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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTCTGGAGAGAATACATGGATTTCAATTAGGCGATAGTACACTGGAATGGAAAAAGAAGAAATGGGATGACTTCAAGGAGAGACTATCCAAGgtaatttctttgctctctctctctctctagtttgagggttttaccctaatgaatacgatttgtcaatgtattttaccag

Basic information

species Zea mays
transcript GRMZM2G351582_T01
intron # 15
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G351582_T01 (Zea mays), 5'ss of exon 15
lower sequence: LOC_Os08g36774.1 (Oryza sativa), 5'ss of exon 14
CTCTGGAGAGAATACATGGATTTCAATTAGGCGATAGTACACTGGAATGGAAAAAGAAGAAATGGGATGACTTCAAGGAGAGACTATCCAAGgta---------atttctttgctc--tctctctctctctagtttgag--ggttttaccctaatgaatacgatttgtcaatgtattttaccag--------
||||| ||||| | |||||||| || || || ||||| ||||||||||||||||||||||||||||| || ||||| || ||| ||||||||||          |||||||| |    | |   |   |||||  |||    |||||     |     | |  |   | |||| | |||  |          
CTCTGCAGAGAGTGCATGGATTCCATTTGGGTGATAGCACACTGGAATGGAAAAAGAAGAAATGGGAGGATTTCAACGATAGATTATCCAAGgtgtgtaatttgatttctttacatggttttatttgttctagcatgattttgttttctttcagaattttcagtagtttaatggagtttttctttctgaatc
















