gi|30088105|gb|CB886310.1|CB886310
EST:     GATTAGAGTCATCCCGTGTTGATTTCTATGAGATTAATGAAGCCTTTTCG                         GCTGTTGCGCTTGCAAATCAAAAACTTCTTGGAATTCCTTCA
genomic: GATTAGAGTCATCCCGTGTTGATTTCTATGAGATTAATGAAGCCTTTTCGgtatgcattg ... gtcaatatagGCTGTTGCGCTTGCAAATCAAAAACTTCTTGGAATTCCTTCA
EST: gi|101395308|gb|EB819584.1|EB819584
EST:     GATTAGAGTCATCCCGTGTTGATTTCTATGAGATTAATGAAGCCTTTTCG                         GCTGTTGCGCTTGCAAATCAAAAACTTCTTGGAATTCCTTCA
genomic: GATTAGAGTCATCCCGTGTTGATTTCTATGAGATTAATGAAGCCTTTTCGgtatgcattg ... gtcaatatagGCTGTTGCGCTTGCAAATCAAAAACTTCTTGGAATTCCTTCA
EST: gi|211193824|gb|FL472434.1|FL472434
EST:     GATTAGAGTCATCCCGTGTTGATTTCTATGAGATTAATGAAGCCTTTTCG                         GCTGTTGCGCTTGCAAATCAAAAGCTTCTTGGAATTCCTTCA
genomic: GATTAGAGTCATCCCGTGTTGATTTCTATGAGATTAATGAAGCCTTTTCGgtatgcattg ... gtcaatatagGCTGTTGCGCTTGCAAATCAAAAACTTCTTGGAATTCCTTCA
EST: gi|78091101|gb|DV519475.1|DV519475
EST:     GATTAGAGTCATCCCGTGTTGATTTCTATGAGATTAATGAAGCCTTTTCG                         GCTGTTGCGCTTGCAAATCAAAAACTTCTTGGAATTCCTTCA
genomic: GATTAGAGTCATCCCGTGTTGATTTCTATGAGATTAATGAAGCCTTTTCGgtatgcattg ... gtcaatatagGCTGTTGCGCTTGCAAATCAAAAACTTCTTGGAATTCCTTCA
EST: gi|31909501|gb|CD650950.1|CD650950
EST:     GATTAGAGTCATCCCGTGTTGATTTCTATGAGATTAATGAAGCCTTTTCG                         GCTGTTGCGCTTGCAAATCAAAAACTTCTTGGAATTCCTTCA
genomic: GATTAGAGTCATCCCGTGTTGATTTCTATGAGATTAATGAAGCCTTTTCGgtatgcattg ... gtcaatatagGCTGTTGCGCTTGCAAATCAAAAACTTCTTGGAATTCCTTCA
EST: gi|110525002|gb|EE029186.1|EE029186
EST:     GATTAGAGTCATCCCGTGTTGATTTCTATGAGATTAATGAAGCCTTTTCG                         GCTGTTGCGCTTGCAAATCAAAAACTTCTTGGAATTCCTTCA
genomic: GATTAGAGTCATCCCGTGTTGATTTCTATGAGATTAATGAAGCCTTTTCGgtatgcattg ... gtcaatatagGCTGTTGCGCTTGCAAATCAAAAACTTCTTGGAATTCCTTCA
EST: gi|166435185|gb|EG112283.1|EG112283
EST:     AGAGTCATCCCGTGTTGATTTCTATGAGATTAATGAAGCCTTTTCG                         GCTGTTGCGCTTGCAAATCAAAAACTTCTTGGAATTCCTTCA
genomic: AGAGTCATCCCGTGTTGATTTCTATGAGATTAATGAAGCCTTTTCGgtatgcattg ... gtcaatatagGCTGTTGCGCTTGCAAATCAAAAACTTCTTGGAATTCCTTCA
EST: gi|93281704|gb|EB673968.1|EB673968
EST:     GATTAGAGTCATCCCGTGTTGATTTCTATGAGATTAATGAAGCCTTTTCG                         GCTGTTGCGCTTGCAAATCAAAAACTTCTTGGAATTCCTTCA
genomic: GATTAGAGTCATCCCGTGTTGATTTCTATGAGATTAATGAAGCCTTTTCGgtatgcattg ... gtcaatatagGCTGTTGCGCTTGCAAATCAAAAACTTCTTGGAATTCCTTCA
EST: gi|78087734|gb|DV516127.1|DV516127
EST:     GATTAGAGTCATCCCGTGTTGATTTCTATGAGATTAATGAAGCCTTTTCG                         GCTGTTGCGCTTGCAAATCAAAAACTTCTTGGAATTCCTTCA
genomic: GATTAGAGTCATCCCGTGTTGATTTCTATGAGATTAATGAAGCCTTTTCGgtatgcattg ... gtcaatatagGCTGTTGCGCTTGCAAATCAAAAACTTCTTGGAATTCCTTCA
EST: gi|76921549|gb|DV168617.1|DV168617
EST:     GATTAGAGTCATCCCGTGTTGATTTCTATGAGATTAATGAAGCCTTTTCG                         GCTGTTGCGCTTGCAAATCAAAAACTTCTTGGAATTCCTTCA
genomic: GATTAGAGTCATCCCGTGTTGATTTCTATGAGATTAATGAAGCCTTTTCGgtatgcattg ... gtcaatatagGCTGTTGCGCTTGCAAATCAAAAACTTCTTGGAATTCCTTCA
EST: gi|33095848|gb|CF055842.1|CF055842
EST:     CATCCCGTGCTGATTTCTATGAGATTAATGAAGCCTTTTCG                         GCTGTTGCGCTTGCAAATCAAAAACTTCTTGGAATTCCTTCA