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|60348538|gb|DN215511.1|DN215511
EST:     TGGAATGGAAAAAGAAGAAATGGGATGACTTCAAGGAGAGACTATCCAAG                         CTTCTGAGTTTACAAGAAGCCTGGACTCTAATAATTGATGATGGATTGGCG
genomic: TGGAATGGAAAAAGAAGAAATGGGATGACTTCAAGGAGAGACTATCCAAGgtaatttctt ... attttaccagCTTCTGAGTTTACAAGAAGCCTGGACTCTAATAATTGATGATGGATTGGCG
EST: gi|6445448|gb|AW179366.1|AW179366
EST:     TGGAATGGAAAAAGAAGAAATGGGATGACTTCAAGGAGAGACTATCCAAG                         CTTCTGAGTTTACAAGAAGCCTGGACTCTAATAATTGATGATGGATTGGCG
genomic: TGGAATGGAAAAAGAAGAAATGGGATGACTTCAAGGAGAGACTATCCAAGgtaatttctt ... attttaccagCTTCTGAGTTTACAAGAAGCCTGGACTCTAATAATTGATGATGGATTGGCG
EST: gi|20513026|gb|BQ280212.1|BQ280212
EST:     TGGAATGGAAAAAGAAGAAATGGGATGACTTCAAGGAGAGACTATCCAAG                         CTTCTGAGTTTACAAGAAGCCTGGACTCTAATAATTGATGATGGATTGGCG
genomic: TGGAATGGAAAAAGAAGAAATGGGATGACTTCAAGGAGAGACTATCCAAGgtaatttctt ... attttaccagCTTCTGAGTTTACAAGAAGCCTGGACTCTAATAATTGATGATGGATTGGCG
EST: gi|78544301|gb|DV621799.1|DV621799
EST:     TGGAATGGAAAAAGAAGAAATGGGATGACTTCAAGGAGAGACTATCCAAG                         CTTCTGAGTTTACAAGAAGCCTGGACTCTAATAATTGATGATGGATTGGCG
genomic: TGGAATGGAAAAAGAAGAAATGGGATGACTTCAAGGAGAGACTATCCAAGgtaatttctt ... attttaccagCTTCTGAGTTTACAAGAAGCCTGGACTCTAATAATTGATGATGGATTGGCG
EST: gi|211282780|gb|FL192971.1|FL192971
EST:     TGGAATGGAAAAAGAAGAAATGGGATGACTTCAAGGAGAGACTATCCAAG                         CTTCTGAGTTTACAAGAAGCCTGGACTCTAATAATTGATGATGGATTGGCG
genomic: TGGAATGGAAAAAGAAGAAATGGGATGACTTCAAGGAGAGACTATCCAAGgtaatttctt ... attttaccagCTTCTGAGTTTACAAGAAGCCTGGACTCTAATAATTGATGATGGATTGGCG
EST: gi|88748313|gb|DY532454.1|DY532454
EST:     TGGAATGGAAAAAGAAGAAATGGGATGACTTCAAGGAGAGACTATCCAAG                         CTTCTGAGTTTACAAGAAGCCTGGACTCTAATAATTGATGATGGATTGGCG
genomic: TGGAATGGAAAAAGAAGAAATGGGATGACTTCAAGGAGAGACTATCCAAGgtaatttctt ... attttaccagCTTCTGAGTTTACAAGAAGCCTGGACTCTAATAATTGATGATGGATTGGCG
EST: gi|20803326|gb|BQ294376.1|BQ294376
EST:     TGGAATGGAAAAAGAAGAAATGGGATGACTTCAAGGAGAGACTATCCAAG                         CTTCTGAGTTTACAAGAAGCCTGGACTCTAATAATTGATGATGGATTGGCG
genomic: TGGAATGGAAAAAGAAGAAATGGGATGACTTCAAGGAGAGACTATCCAAGgtaatttctt ... attttaccagCTTCTGAGTTTACAAGAAGCCTGGACTCTAATAATTGATGATGGATTGGCG
EST: gi|78085694|gb|DV514087.1|DV514087
EST:     TGGAATGGAAAAAGAAGAAATGGGATGACTTCAAGGAGAGACTATCCAAG                         CTTCTGAGTTTACAAGAAGCCTGGACTCTAATAATTGATGATGGATTGGCG
genomic: TGGAATGGAAAAAGAAGAAATGGGATGACTTCAAGGAGAGACTATCCAAGgtaatttctt ... attttaccagCTTCTGAGTTTACAAGAAGCCTGGACTCTAATAATTGATGATGGATTGGCG
EST: gi|31611962|gb|CD568584.1|CD568584
EST:     TGGAATGGAAAAAGAAGAAATGGGATGACTTCAAGGAGAGACTATCCAAG                         CTTCTGAGTTTACAAGAAGCCTGGACTCTAATAATTGATGATGGATTGGCG
genomic: TGGAATGGAAAAAGAAGAAATGGGATGACTTCAAGGAGAGACTATCCAAGgtaatttctt ... attttaccagCTTCTGAGTTTACAAGAAGCCTGGACTCTAATAATTGATGATGGATTGGCG
EST: gi|29945539|gb|CB815690.1|CB815690
EST:     TGGAATGGAAAAAGAAGAAATGGGATGACTTCAAGGAGAGACTATCCAAG                         CTTCTGAGTTTACAAGAAGCCTGGACTCTAATAATTGATGATGGATTGGCG
genomic: TGGAATGGAAAAAGAAGAAATGGGATGACTTCAAGGAGAGACTATCCAAGgtaatttctt ... attttaccagCTTCTGAGTTTACAAGAAGCCTGGACTCTAATAATTGATGATGGATTGGCG
EST: gi|211282779|gb|FL192970.1|FL192970
EST:     TGGAATGGAAAAAGAAGAAATGGGATGACTTCAAGGAGAGACTATCCAAG                         CTTCTGAGTTTACAAGAAGCCTGGACTCTAATAATTGATGATGGATTGGCG
genomic: TGGAATGGAAAAAGAAGAAATGGGATGACTTCAAGGAGAGACTATCCAAGgtaatttctt ... attttaccagCTTCTGAGTTTACAAGAAGCCTGGACTCTAATAATTGATGATGGATTGGCG
EST: gi|31611961|gb|CD568583.1|CD568583
EST:     TGGAATGGAAAAAGAAGAAATGGGATGACTTCAAGGAGAGACTATCCAAG                         CTTCTGAGTTTACAAGAAGCCTGGACTCTAATAATTGATGATGGATTGGCG
genomic: TGGAATGGAAAAAGAAGAAATGGGATGACTTCAAGGAGAGACTATCCAAGgtaatttctt ... attttaccagCTTCTGAGTTTACAAGAAGCCTGGACTCTAATAATTGATGATGGATTGGCG
EST: gi|37401209|gb|CF637968.1|CF637968
EST:     TGGAATGGAAAAAGAAGAAATGGGATGACTTCAAGGAGAGACTATCCAAG                         CTTCTGAGTTTACAAGAAGCCTGGACTCTAATAATTGATGATGGATTGGCG
genomic: TGGAATGGAAAAAGAAGAAATGGGATGACTTCAAGGAGAGACTATCCAAGgtaatttctt ... attttaccagCTTCTGAGTTTACAAGAAGCCTGGACTCTAATAATTGATGATGGATTGGCG
EST: gi|67020485|gb|CO449234.1|CO449234
EST:     TGGAATGGAAAAAGAAGAAATGGGATGACTTCAAGGAGAGACTATCCAAG                         CTTCTGAGTTTACAAGAAGCCTGNACTCTAAATA-TTGATGATGGATTGGC