genomic: CATCCCGTGTTGATTTCTATGAGATTAATGAAGCCTTTTCGgtatgcattg ... gtcaatatagGCTGTTGCGCTTGCAAATCAAAAACTTCTTGGAATTCCTTCA
EST: gi|31909499|gb|CD650949.1|CD650949
EST:     GATTAGAGTCATCCCGTGTTGATTTCTATGAGATTAATGAAGCCTTTTCG                         GCTGTTGCGCTTGCAAATCAAAAACTTCTTGGAATTCCTTCA
genomic: GATTAGAGTCATCCCGTGTTGATTTCTATGAGATTAATGAAGCCTTTTCGgtatgcattg ... gtcaatatagGCTGTTGCGCTTGCAAATCAAAAACTTCTTGGAATTCCTTCA
EST: gi|76284259|gb|DV023827.1|DV023827
EST:     GATTAGAGTCATCCCGTGTTGATTTCTATGAGATTAATGAAGCCTTTTCG                         GCTGTTGCGCTTGCAAATCAAAAACTTCTTGGAATTCCTTCA
genomic: GATTAGAGTCATCCCGTGTTGATTTCTATGAGATTAATGAAGCCTTTTCGgtatgcattg ... gtcaatatagGCTGTTGCGCTTGCAAATCAAAAACTTCTTGGAATTCCTTCA
EST: gi|30306466|gb|CD001139.1|CD001139
EST:     GATTAGAGTCATCCCGTGTTGATTTCTATGAGATTAATGAAGCCTTTTCG                         GCTGTTGCGCTTGCAAATCAAAAACTTCTTGGAATTCCTTCA
genomic: GATTAGAGTCATCCCGTGTTGATTTCTATGAGATTAATGAAGCCTTTTCGgtatgcattg ... gtcaatatagGCTGTTGCGCTTGCAAATCAAAAACTTCTTGGAATTCCTTCA
EST: gi|149016999|gb|EE154316.2|EE154316
EST:     GATTAGAGTCATCCCGTGTTGATTTCTATGAGATTAATGAAGCCTTTTCG                         GCTGTTGCGCTTGCAAATCAAAAACTTCTTGGAATTCCTTCA
genomic: GATTAGAGTCATCCCGTGTTGATTTCTATGAGATTAATGAAGCCTTTTCGgtatgcattg ... gtcaatatagGCTGTTGCGCTTGCAAATCAAAAACTTCTTGGAATTCCTTCA
EST: gi|76936635|gb|DV174816.1|DV174816
EST:     GATTAGAGTCATCCCGTGTTGATTTCTATGAGATTAATGAAGCCTTTTCG                         GCTGTTGCGCTTGCAAATCAAAAACTTCTTGGAATTCCTTCA
genomic: GATTAGAGTCATCCCGTGTTGATTTCTATGAGATTAATGAAGCCTTTTCGgtatgcattg ... gtcaatatagGCTGTTGCGCTTGCAAATCAAAAACTTCTTGGAATTCCTTCA
EST: gi|211206261|gb|FL471226.1|FL471226
EST:     GATTGGGGTCATCCCGTGTGGATTTCTTTGAGATTAATGAAGCATTTTCG                         GCTGTTGCGCTTGCAAATCAAAAACTTCTTGGAATTCCTTCA
genomic: GATTAGAGTCATCCCGTGTTGATTTCTATGAGATTAATGAAGCCTTTTCGgtatgcattg ... gtcaatatagGCTGTTGCGCTTGCAAATCAAAAACTTCTTGGAATTCCTTCA
EST: gi|29544660|gb|CB605040.1|CB605040
EST:     GATTAGAGTCATCCCGTGTTGATTTCTATGAGATTAATGAAGCCTTTTCG                         GCTGTTGCGCTTGCAAATCAAAAACTTCTTGGAATTCCTTCA
genomic: GATTAGAGTCATCCCGTGTTGATTTCTATGAGATTAATGAAGCCTTTTCGgtatgcattg ... gtcaatatagGCTGTTGCGCTTGCAAATCAAAAACTTCTTGGAATTCCTTCA
EST: gi|32864390|gb|CF004072.1|CF004072
EST:     GATTAGAGTCATCCCGTGTTGATTTCTATGAGATTAATGAAGCCTTTTCG                         GCTGTTGCGCTTGCAAATCAAAAACTTCTTGGAATTCCTTCA
genomic: GATTAGAGTCATCCCGTGTTGATTTCTATGAGATTAATGAAGCCTTTTCGgtatgcattg ... gtcaatatagGCTGTTGCGCTTGCAAATCAAAAACTTCTTGGAATTCCTTCA
EST: gi|76017958|gb|DT945128.1|DT945128
EST:     GATTAGAGTCATCCCGTGTTGATTTCTATGAGATTAATGAAGCCTTTTCG                         GCTGTTGCGCTTGCAAATCAAAAACTTCTTGGAATTCCTTCA
genomic: GATTAGAGTCATCCCGTGTTGATTTCTATGAGATTAATGAAGCCTTTTCGgtatgcattg ... gtcaatatagGCTGTTGCGCTTGCAAATCAAAAACTTCTTGGAATTCCTTCA
EST: gi|32862142|gb|CF001824.1|CF001824
EST:     GATTAGAGTCATCCCGTGTTGATTTCTATGAGATTAATGAAGCCTTTTCG                         GCTGTTGCGCTTGCAAATCAAAAACTTCTTGGAATTCCTTCA
genomic: GATTAGAGTCATCCCGTGTTGATTTCTATGAGATTAATGAAGCCTTTTCGgtatgcattg ... gtcaatatagGCTGTTGCGCTTGCAAATCAAAAACTTCTTGGAATTCCTTCA