genomic: TGGAATGGAAAAAGAAGAAATGGGATGACTTCAAGGAGAGACTATCCAAGgtaatttctt ... attttaccagCTTCTGAGTTTACAAGAAGCCTGGACTCTAA-TAATTGATGATGGATTGGC
EST: gi|60353658|gb|DN220631.1|DN220631
EST:     TGGAATGGAAAAAGAAGAAATGGGATGACTTCAAGGAGAGACTATCCAAG                         CTTCTGAGTTTACAAGAAGCCTGGACTCTAATAATTGATGATGGATTGGCG
genomic: TGGAATGGAAAAAGAAGAAATGGGATGACTTCAAGGAGAGACTATCCAAGgtaatttctt ... attttaccagCTTCTGAGTTTACAAGAAGCCTGGACTCTAATAATTGATGATGGATTGGCG
EST: gi|60395671|gb|DN228541.1|DN228541
EST:     TGGAATGGAAAAAGAAGAAATGGGATGACTTCAAGGAGAGACTATCCAAG                         CTTCTGAGTTTACAAGAAGCCTGGACTCTAATAATTGATGATGGATTGGCG
genomic: TGGAATGGAAAAAGAAGAAATGGGATGACTTCAAGGAGAGACTATCCAAGgtaatttctt ... attttaccagCTTCTGAGTTTACAAGAAGCCTGGACTCTAATAATTGATGATGGATTGGCG
EST: gi|29946582|gb|CB816222.1|CB816222
EST:     TGGAATGGAAAAAGAAGAAATGGGATGACTTCAAGGAGAGACTATCCAAG                         CTTCTGAGTTTACAAGAAGCCTGGACTCTAATAATTGATGATGGATTGGCG
genomic: TGGAATGGAAAAAGAAGAAATGGGATGACTTCAAGGAGAGACTATCCAAGgtaatttctt ... attttaccagCTTCTGAGTTTACAAGAAGCCTGGACTCTAATAATTGATGATGGATTGGCG
EST: gi|37401269|gb|CF637997.1|CF637997
EST:     TGGAATGGAAAAAGAAGAAATGGGATGACTTCAAGGAGAGACTATCCAAG                         CTTCTGAGTTTACAAGAAGCCTGGACTCTAATAATTGATGATGGATTGGCG
genomic: TGGAATGGAAAAAGAAGAAATGGGATGACTTCAAGGAGAGACTATCCAAGgtaatttctt ... attttaccagCTTCTGAGTTTACAAGAAGCCTGGACTCTAATAATTGATGATGGATTGGCG
EST: gi|149027381|gb|EE046513.2|EE046513
EST:     TGGAATGGAAAAAGAAGAAATGGGATGACTTCAAGGAGAGACTATCCAAG                         CTTCTGAGTTTACAAGAAGCCTGGACTCTAATAATTGATGATGGATTGGCG
genomic: TGGAATGGAAAAAGAAGAAATGGGATGACTTCAAGGAGAGACTATCCAAGgtaatttctt ... attttaccagCTTCTGAGTTTACAAGAAGCCTGGACTCTAATAATTGATGATGGATTGGCG
EST: gi|78543967|gb|DV621465.1|DV621465
EST:     TGGAATGGAAAAAGAAGAAATGGGATGACTTCAAGGAGAGACTATCCAAG                         CTTCTGAGTTTACAAGAAGCCTGGACTCTAATAATTGATGATGGATTGGCG
genomic: TGGAATGGAAAAAGAAGAAATGGGATGACTTCAAGGAGAGACTATCCAAGgtaatttctt ... attttaccagCTTCTGAGTTTACAAGAAGCCTGGACTCTAATAATTGATGATGGATTGGCG
EST: gi|60350354|gb|DN217327.1|DN217327
EST:     TGGAATGGAAAAAGAAGAAATGGGATGACTTCAAGGAGAGACTATCCAAG                         CTTCTGAGTTTACAAGAAGCCTGGACTCTAATAATTGATGATGGATTGGCG
genomic: TGGAATGGAAAAAGAAGAAATGGGATGACTTCAAGGAGAGACTATCCAAGgtaatttctt ... attttaccagCTTCTGAGTTTACAAGAAGCCTGGACTCTAATAATTGATGATGGATTGGCG
EST: gi|88755471|gb|DY539612.1|DY539612
EST:     TGGAATGGAAAAAGAAGAAATGGGATGACTTCAAGGAGAGACTATCCAAG                         CTTCTGAGTTTACAAGAAGCCTGGACTCTAATAATTGATGATGGATTGGCG
genomic: TGGAATGGAAAAAGAAGAAATGGGATGACTTCAAGGAGAGACTATCCAAGgtaatttctt ... attttaccagCTTCTGAGTTTACAAGAAGCCTGGACTCTAATAATTGATGATGGATTGGCG
EST: gi|28568977|gb|CB280852.1|CB280852
EST:     TGGAATGGAAAAAGAAGAAATGGGATGACTTCAAGGAGAGACTATCCAAG                         CTTCTGAGTTTACAAGAAGCCTGGACTCTAATAATTGATGATGGATTGGCG
genomic: TGGAATGGAAAAAGAAGAAATGGGATGACTTCAAGGAGAGACTATCCAAGgtaatttctt ... attttaccagCTTCTGAGTTTACAAGAAGCCTGGACTCTAATAATTGATGATGGATTGGCG
EST: gi|7135394|gb|AW498064.1|AW498064
EST:     TGGAATGGAAAAAGAAGAAATGGGATGACTTCAAGGAGAGACTATCCAAG                         CTTCTGAGTTTACAAGAAGCCTGGACTCTAATAATTGATGATGGATTGGCG
genomic: TGGAATGGAAAAAGAAGAAATGGGATGACTTCAAGGAGAGACTATCCAAGgtaatttctt ... attttaccagCTTCTGAGTTTACAAGAAGCCTGGACTCTAATAATTGATGATGGATTGGCG
EST: gi|7135020|gb|AW497876.1|AW497876
EST:     TGGAATGGAAAAAGAAGAAATGGGATGACTTCAAGGAGAGACTATCCAAG                         CTTCTGAGTTTACAAGAAGCCTGGACTCTAATAATTGATGATGGATTGGCG
genomic: TGGAATGGAAAAAGAAGAAATGGGATGACTTCAAGGAGAGACTATCCAAGgtaatttctt ... attttaccagCTTCTGAGTTTACAAGAAGCCTGGACTCTAATAATTGATGATGGATTGGCG
EST: gi|60357973|gb|DN224946.1|DN224946
EST:     TGGAATGGAAAAAGAAGAAATGGGATGACTTCAAGGAGAGACTATCCAAG                         CTTCTGAGTTTACAAGAAGCCTGGACTCTAATAATTGATGATGGATTGGCG
genomic: TGGAATGGAAAAAGAAGAAATGGGATGACTTCAAGGAGAGACTATCCAAGgtaatttctt ... attttaccagCTTCTGAGTTTACAAGAAGCCTGGACTCTAATAATTGATGATGGATTGGCG
EST: gi|211282781|gb|FL192972.1|FL192972
EST:     TGGAATGGAAAAAGAAGAAATGGGATGACTTCAAGGAGAGACTATCCAAG                         CTTCTGAGTTTACAAGAAGCCTGGACTCTAATAATTGATGATGGATTGGCG
genomic: TGGAATGGAAAAAGAAGAAATGGGATGACTTCAAGGAGAGACTATCCAAGgtaatttctt ... attttaccagCTTCTGAGTTTACAAGAAGCCTGGACTCTAATAATTGATGATGGATTGGCG