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), 42 (downstream exon)
Score: 101

TTTTACAACCACTCCAGCACTTGCAATACCAAAGGCTATCGCAAATGCTGGATTAGAGTCATCCCGTGTTGATTTCTATGAGATTAATGAAGCCTTTTCGgtatgcattg ... gtcaatatagGCTGTTGCGCTTGCAAATCAAAAACTTCTTGGAATTCCTTCA


Block sizes: 48 (upstream exon), 42 (downstream exon)
Score: 121

TTTTACAACCACTCCAGCACTTGCAATACCAAAGGCTATCGCAAATGCTGGATTAGAGTCATCCCGTGTTGATTTCTATGAGATTAATGAAGCCTTTTCGgtatgcattg ... gtcaatatagGCTGTTGCGCTTGCAAATCAAAAACTTCTTGGAATTCCTTCA


Block sizes: 49 (upstream exon), 42 (downstream exon)
Score: 86

TTTTACAACCACTCCAGCACTTGCAATACCAAAGGCTATCGCAAATGCTGGATTAGAGTCATCCCGTGTTGATTTCTATGAGATTAATGAAGCCTTTTCGgtatgcattg ... gtcaatatagGCTGTTGCGCTTGCAAATCAAAAACTTCTTGGAATTCCTTCA


Block sizes: 49 (upstream exon), 42 (downstream exon)
Score: 60

TTTTACAACCACTCCAGCACTTGCAATACCAAAGGCTATCGCAAATGCTGGATTAGAGTCATCCCGTGTTGATTTCTATGAGATTAATGAAGCCTTTTCGgtatgcattg ... gtcaatatagGCTGTTGCGCTTGCAAATCAAAAACTTCTTGGAATTCCTTCA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttattttacttattactttttttgtaataatgtcttttttacttgtcaatatagGCTGTTGCGCTTGCAAATCAAAAACTTCTTGGAATTCCTTCA
                                 tcttttttacttgtc  CT-rich tract
     tttacttattactttt  TA-rich tract