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: 115

CTCTGGAGAGAATACATGGATTTCAATTAGGCGATAGTACACTGGAATGGAAAAAGAAGAAATGGGATGACTTCAAGGAGAGACTATCCAAGgtaatttctt ... attttaccagCTTCTGAGTTTACAAGAAGCCTGGACTCTAATAATTGATGATGGATTGGCGGCTTCATTTGTGGCCCCGGCTACTGATTCGTTAGAAGATGACAGCCAAC


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 74

CTCTGGAGAGAATACATGGATTTCAATTAGGCGATAGTACACTGGAATGGAAAAAGAAGAAATGGGATGACTTCAAGGAGAGACTATCCAAGgtaatttctt ... attttaccagCTTCTGAGTTTACAAGAAGCCTGGACTCTAATAATTGATGATGGATTGGCGGCTTCATTTGTGGCCCCGGCTACTGATTCGTTAGAAGATGACAGCCAAC


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 47

CTCTGGAGAGAATACATGGATTTCAATTAGGCGATAGTACACTGGAATGGAAAAAGAAGAAATGGGATGACTTCAAGGAGAGACTATCCAAGgtaatttctt ... attttaccagCTTCTGAGTTTACAAGAAGCCTGGACTCTAATAATTGATGATGGATTGGCGGCTTCATTTGTGGCCCCGGCTACTGATTCGTTAGAAGATGACAGCCAAC


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 64

CTCTGGAGAGAATACATGGATTTCAATTAGGCGATAGTACACTGGAATGGAAAAAGAAGAAATGGGATGACTTCAAGGAGAGACTATCCAAGgtaatttctt ... attttaccagCTTCTGAGTTTACAAGAAGCCTGGACTCTAATAATTGATGATGGATTGGCGGCTTCATTTGTGGCCCCGGCTACTGATTCGTTAGAAGATGACAGCCAAC


Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTCTGGAGAGAATACATGGATTTCAATTAGGCGATAGTACACTGGAATGGAAAAAGAAGAAATGGGATGACTTCAAGGAGAGACTATCCAAGgtaatttctttgctctctctctctctctagtttgagggttttaccctaatgaatacgatttgtcaatgtattttaccag

- - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA